[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/15076797/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/15082576/transformed.cor.cli.txt"

nPatients in clinical file=304, in cluster file=295, common to both=292
[1]  63 292
[1] "AMP PEAK  1(1P31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           96                           196 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           96                           196 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          157                           135 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          157                           135 
[1] "AMP PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        152                         140 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        152                         140 
[1] "AMP PEAK  4(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           79                           213 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           79                           213 
[1] "AMP PEAK  5(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           41                           251 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           41                           251 
[1] "AMP PEAK  6(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                           226                             66 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                           226                             66 
[1] "AMP PEAK  7(3Q28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                        223                          69 
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                        223                          69 
[1] "AMP PEAK  8(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                         21                         271 
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                         21                         271 
[1] "AMP PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           137                            155 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           137                            155 
[1] "AMP PEAK 10(6P21.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                            82                            210 
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                            82                            210 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           52                           240 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           52                           240 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           126                            166 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           126                            166 
[1] "AMP PEAK 13(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           63                           229 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           63                           229 
[1] "AMP PEAK 14(11P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                          23                          269 
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                          23                          269 
[1] "AMP PEAK 15(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            41                            251 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            41                            251 
[1] "AMP PEAK 16(11Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                            47                            245 
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                            47                            245 
[1] "AMP PEAK 17(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                            65                            227 
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                            65                            227 
[1] "AMP PEAK 18(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          69                          223 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          69                          223 
[1] "AMP PEAK 19(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                            76                            216 
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                            76                            216 
[1] "AMP PEAK 20(16P13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                             65                             227 
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                             65                             227 
[1] "AMP PEAK 21(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                          54                          238 
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                          54                          238 
[1] "AMP PEAK 22(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            73                            219 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            73                            219 
[1] "AMP PEAK 23(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                            38                            254 
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                            38                            254 
[1] "AMP PEAK 24(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                            42                            250 
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                            42                            250 
[1] "AMP PEAK 25(19Q13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                             91                             201 
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                             91                             201 
[1] "AMP PEAK 26(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                            134                             158 
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                            134                             158 
[1] "AMP PEAK 27(21Q22.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                             48                             244 
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                             48                             244 
[1] "AMP PEAK 28(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         75                         217 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         75                         217 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            40                            252 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            40                            252 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           33                           259 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           33                           259 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           65                           227 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           65                           227 
[1] "DEL PEAK  4(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          128                           164 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          128                           164 
[1] "DEL PEAK  5(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                          132                           160 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                          132                           160 
[1] "DEL PEAK  6(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                          100                           192 
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                          100                           192 
[1] "DEL PEAK  7(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           97                           195 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           97                           195 
[1] "DEL PEAK  8(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                          111                           181 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                          111                           181 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           75                           217 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           75                           217 
[1] "DEL PEAK 10(5Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                           71                           221 
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                           71                           221 
[1] "DEL PEAK 11(6P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                           46                           246 
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                           46                           246 
[1] "DEL PEAK 12(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        100                         192 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        100                         192 
[1] "DEL PEAK 13(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                         60                         232 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                         60                         232 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          103                           189 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          103                           189 
[1] "DEL PEAK 15(8P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                           96                           196 
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                           96                           196 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             86                             206 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             86                             206 
[1] "DEL PEAK 17(11P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                           101                            191 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                           101                            191 
[1] "DEL PEAK 18(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                           161                            131 
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                           161                            131 
[1] "DEL PEAK 19(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                         159                          133 
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                         159                          133 
[1] "DEL PEAK 20(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                             97                             195 
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                             97                             195 
[1] "DEL PEAK 21(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           117                            175 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           117                            175 
[1] "DEL PEAK 22(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                             50                             242 
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                             50                             242 
[1] "DEL PEAK 23(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            68                            224 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            68                            224 
[1] "DEL PEAK 24(16Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                            53                            239 
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                            53                            239 
[1] "DEL PEAK 25(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            55                            237 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            55                            237 
[1] "DEL PEAK 26(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                         108                          184 
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                         108                          184 
[1] "DEL PEAK 27(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                            51                            241 
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                            51                            241 
[1] "DEL PEAK 28(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            82                            210 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            82                            210 
[1] "DEL PEAK 29(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                           103                            189 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                           103                            189 
[1] "DEL PEAK 30(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                             37                             255 
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                             37                             255 
[1] "DEL PEAK 31(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            35                            257 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            35                            257 
[1] "DEL PEAK 32(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                            58                            234 
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                            58                            234 
[1] "DEL PEAK 33(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             87                             205 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             87                             205 
[1] "DEL PEAK 34(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           71                           221 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           71                           221 
[1] "DEL PEAK 35(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            59                            233 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            59                            233 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                                  
 [2] "VITAL_STATUS"                                    
 [3] "DAYS_TO_DEATH"                                   
 [4] "DAYS_TO_LAST_FOLLOWUP"                           
 [5] "PRIMARY_SITE_OF_DISEASE"                         
 [6] "NEOPLASM_DISEASESTAGE"                           
 [7] "PATHOLOGY_T_STAGE"                               
 [8] "PATHOLOGY_N_STAGE"                               
 [9] "PATHOLOGY_M_STAGE"                               
[10] "DCC_UPLOAD_DATE"                                 
[11] "GENDER"                                          
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"            
[13] "HISTOLOGICAL_TYPE"                               
[14] "RADIATIONS_RADIATION_REGIMENINDICATION"          
[15] "NUMBER_PACK_YEARS_SMOKED"                        
[16] "NUMBER_OF_LYMPH_NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCH_NUMBER"                                    
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASM_HISTOLOGIC_GRADE"                       
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_TOTAL_DOSE"                            
[30] "RADIATION_THERAPY_TYPE"                          
[31] "RADIATION_THERAPY_STATUS"                        
[32] "RADIATION_THERAPY_SITE"                          
[33] "RADIATION_ADJUVANT_UNITS"                        
[34] "PREGNANCIES_COUNT_TOTAL"                         
[35] "PREGNANCIES_COUNT_STILLBIRTH"                    
[36] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[38] "PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[39] "PREGNANCIES_COUNT_ECTOPIC"                       
[40] "PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[41] "LYMPH_NODE_LOCATION"                             
[42] "POS_LYMPH_NODE_LOCATION"                         
[43] "MENOPAUSE_STATUS"                                
[44] "LYMPHOVASCULAR_INVOLVEMENT"                      
[45] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[46] "LYMPH_NODES_EXAMINED"                            
[47] "KERATINIZATION_SQUAMOUS_CELL"                    
[48] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[49] "HYSTERECTOMY_TYPE"                               
[50] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[51] "HEIGHT_CM_AT_DIAGNOSIS"                          
[52] "FEDPET_OR_CT_RESULTS"                            
[53] "CORPUS_INVOLVEMENT"                              
[54] "CHEMO_CONCURRENT_TYPE"                           
[55] "CERVIX_SUV_RESULTS"                              
[56] "CAUSE_OF_DEATH"                                  
[57] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[58] "AGE_AT_DIAGNOSIS"                                
[59] "STAGE_EVENT.CLINICAL_STAGE"                      

Input Data has 59 rows and 292 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=202,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 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:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH_NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TUMOR_SAMPLE_PROCUREMENT_COUNTRY':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASM_HISTOLOGIC_GRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_TREATMENT_ADJUVANT is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 29:'RADIATION_TOTAL_DOSE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 31:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'RADIATION_THERAPY_SITE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 33:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 40:'PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT excluded in the analysis because there is no case of (both >= 3) in the table below"
              BILATERAL PELVIC WALL INVOLVEMENT ON IMAGING
freq.values   "1"                                         
freq.contrast "10"                                        
both >= 3     "FALSE"                                     
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "10"                                                                                                                               
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NEGATIVE NO EXTENTION NO PELVIC SPREAD
freq.values   "1"                       "2"      "1"          "1"             
freq.contrast "10"                      "9"      "10"         "10"            
both >= 3     "FALSE"                   "FALSE"  "FALSE"      "FALSE"         
              PELVIC SPREAD
freq.values   "1"          
freq.contrast "10"         
both >= 3     "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "10"                                                                        
both >= 3     "FALSE"                                                                     
              THE PELVIC NODULES SHOW CIRCUMSCRIBED AREA OF ADIPOSE TISSUE WITH LOCAL FAT NECROSIS. NO EVIDENCE OF MALIGNANCY WITHIN THIS PELVIC NODULE.
freq.values   "1"                                                                                                                                       
freq.contrast "10"                                                                                                                                      
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "10"                                                                     
both >= 3     "FALSE"                                                                  
Variable 41:'LYMPH_NODE_LOCATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "LYMPH_NODE_LOCATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 42:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 45:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'LYMPH_NODES_EXAMINED':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 48:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HYSTERECTOMY_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 50:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 51:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 52:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "FEDPET_OR_CT_RESULTS is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 53:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 54:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CHEMO_CONCURRENT_TYPE excluded in the analysis because there is no case of (both >= 3) in the table below"
              CARBOPLATIN CISPLATIN OTHER  
freq.values   "1"         "15"      "1"    
freq.contrast "16"        "2"       "16"   
both >= 3     "FALSE"     "FALSE"   "FALSE"
Variable 55:'CERVIX_SUV_RESULTS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 56:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CAUSE_OF_DEATH is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 57:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 58:'AGE_AT_DIAGNOSIS':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 59:'STAGE_EVENT.CLINICAL_STAGE':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 292 columns, 1 survival variables, and 43 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                                  
 [2] "PATHOLOGY_T_STAGE"                               
 [3] "PATHOLOGY_N_STAGE"                               
 [4] "PATHOLOGY_M_STAGE"                               
 [5] "HISTOLOGICAL_TYPE"                               
 [6] "RADIATIONS_RADIATION_REGIMENINDICATION"          
 [7] "NUMBER_PACK_YEARS_SMOKED"                        
 [8] "NUMBER_OF_LYMPH_NODES"                           
 [9] "RACE"                                            
[10] "ETHNICITY"                                       
[11] "WEIGHT_KG_AT_DIAGNOSIS"                          
[12] "TUMOR_STATUS"                                    
[13] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[14] "NEOPLASM_HISTOLOGIC_GRADE"                       
[15] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[16] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[17] "TOBACCO_SMOKING_HISTORY"                         
[18] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[19] "RADIATION_TOTAL_DOSE"                            
[20] "RADIATION_THERAPY_TYPE"                          
[21] "RADIATION_THERAPY_STATUS"                        
[22] "RADIATION_THERAPY_SITE"                          
[23] "RADIATION_ADJUVANT_UNITS"                        
[24] "PREGNANCIES_COUNT_TOTAL"                         
[25] "PREGNANCIES_COUNT_STILLBIRTH"                    
[26] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[27] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[28] "PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[29] "PREGNANCIES_COUNT_ECTOPIC"                       
[30] "POS_LYMPH_NODE_LOCATION"                         
[31] "MENOPAUSE_STATUS"                                
[32] "LYMPHOVASCULAR_INVOLVEMENT"                      
[33] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[34] "LYMPH_NODES_EXAMINED"                            
[35] "KERATINIZATION_SQUAMOUS_CELL"                    
[36] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[37] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[38] "HEIGHT_CM_AT_DIAGNOSIS"                          
[39] "CORPUS_INVOLVEMENT"                              
[40] "CERVIX_SUV_RESULTS"                              
[41] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[42] "AGE_AT_DIAGNOSIS"                                
[43] "STAGE_EVENT.CLINICAL_STAGE"                      
YEARS_TO_BIRTH, nv=61, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
134  68  21   8 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
134  68  21   8 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
134  68  21   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
134  68  21   8 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=73, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=7, binary=FALSE, numeric=FALSE
NEOPLASM_HISTOLOGIC_GRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=22, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=28, binary=FALSE, numeric=TRUE
RADIATION_TOTAL_DOSE, nv=43, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_SITE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_ADJUVANT_UNITS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=15, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=12, binary=FALSE, numeric=TRUE
PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=49, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=35, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=17, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=15, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=61, binary=FALSE, numeric=TRUE
STAGE_EVENT.CLINICAL_STAGE, nv=17, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P31.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P31.3) MUTATED    68  23
  AMP PEAK  1(1P31.3) WILD-TYPE 145  42
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           91                           187 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           23                            42 
$`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-A1ML TCGA-C5-A2LZ TCGA-C5-A3HF 
       38.99         0.46         2.43        20.91       100.14        17.85 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      154.32       101.82        13.61         2.73        50.99        45.83 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DS-A0VL TCGA-DS-A0VN 
       23.51        27.52         1.12        44.94         2.66       118.65 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A411 
        8.28        39.55        37.35        31.36        25.02        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A97N 
       14.50        26.01        13.91        15.02        14.96         0.36 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
        1.51         0.59         0.59        16.08         1.18         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A69L TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.10         0.07         0.03        19.79         1.45         1.58 
TCGA-FU-A40J TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VK 
        1.35        20.78        14.93       117.40        36.36        20.48 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A7HU 
       18.15       195.85        30.31         7.99         0.30        13.35 
TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-PN-A8MA 
       20.28        11.38        13.87        34.62        35.05         2.96 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG 
       16.41         9.04        17.56        19.59        93.99        12.16 
TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A953 
       37.78        19.96        11.51        57.93        31.27        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UD 
       50.63        48.07        45.34        44.94        25.74        19.69 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9V0 TCGA-ZJ-AAXA 
       46.92        40.96        14.53        27.25        18.84         1.41 
TCGA-ZX-AA5X 
        3.91 

$`AMP PEAK  1(1P31.3) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ 
       12.39        23.67        11.44        68.84        18.74       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 
      177.04       173.29         5.46        19.86        67.46        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A1MP 
       35.01        57.73        53.16        35.61        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CK 
       33.24        52.01        18.02        20.42       210.67       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT 
       94.95         9.34         8.35       146.86        99.91        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        11.87        58.88        50.76        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88        36.76       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3Y4 
       17.52        12.36        30.90        31.53        13.05        14.50 
TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.40        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.99        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB 
        6.64        19.27         0.43         1.45         0.13         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK 
        4.04         0.03         0.36        47.77         0.10         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF 
       20.35         7.92         6.94        14.70         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17        31.36        36.26 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 
        9.01        25.41        10.82        21.67         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81        96.95        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        28.37 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
        8.28        21.11        11.28         0.89        12.49         0.82 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A8JM 
       22.52        17.82        19.56         9.17         8.52         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
       54.81        20.84         5.49        15.58        15.95        16.14 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       14.07        15.88         9.34        15.39        19.36         3.88 
TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI 
       11.67        66.05        10.03        40.50        26.43        18.05 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94W 
       59.51        32.15        46.03        36.13        39.78        36.26 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A958 
       16.64         4.73        24.39        39.78        50.86        50.14 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UO 
       43.40        42.41        21.30        22.72         1.71        41.42 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       43.27        35.97        20.09        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       67.20         5.16        14.04        14.89         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXU 
        0.16 

  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 
                       195.85                        210.67 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                        19.79                         19.86 
[1] "0.0 - 195.8 (19.8)" "0.0 - 210.7 (19.9)"
[1] "hr=" "1.2"
D1V2, continuous
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  1(1P31.3) MUTATED   38 23 10  2
  AMP PEAK  1(1P31.3) WILD-TYPE 96 45 11  6
D1V3, multiclass
    clus
vv   AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  T1                          38                            96
  T2                          23                            45
  T3                          10                            11
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   38 15
  AMP PEAK  1(1P31.3) WILD-TYPE 89 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     38   15
  AMP PEAK  1(1P31.3) WILD-TYPE   89   40
   clus
vv  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  0                          38                            89
  1                          15                            40
[1] 2 2
[1] FALSE
D1V5, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   36  2
  AMP PEAK  1(1P31.3) WILD-TYPE 71  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     36    2
  AMP PEAK  1(1P31.3) WILD-TYPE   71    8
   clus
vv  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  0                          36                            71
  1                           2                             8
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1P31.3) MUTATED               1                               87
  AMP PEAK  1(1P31.3) WILD-TYPE             4                              154
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  1(1P31.3) MUTATED                                               1
  AMP PEAK  1(1P31.3) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  1(1P31.3) MUTATED                                     4
  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                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  1(1P31.3) MUTATED                                              3
  AMP PEAK  1(1P31.3) WILD-TYPE                                           12
D1V6, multiclass
                                               clus
vv                                              AMP PEAK  1(1P31.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              AMP PEAK  1(1P31.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P31.3) MUTATED     9  87
  AMP PEAK  1(1P31.3) WILD-TYPE  21 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      9   87
  AMP PEAK  1(1P31.3) WILD-TYPE   21  175
     clus
vv    AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  NO                            9                            21
  YES                          87                           175
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P31.3) MUTATED                                  1     8
  AMP PEAK  1(1P31.3) WILD-TYPE                                7    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P31.3) MUTATED                          11
  AMP PEAK  1(1P31.3) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  1(1P31.3) MUTATED                                           0    63
  AMP PEAK  1(1P31.3) WILD-TYPE                                         2   138
D1V10, multiclass
                                           clus
vv                                          AMP PEAK  1(1P31.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              63
                                           clus
vv                                          AMP PEAK  1(1P31.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               138
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P31.3) MUTATED     4  57
  AMP PEAK  1(1P31.3) WILD-TYPE  19 104
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      4   57
  AMP PEAK  1(1P31.3) WILD-TYPE   19  104
                        clus
vv                       AMP PEAK  1(1P31.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       AMP PEAK  1(1P31.3) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           104
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   40 14
  AMP PEAK  1(1P31.3) WILD-TYPE 94 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     40   14
  AMP PEAK  1(1P31.3) WILD-TYPE   94   27
            clus
vv           AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  TUMOR FREE                          40                            94
  WITH TUMOR                          14                            27
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  1(1P31.3) MUTATED       17      2       1      5       3
  AMP PEAK  1(1P31.3) WILD-TYPE     36      3       0      6       4
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK  1(1P31.3) MUTATED              62       6
  AMP PEAK  1(1P31.3) WILD-TYPE           139       8
D1V14, multiclass
               clus
vv              AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  BRAZIL                                 17                            36
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  5                             6
  UKRAINE                                 3                             4
  UNITED STATES                          62                           139
  VIETNAM                                 6                             8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  1(1P31.3) MUTATED    4 43 40  0  8
  AMP PEAK  1(1P31.3) WILD-TYPE 14 86 73  1 16
D1V15, multiclass
    clus
vv   AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  G1                           4                            14
  G2                          43                            86
  G3                          40                            73
  G4                           0                             1
  GX                           8                            16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V16, continuous
D1V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  1(1P31.3) MUTATED                                            11
  AMP PEAK  1(1P31.3) WILD-TYPE                                          26
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  1(1P31.3) MUTATED                                        5
  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                                               3
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  1(1P31.3) MUTATED               19                  47
  AMP PEAK  1(1P31.3) WILD-TYPE             43                  95
D1V18, multiclass
                                                 clus
vv                                                AMP PEAK  1(1P31.3) 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                                                           19
  LIFELONG NON-SMOKER                                                      47
                                                 clus
vv                                                AMP PEAK  1(1P31.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             3
  CURRENT SMOKER                                                             43
  LIFELONG NON-SMOKER                                                        95
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V19, continuous
D1V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  1(1P31.3) MUTATED             7       33             2        4
  AMP PEAK  1(1P31.3) WILD-TYPE          12       69            10       21
D1V21, multiclass
               clus
vv              AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               33                            69
  EXTERNAL BEAM                           2                            10
  INTERNAL                                4                            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"
D1V22, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED    6  1
  AMP PEAK  1(1P31.3) WILD-TYPE 19  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      6    1
  AMP PEAK  1(1P31.3) WILD-TYPE   19    2
                         clus
vv                        AMP PEAK  1(1P31.3) MUTATED
  COMPLETED AS PLANNED                              6
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        AMP PEAK  1(1P31.3) WILD-TYPE
  COMPLETED AS PLANNED                               19
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  1(1P31.3) MUTATED                    0                0
  AMP PEAK  1(1P31.3) WILD-TYPE                  2                2
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  1(1P31.3) MUTATED                    13            11
  AMP PEAK  1(1P31.3) WILD-TYPE                  23            22
D1V23, multiclass
                     clus
vv                    AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              0                             2
  PRIMARY TUMOR FIELD                          13                            23
  REGIONAL SITE                                11                            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"
D1V24, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   20  2
  AMP PEAK  1(1P31.3) WILD-TYPE 36  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     20    2
  AMP PEAK  1(1P31.3) WILD-TYPE   36    3
     clus
vv    AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  CGY                          20                            36
  GY                            2                             3
[1] 2 2
[1] FALSE
D1V25, continuous
D1V26, continuous
D1V27, continuous
D1V28, continuous
D1V29, continuous
D1V30, 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                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  1(1P31.3) MUTATED                        10                       0
  AMP PEAK  1(1P31.3) WILD-TYPE                      25                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  1(1P31.3) MUTATED                         2
  AMP PEAK  1(1P31.3) WILD-TYPE                       6
D1V31, multiclass
                                     clus
vv                                    AMP PEAK  1(1P31.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                      10
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    AMP PEAK  1(1P31.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        25
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                                7
  AMP PEAK  1(1P31.3) WILD-TYPE                                             18
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  1(1P31.3) MUTATED                                                                                  38
  AMP PEAK  1(1P31.3) WILD-TYPE                                                                                43
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  1(1P31.3) MUTATED                                                                                             32
  AMP PEAK  1(1P31.3) WILD-TYPE                                                                                           88
D1V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  1(1P31.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          32
                                                                                              clus
vv                                                                                             AMP PEAK  1(1P31.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       43
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V33, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   22 24
  AMP PEAK  1(1P31.3) WILD-TYPE 48 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     22   24
  AMP PEAK  1(1P31.3) WILD-TYPE   48   49
         clus
vv        AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  ABSENT                           22                            48
  PRESENT                          24                            49
[1] 2 2
[1] FALSE
D1V34, continuous
D1V35, continuous
D1V36, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   19 37
  AMP PEAK  1(1P31.3) WILD-TYPE 29 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     19   37
  AMP PEAK  1(1P31.3) WILD-TYPE   29   79
                                          clus
vv                                         AMP PEAK  1(1P31.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          37
                                          clus
vv                                         AMP PEAK  1(1P31.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            79
[1] 2 2
[1] FALSE
D1V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  1(1P31.3) MUTATED              3           9         30
  AMP PEAK  1(1P31.3) WILD-TYPE           12          44         54
D1V38, multiclass
              clus
vv             AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                            9                            44
  NEVER USED                            30                            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"
D1V39, continuous
D1V40, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   26  6
  AMP PEAK  1(1P31.3) WILD-TYPE 66 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     26    6
  AMP PEAK  1(1P31.3) WILD-TYPE   66   11
         clus
vv        AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  ABSENT                           26                            66
  PRESENT                           6                            11
[1] 2 2
[1] FALSE
D1V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  1(1P31.3) MUTATED      1   9   22    6  2   5    3    2  11  2   1
  AMP PEAK  1(1P31.3) WILD-TYPE    0  25   47   24  4   5    4    7  25  0   1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK  1(1P31.3) MUTATED     7  2   0  8
  AMP PEAK  1(1P31.3) WILD-TYPE  10  6   1  8
D1V42, multiclass
      clus
vv     AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  T1A1                           1                             0
  T1B                            9                            25
  T1B1                          22                            47
  T1B2                           6                            24
  T2                             2                             4
  T2A                            5                             5
  T2A1                           3                             4
  T2A2                           2                             7
  T2B                           11                            25
  T3                             2                             0
  T3A                            1                             1
  T3B                            7                            10
  T4                             2                             6
  TIS                            0                             1
  TX                             8                             8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  1(1P31.3) MUTATED         2        0         1         0       13
  AMP PEAK  1(1P31.3) WILD-TYPE       3        1         0         1       20
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  1(1P31.3) MUTATED          25         6        2         2
  AMP PEAK  1(1P31.3) WILD-TYPE        52        30        2         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  1(1P31.3) MUTATED            2          3        12         1
  AMP PEAK  1(1P31.3) WILD-TYPE          3          4        31         0
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  1(1P31.3) MUTATED            2         17         3         3
  AMP PEAK  1(1P31.3) WILD-TYPE          1         25         4         9
D1V44, multiclass
            clus
vv           AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IA1                            1                             0
  STAGE IA2                            0                             1
  STAGE IB                            13                            20
  STAGE IB1                           25                            52
  STAGE IB2                            6                            30
  STAGE II                             2                             2
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           3                             4
  STAGE IIB                           12                            31
  STAGE III                            1                             0
  STAGE IIIA                           2                             1
  STAGE IIIB                          17                            25
  STAGE IVA                            3                             4
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED   111  36
  AMP PEAK  2(1Q21.3) WILD-TYPE 102  29
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          147                           131 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           36                            29 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       12.39        49.48        57.04        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-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CH 
        3.58        44.22        78.35       100.14        17.85       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 
      101.82       134.33        15.48        94.95        13.61         2.73 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KL 
       45.83         8.35        23.51        27.52         1.12        44.94 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WH 
       87.75        58.88         2.66       117.99        22.98        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        39.55        37.35        30.90        31.53        31.36 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.56        14.50        26.01        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PI 
       14.96        13.58         0.36        12.59         1.51        19.27 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        0.59         0.59        16.08         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.10         0.03         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A40J 
        8.32        15.55        23.84         2.17         1.45         1.35 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LC 
       25.41        10.82        20.78        14.93         9.44       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 
       78.71        81.96        36.36        21.44        20.48         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 
       18.15       195.85        30.31         7.99        11.28         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
        0.82        22.52        20.28         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DW 
       13.87        35.05         2.96        16.41        15.95        17.56 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB 
        9.34        15.39        19.59        93.99        12.16        10.03 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC 
       26.43        19.96        59.51        32.15        46.03        11.51 
TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A952 
       57.93        31.27        16.64         4.73        39.78        50.86 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       50.63        48.07        50.14        45.34        44.94        43.40 
TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL 
       25.74        22.72        19.69        46.92        40.96        14.53 
TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UV TCGA-VS-A9V0 TCGA-VS-A9V3 TCGA-WL-A834 
       27.25        43.27         3.42        18.84        14.89        26.01 
TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       29.26         1.41         3.91 

$`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        33.24        52.01        18.02        20.42       210.67 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77       131.11         9.34 
TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       50.99       146.86        99.91        20.81        20.91        11.87 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        50.76        40.04        36.76       118.65        16.83 
TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       16.18        12.36        13.05        25.02        14.50        26.40 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A78R 
       12.66        12.82         7.46        14.89        26.79        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 
       45.96        26.27         6.64         0.43         1.45         0.13 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.07         4.04         0.03         0.36         0.07         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
       20.35         7.92         1.22         0.92        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.12         9.01        21.67       147.39       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VL 
       96.95        29.85        27.42         3.29        24.56        15.58 
TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3Y 
       28.37        21.11         0.89        12.49        13.35        17.82 
TCGA-MA-AA3Z TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       19.56        34.62         5.42        54.81        20.84         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73S 
       15.58         9.04        16.14        14.07        15.88        19.36 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI 
        3.88        11.67        66.05        40.50        37.78        18.05 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A953 TCGA-VS-A9U7 
       36.13        39.78        36.26        24.39        15.68        42.41 
TCGA-VS-A9UB TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU 
       21.30         1.71        41.42        35.97        20.09        14.53 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.25        67.20         5.16        14.04         4.34        16.24 
TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
       15.42        67.59        19.13         0.69         0.16 

  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 
                       195.85                        210.67 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        19.96                         19.56 
[1] "0.0 - 195.8 (20.0)" "0.0 - 210.7 (19.6)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  2(1Q21.3) MUTATED   61 43 15  4
  AMP PEAK  2(1Q21.3) WILD-TYPE 73 25  6  4
D2V3, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                          61                            73
  T2                          43                            25
  T3                          15                             6
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   63 30
  AMP PEAK  2(1Q21.3) WILD-TYPE 64 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     63   30
  AMP PEAK  2(1Q21.3) WILD-TYPE   64   25
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                          63                            64
  1                          30                            25
[1] 2 2
[1] FALSE
D2V5, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   58  8
  AMP PEAK  2(1Q21.3) WILD-TYPE 49  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     58    8
  AMP PEAK  2(1Q21.3) WILD-TYPE   49    2
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                          58                            49
  1                           8                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED               3                              135
  AMP PEAK  2(1Q21.3) WILD-TYPE             2                              106
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                               3
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                                    11
  AMP PEAK  2(1Q21.3) WILD-TYPE                                  11
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  2(1Q21.3) MUTATED                                           0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                              5
  AMP PEAK  2(1Q21.3) WILD-TYPE                                           10
D2V6, multiclass
                                               clus
vv                                              AMP PEAK  2(1Q21.3) MUTATED
  ADENOSQUAMOUS                                                           3
  CERVICAL SQUAMOUS CELL CARCINOMA                                      135
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
                                               clus
vv                                              AMP PEAK  2(1Q21.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        106
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             10
[1] 6 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    17 140
  AMP PEAK  2(1Q21.3) WILD-TYPE  13 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     17  140
  AMP PEAK  2(1Q21.3) WILD-TYPE   13  122
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           17                            13
  YES                         140                           122
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q21.3) MUTATED                                  1    12
  AMP PEAK  2(1Q21.3) WILD-TYPE                                7     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1Q21.3) MUTATED                          21
  AMP PEAK  2(1Q21.3) WILD-TYPE                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           0   105
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         2    96
D2V10, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                              12
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             105
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  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"
D2V11, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   10 85
  AMP PEAK  2(1Q21.3) WILD-TYPE 13 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     10   85
  AMP PEAK  2(1Q21.3) WILD-TYPE   13   76
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                          85
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                            76
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   68 28
  AMP PEAK  2(1Q21.3) WILD-TYPE 66 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     68   28
  AMP PEAK  2(1Q21.3) WILD-TYPE   66   13
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  TUMOR FREE                          68                            66
  WITH TUMOR                          28                            13
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  2(1Q21.3) MUTATED       31      2       1      7       3
  AMP PEAK  2(1Q21.3) WILD-TYPE     22      3       0      4       4
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK  2(1Q21.3) MUTATED             104       9
  AMP PEAK  2(1Q21.3) WILD-TYPE            97       5
D2V14, multiclass
               clus
vv              AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  BRAZIL                                 31                            22
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  7                             4
  UKRAINE                                 3                             4
  UNITED STATES                         104                            97
  VIETNAM                                 9                             5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  2(1Q21.3) MUTATED    7 67 67  1 11
  AMP PEAK  2(1Q21.3) WILD-TYPE 11 62 46  0 13
D2V15, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  G1                           7                            11
  G2                          67                            62
  G3                          67                            46
  G4                           1                             0
  GX                          11                            13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V16, continuous
D2V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  2(1Q21.3) MUTATED                                            18
  AMP PEAK  2(1Q21.3) WILD-TYPE                                          19
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  2(1Q21.3) MUTATED                                        5
  AMP PEAK  2(1Q21.3) WILD-TYPE                                      4
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  2(1Q21.3) MUTATED                                                 2
  AMP PEAK  2(1Q21.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  2(1Q21.3) MUTATED               36                  77
  AMP PEAK  2(1Q21.3) WILD-TYPE             26                  65
D2V18, multiclass
                                                 clus
vv                                                AMP PEAK  2(1Q21.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           36
  LIFELONG NON-SMOKER                                                      77
                                                 clus
vv                                                AMP PEAK  2(1Q21.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             26
  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"
D2V19, continuous
D2V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  2(1Q21.3) MUTATED            14       56             3        9
  AMP PEAK  2(1Q21.3) WILD-TYPE           5       46             9       16
D2V21, multiclass
               clus
vv              AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  COMBINATION                            14                             5
  EXTERNAL                               56                            46
  EXTERNAL BEAM                           3                             9
  INTERNAL                                9                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V22, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   15  1
  AMP PEAK  2(1Q21.3) WILD-TYPE 10  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     15    1
  AMP PEAK  2(1Q21.3) WILD-TYPE   10    2
                         clus
vv                        AMP PEAK  2(1Q21.3) MUTATED
  COMPLETED AS PLANNED                             15
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        AMP PEAK  2(1Q21.3) WILD-TYPE
  COMPLETED AS PLANNED                               10
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  2(1Q21.3) MUTATED                    1                0
  AMP PEAK  2(1Q21.3) WILD-TYPE                  1                2
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  2(1Q21.3) MUTATED                    21            18
  AMP PEAK  2(1Q21.3) WILD-TYPE                  15            15
D2V23, multiclass
                     clus
vv                    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  DISTANT RECURRENCE                            1                             1
  LOCAL RECURRENCE                              0                             2
  PRIMARY TUMOR FIELD                          21                            15
  REGIONAL SITE                                18                            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V24, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   32  3
  AMP PEAK  2(1Q21.3) WILD-TYPE 24  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     32    3
  AMP PEAK  2(1Q21.3) WILD-TYPE   24    2
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  CGY                          32                            24
  GY                            3                             2
[1] 2 2
[1] FALSE
D2V25, continuous
D2V26, continuous
D2V27, continuous
D2V28, continuous
D2V29, continuous
D2V30, 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                                     2
  AMP PEAK  2(1Q21.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  2(1Q21.3) MUTATED                        18                       0
  AMP PEAK  2(1Q21.3) WILD-TYPE                      17                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  2(1Q21.3) MUTATED                         4
  AMP PEAK  2(1Q21.3) WILD-TYPE                       4
D2V31, multiclass
                                     clus
vv                                    AMP PEAK  2(1Q21.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  OTHER LOCATION, SPECIFY                                      18
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       4
                                     clus
vv                                    AMP PEAK  2(1Q21.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                        17
  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  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                                               13
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             12
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  2(1Q21.3) MUTATED                                                                                  49
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                                32
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  2(1Q21.3) MUTATED                                                                                             63
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                                           57
D2V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  2(1Q21.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          63
                                                                                              clus
vv                                                                                             AMP PEAK  2(1Q21.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       32
  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"
D2V33, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   35 40
  AMP PEAK  2(1Q21.3) WILD-TYPE 35 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     35   40
  AMP PEAK  2(1Q21.3) WILD-TYPE   35   33
         clus
vv        AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ABSENT                           35                            35
  PRESENT                          40                            33
[1] 2 2
[1] FALSE
D2V34, continuous
D2V35, continuous
D2V36, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   25 63
  AMP PEAK  2(1Q21.3) WILD-TYPE 23 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     25   63
  AMP PEAK  2(1Q21.3) WILD-TYPE   23   53
                                          clus
vv                                         AMP PEAK  2(1Q21.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          63
                                          clus
vv                                         AMP PEAK  2(1Q21.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            53
[1] 2 2
[1] FALSE
D2V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  2(1Q21.3) MUTATED              5          26         47
  AMP PEAK  2(1Q21.3) WILD-TYPE           10          27         37
D2V38, multiclass
              clus
vv             AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  CURRENT USER                           5                            10
  FORMER USER                           26                            27
  NEVER USED                            47                            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"
D2V39, continuous
D2V40, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   44 10
  AMP PEAK  2(1Q21.3) WILD-TYPE 48  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     44   10
  AMP PEAK  2(1Q21.3) WILD-TYPE   48    7
         clus
vv        AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ABSENT                           44                            48
  PRESENT                          10                             7
[1] 2 2
[1] FALSE
D2V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  2(1Q21.3) MUTATED      0  11   36   14  3   8    7    2  23  2   2
  AMP PEAK  2(1Q21.3) WILD-TYPE    1  23   33   16  3   2    0    7  13  0   0
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK  2(1Q21.3) MUTATED    11  4   0 12
  AMP PEAK  2(1Q21.3) WILD-TYPE   6  4   1  4
D2V42, multiclass
      clus
vv     AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1A1                           0                             1
  T1B                           11                            23
  T1B1                          36                            33
  T1B2                          14                            16
  T2                             3                             3
  T2A                            8                             2
  T2A1                           7                             0
  T2A2                           2                             7
  T2B                           23                            13
  T3                             2                             0
  T3A                            2                             0
  T3B                           11                             6
  T4                             4                             4
  TIS                            0                             1
  TX                            12                             4
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  2(1Q21.3) MUTATED         3        0         0         0       19
  AMP PEAK  2(1Q21.3) WILD-TYPE       2        1         1         1       14
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED          35        16        2         4
  AMP PEAK  2(1Q21.3) WILD-TYPE        42        20        2         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  2(1Q21.3) MUTATED            5          3        24         1
  AMP PEAK  2(1Q21.3) WILD-TYPE          0          4        19         0
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  2(1Q21.3) MUTATED            3         26         4         8
  AMP PEAK  2(1Q21.3) WILD-TYPE          0         16         3         4
D2V44, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            19                            14
  STAGE IB1                           35                            42
  STAGE IB2                           16                            20
  STAGE II                             2                             2
  STAGE IIA                            4                             4
  STAGE IIA1                           5                             0
  STAGE IIA2                           3                             4
  STAGE IIB                           24                            19
  STAGE III                            1                             0
  STAGE IIIA                           3                             0
  STAGE IIIB                          26                            16
  STAGE IVA                            4                             3
  STAGE IVB                            8                             4
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(1Q44) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  3(1Q44) MUTATED   107  36
  AMP PEAK  3(1Q44) WILD-TYPE 106  29
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        143                         135 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         36                          29 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       12.39        49.48        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-A1ML TCGA-C5-A1MP 
       38.99        35.61         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HF 
       44.22        83.05        78.35       100.14        52.01        17.85 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UI TCGA-C5-A7X8 
      154.32       101.82       134.33        15.48        94.95         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH 
       50.99        45.83         8.35        23.51        27.52         1.12 
TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       44.94        87.75        58.88         2.66       117.99        22.98 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3QD 
       17.52         8.28        37.35        30.90        31.36        13.05 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.56        14.50        26.01        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ 
        1.51        19.27         0.59         0.59        16.08         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A3L1 
       47.77         2.24         0.10         0.10         0.03         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO 
       14.70        19.79         8.32        15.55        23.84         2.17 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.45         1.35        25.41        10.82        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VJ 
        9.44       117.40        81.96        29.85        36.36        21.44 
TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       20.48         8.28        18.15       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MA-AA42 
       11.28         0.30         0.82        20.28         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       11.38        13.87        35.05         2.96        16.41        15.95 
TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG 
       17.56         9.34        15.39        19.59        93.99        12.16 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       10.03        40.50        26.43        19.96        59.51        32.15 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A954 
       11.51        57.93        31.27        16.64         4.73        50.63 
TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UD 
       48.07        45.34        44.94        43.40        25.74        19.69 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UV TCGA-VS-A9V2 
       40.96        14.53        27.25        43.27         3.42        14.04 
TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       14.89        26.01        29.26         1.41         3.91 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BQ TCGA-C5-A1M5 
       57.04        23.67        11.44        68.84        19.86        67.46 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV 
       30.21        35.01        57.73        40.93        73.18        73.45 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CM 
       38.43        33.24        18.02        20.42       210.67        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19       155.77       131.11         9.34        13.61 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
      146.86        99.91        20.81        20.91        11.87        58.88 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       50.76        40.04        36.76       118.65        16.83        16.18 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       39.55        12.36        31.53        25.02        14.50        26.40 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2H1 
       12.66        12.82         7.46        14.89        26.79        26.27 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC 
        6.64         0.43         1.45         0.13         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.03         0.36         0.07         0.10        20.35         7.92 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        1.22         0.92        31.36        36.26         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH 
       21.67       147.39       137.16        66.81        96.95        78.71 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ 
       27.42         3.29        24.56        15.58        28.37        21.11 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.89        12.49        13.35        22.52        17.82        19.56 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
       34.62         5.42        54.81        20.84         5.49        15.58 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 
        9.04        16.14        14.07        15.88        19.36         3.88 
TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8Q9 TCGA-VS-A8QA 
       11.67        66.05        37.78        18.05        46.03        36.13 
TCGA-VS-A8QH TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       39.78        36.26        24.39        39.78        50.86        15.68 
TCGA-VS-A958 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ 
       50.14        42.41        21.30        22.72        46.92         1.71 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.42        35.97        20.09        14.53        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       18.84         5.16         4.34        16.24        15.42        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
       19.13         0.69         0.16 

  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                       0.03                        0.03 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     195.85                      210.67 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                      19.59                       20.35 
[1] "0.0 - 195.8 (19.6)" "0.0 - 210.7 (20.4)"
[1] "hr=" "1.2"
D3V2, continuous
                             vv
clus                          T1 T2 T3 T4
  AMP PEAK  3(1Q44) MUTATED   60 40 15  3
  AMP PEAK  3(1Q44) WILD-TYPE 74 28  6  5
D3V3, multiclass
    clus
vv   AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  T1                        60                          74
  T2                        40                          28
  T3                        15                           6
  T4                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   61 30
  AMP PEAK  3(1Q44) WILD-TYPE 66 25
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     61   30
  AMP PEAK  3(1Q44) WILD-TYPE   66   25
   clus
vv  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  0                        61                          66
  1                        30                          25
[1] 2 2
[1] FALSE
D3V5, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   58  8
  AMP PEAK  3(1Q44) WILD-TYPE 49  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     58    8
  AMP PEAK  3(1Q44) WILD-TYPE   49    2
   clus
vv  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  0                        58                          49
  1                         8                           2
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(1Q44) MUTATED               3                              132
  AMP PEAK  3(1Q44) WILD-TYPE             2                              109
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  3(1Q44) MUTATED                                               3
  AMP PEAK  3(1Q44) WILD-TYPE                                             3
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  3(1Q44) MUTATED                                    11
  AMP PEAK  3(1Q44) WILD-TYPE                                  11
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  3(1Q44) MUTATED                                           0
  AMP PEAK  3(1Q44) WILD-TYPE                                         3
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  3(1Q44) MUTATED                                              3
  AMP PEAK  3(1Q44) WILD-TYPE                                           12
D3V6, multiclass
                                               clus
vv                                              AMP PEAK  3(1Q44) MUTATED
  ADENOSQUAMOUS                                                         3
  CERVICAL SQUAMOUS CELL CARCINOMA                                    132
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                  11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          3
                                               clus
vv                                              AMP PEAK  3(1Q44) WILD-TYPE
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      109
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    20 132
  AMP PEAK  3(1Q44) WILD-TYPE  10 130
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     20  132
  AMP PEAK  3(1Q44) WILD-TYPE   10  130
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         20                          10
  YES                       132                         130
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(1Q44) MUTATED                                  1    13
  AMP PEAK  3(1Q44) WILD-TYPE                                7     5
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1Q44) MUTATED                          18
  AMP PEAK  3(1Q44) WILD-TYPE                        10
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q44) MUTATED                                           0   105
  AMP PEAK  3(1Q44) WILD-TYPE                                         2    96
D3V10, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                            13
  BLACK OR AFRICAN AMERICAN                                        18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                           105
                                           clus
vv                                          AMP PEAK  3(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    7
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  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"
D3V11, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED    9 85
  AMP PEAK  3(1Q44) WILD-TYPE 14 76
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED      9   85
  AMP PEAK  3(1Q44) WILD-TYPE   14   76
                        clus
vv                       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             9                          14
  NOT HISPANIC OR LATINO                        85                          76
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   67 26
  AMP PEAK  3(1Q44) WILD-TYPE 67 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     67   26
  AMP PEAK  3(1Q44) WILD-TYPE   67   15
            clus
vv           AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  TUMOR FREE                        67                          67
  WITH TUMOR                        26                          15
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  3(1Q44) MUTATED       26      2       1      5       3
  AMP PEAK  3(1Q44) WILD-TYPE     27      3       0      6       4
                             vv
clus                          UNITED STATES VIETNAM
  AMP PEAK  3(1Q44) MUTATED             105      10
  AMP PEAK  3(1Q44) WILD-TYPE            96       4
D3V14, multiclass
               clus
vv              AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  BRAZIL                               26                          27
  CANADA                                2                           3
  NIGERIA                               1                           0
  RUSSIA                                5                           6
  UKRAINE                               3                           4
  UNITED STATES                       105                          96
  VIETNAM                              10                           4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  AMP PEAK  3(1Q44) MUTATED    6 68 65  0 10
  AMP PEAK  3(1Q44) WILD-TYPE 12 61 48  1 14
D3V15, multiclass
    clus
vv   AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  G1                         6                          12
  G2                        68                          61
  G3                        65                          48
  G4                         0                           1
  GX                        10                          14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V16, continuous
D3V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  3(1Q44) MUTATED                                            16
  AMP PEAK  3(1Q44) WILD-TYPE                                          21
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  3(1Q44) MUTATED                                        5
  AMP PEAK  3(1Q44) WILD-TYPE                                      4
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  3(1Q44) MUTATED                                                 2
  AMP PEAK  3(1Q44) WILD-TYPE                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  3(1Q44) MUTATED               36                  73
  AMP PEAK  3(1Q44) WILD-TYPE             26                  69
D3V18, multiclass
                                                 clus
vv                                                AMP PEAK  3(1Q44) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                            16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         2
  CURRENT SMOKER                                                         36
  LIFELONG NON-SMOKER                                                    73
                                                 clus
vv                                                AMP PEAK  3(1Q44) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    4
  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"
D3V19, continuous
D3V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  3(1Q44) MUTATED            16       53             4        7
  AMP PEAK  3(1Q44) WILD-TYPE           3       49             8       18
D3V21, multiclass
               clus
vv              AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  COMBINATION                          16                           3
  EXTERNAL                             53                          49
  EXTERNAL BEAM                         4                           8
  INTERNAL                              7                          18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V22, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   17  2
  AMP PEAK  3(1Q44) WILD-TYPE  8  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     17    2
  AMP PEAK  3(1Q44) WILD-TYPE    8    1
                         clus
vv                        AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  COMPLETED AS PLANNED                           17                           8
  TREATMENT NOT COMPLETED                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                          DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  3(1Q44) MUTATED                    1                0
  AMP PEAK  3(1Q44) WILD-TYPE                  1                2
                             vv
clus                          PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  3(1Q44) MUTATED                    17            16
  AMP PEAK  3(1Q44) WILD-TYPE                  19            17
D3V23, multiclass
                     clus
vv                    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  DISTANT RECURRENCE                          1                           1
  LOCAL RECURRENCE                            0                           2
  PRIMARY TUMOR FIELD                        17                          19
  REGIONAL SITE                              16                          17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V24, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   27  3
  AMP PEAK  3(1Q44) WILD-TYPE 29  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     27    3
  AMP PEAK  3(1Q44) WILD-TYPE   29    2
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  CGY                        27                          29
  GY                          3                           2
[1] 2 2
[1] FALSE
D3V25, continuous
D3V26, continuous
D3V27, continuous
D3V28, continuous
D3V29, continuous
D3V30, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  3(1Q44) MUTATED                                     1
  AMP PEAK  3(1Q44) WILD-TYPE                                   1
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  3(1Q44) MUTATED                                     3
  AMP PEAK  3(1Q44) WILD-TYPE                                   4
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  3(1Q44) MUTATED                        20                       0
  AMP PEAK  3(1Q44) WILD-TYPE                      15                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  3(1Q44) MUTATED                         4
  AMP PEAK  3(1Q44) WILD-TYPE                       4
D3V31, multiclass
                                     clus
vv                                    AMP PEAK  3(1Q44) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         3
  OTHER LOCATION, SPECIFY                                    20
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     4
                                     clus
vv                                    AMP PEAK  3(1Q44) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      15
  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  3(1Q44) MUTATED                                               0
  AMP PEAK  3(1Q44) WILD-TYPE                                             2
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  3(1Q44) MUTATED                                               15
  AMP PEAK  3(1Q44) WILD-TYPE                                             10
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  3(1Q44) MUTATED                                                                                  48
  AMP PEAK  3(1Q44) WILD-TYPE                                                                                33
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  3(1Q44) MUTATED                                                                                             58
  AMP PEAK  3(1Q44) WILD-TYPE                                                                                           62
D3V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  3(1Q44) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                      15
  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)                        58
                                                                                              clus
vv                                                                                             AMP PEAK  3(1Q44) 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)                                     33
  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"
D3V33, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   30 43
  AMP PEAK  3(1Q44) WILD-TYPE 40 30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     30   43
  AMP PEAK  3(1Q44) WILD-TYPE   40   30
         clus
vv        AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  ABSENT                         30                          40
  PRESENT                        43                          30
[1] 2 2
[1] FALSE
D3V34, continuous
D3V35, continuous
D3V36, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   23 63
  AMP PEAK  3(1Q44) WILD-TYPE 25 53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     23   63
  AMP PEAK  3(1Q44) WILD-TYPE   25   53
                                          clus
vv                                         AMP PEAK  3(1Q44) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        63
                                          clus
vv                                         AMP PEAK  3(1Q44) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          53
[1] 2 2
[1] FALSE
D3V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  3(1Q44) MUTATED              5          29         40
  AMP PEAK  3(1Q44) WILD-TYPE           10          24         44
D3V38, multiclass
              clus
vv             AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  CURRENT USER                         5                          10
  FORMER USER                         29                          24
  NEVER USED                          40                          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"
D3V39, continuous
D3V40, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   44  9
  AMP PEAK  3(1Q44) WILD-TYPE 48  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     44    9
  AMP PEAK  3(1Q44) WILD-TYPE   48    8
         clus
vv        AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  ABSENT                         44                          48
  PRESENT                         9                           8
[1] 2 2
[1] FALSE
D3V41, continuous
                             vv
clus                          T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  3(1Q44) MUTATED      0  10   35   15  4   8    6    2  20  2   1
  AMP PEAK  3(1Q44) WILD-TYPE    1  24   34   15  2   2    1    7  16  0   1
                             vv
clus                          T3B T4 TIS TX
  AMP PEAK  3(1Q44) MUTATED    12  3   0 11
  AMP PEAK  3(1Q44) WILD-TYPE   5  5   1  5
D3V42, multiclass
      clus
vv     AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  T1A1                         0                           1
  T1B                         10                          24
  T1B1                        35                          34
  T1B2                        15                          15
  T2                           4                           2
  T2A                          8                           2
  T2A1                         6                           1
  T2A2                         2                           7
  T2B                         20                          16
  T3                           2                           0
  T3A                          1                           1
  T3B                         12                           5
  T4                           3                           5
  TIS                          0                           1
  TX                          11                           5
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  3(1Q44) MUTATED         3        0         0         0       16
  AMP PEAK  3(1Q44) WILD-TYPE       2        1         1         1       17
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK  3(1Q44) MUTATED          35        17        2         4          4
  AMP PEAK  3(1Q44) WILD-TYPE        42        19        2         4          1
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  AMP PEAK  3(1Q44) MUTATED            3        23         1          2
  AMP PEAK  3(1Q44) WILD-TYPE          4        20         0          1
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  3(1Q44) MUTATED           28         3         7
  AMP PEAK  3(1Q44) WILD-TYPE         14         4         5
D3V44, multiclass
            clus
vv           AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  STAGE I                            3                           2
  STAGE IA                           0                           1
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                          16                          17
  STAGE IB1                         35                          42
  STAGE IB2                         17                          19
  STAGE II                           2                           2
  STAGE IIA                          4                           4
  STAGE IIA1                         4                           1
  STAGE IIA2                         3                           4
  STAGE IIB                         23                          20
  STAGE III                          1                           0
  STAGE IIIA                         2                           1
  STAGE IIIB                        28                          14
  STAGE IVA                          3                           4
  STAGE IVB                          7                           5
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(2P24.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P24.3) MUTATED    59  17
  AMP PEAK  4(2P24.3) WILD-TYPE 154  48
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           76                           202 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           17                            48 
$`AMP PEAK  4(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        33.24       131.11         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH 
        2.73        50.99        45.83        23.51        27.52         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A3HR TCGA-EA-A411 
       58.88        44.94        22.98        17.52        30.90        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF 
       14.50        26.01        12.66        14.89        13.91        14.96 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2RA TCGA-EK-A2RJ 
       12.59        26.27         1.51        19.27        16.08         1.18 
TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG 
        2.24         0.10         7.92         6.94        23.84         0.92 
TCGA-FU-A3HY TCGA-FU-A40J TCGA-IR-A3LA TCGA-IR-A3LC TCGA-JW-A5VJ TCGA-JX-A5QV 
       31.36         1.35       137.16       117.40        21.44         7.99 
TCGA-LP-A7HU TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       13.35        19.56         9.17         5.49        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8EJ 
       15.95        19.36        11.67        93.99        18.05        19.96 
TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 TCGA-VS-A959 TCGA-VS-A9U5 
       57.93        16.64         4.73        50.86        45.34        44.94 
TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL 
       43.40        21.30        22.72        19.69        40.96        14.53 
TCGA-VS-A9UP TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 
       43.27        14.89        16.24        26.01 

$`AMP PEAK  4(2P24.3) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       12.39        49.48        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK 
       46.32        30.21        35.01        53.16        38.99         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35       100.14        38.43        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A8XI 
       20.35       147.35        17.19       155.77        94.95         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK 
      146.86        99.91        20.81        20.91        11.87        50.76 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
      118.65        16.83        16.18         8.28        39.55        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       37.35        31.53        31.36        13.05        25.02        14.50 
TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       26.40        12.82         7.46        26.79        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PL 
       13.58        13.48         0.36        45.96         6.64         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         0.59         1.45         0.13         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK 
        0.03         0.36        47.77         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        0.03        20.35        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        1.22         2.17        36.26         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        10.82        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
      147.39        66.81        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       195.85        30.31 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W 
       11.28         0.89        12.49         0.30         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       20.28        17.82         8.52        11.38        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A6DT 
        5.42        54.81        35.05        20.84         2.96         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        15.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59         3.88        12.16        66.05        10.03        40.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       37.78        26.43        59.51        32.15        46.03        36.13 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 
       11.51        39.78        31.27        36.26        24.39        39.78 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U7 TCGA-VS-A9UA 
       15.68        50.63        48.07        50.14        42.41        25.74 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
       46.92         1.71        27.25        41.42        35.97        20.09 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       14.04         4.34        15.42        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                       137.16                        210.67 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                       19.460                        20.185 
[1] "0.1 - 137.2 (19.5)" "0.0 - 210.7 (20.2)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(2P24.3) MUTATED    33  23   5   2
  AMP PEAK  4(2P24.3) WILD-TYPE 101  45  16   6
D4V3, multiclass
    clus
vv   AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  T1                          33                           101
  T2                          23                            45
  T3                           5                            16
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   35 13
  AMP PEAK  4(2P24.3) WILD-TYPE 92 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     35   13
  AMP PEAK  4(2P24.3) WILD-TYPE   92   42
   clus
vv  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  0                          35                            92
  1                          13                            42
[1] 2 2
[1] FALSE
D4V5, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   31  4
  AMP PEAK  4(2P24.3) WILD-TYPE 76  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     31    4
  AMP PEAK  4(2P24.3) WILD-TYPE   76    6
   clus
vv  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  0                          31                            76
  1                           4                             6
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(2P24.3) MUTATED               2                               62
  AMP PEAK  4(2P24.3) WILD-TYPE             3                              179
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  4(2P24.3) MUTATED                                               1
  AMP PEAK  4(2P24.3) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  4(2P24.3) MUTATED                                     7
  AMP PEAK  4(2P24.3) WILD-TYPE                                  15
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  4(2P24.3) MUTATED                                           2
  AMP PEAK  4(2P24.3) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  4(2P24.3) MUTATED                                              5
  AMP PEAK  4(2P24.3) WILD-TYPE                                           10
D4V6, multiclass
                                               clus
vv                                              AMP PEAK  4(2P24.3) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       62
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
                                               clus
vv                                              AMP PEAK  4(2P24.3) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        179
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             10
[1] 6 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(2P24.3) MUTATED     5  74
  AMP PEAK  4(2P24.3) WILD-TYPE  25 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      5   74
  AMP PEAK  4(2P24.3) WILD-TYPE   25  188
     clus
vv    AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  NO                            5                            25
  YES                          74                           188
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(2P24.3) MUTATED                                  2     3
  AMP PEAK  4(2P24.3) WILD-TYPE                                6    15
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(2P24.3) MUTATED                           5
  AMP PEAK  4(2P24.3) WILD-TYPE                        23
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(2P24.3) MUTATED                                           1    57
  AMP PEAK  4(2P24.3) WILD-TYPE                                         1   144
D4V10, multiclass
                                           clus
vv                                          AMP PEAK  4(2P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              57
                                           clus
vv                                          AMP PEAK  4(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                            23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               144
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED     5  40
  AMP PEAK  4(2P24.3) WILD-TYPE  18 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      5   40
  AMP PEAK  4(2P24.3) WILD-TYPE   18  121
                        clus
vv                       AMP PEAK  4(2P24.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       AMP PEAK  4(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           121
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   35 12
  AMP PEAK  4(2P24.3) WILD-TYPE 99 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     35   12
  AMP PEAK  4(2P24.3) WILD-TYPE   99   29
            clus
vv           AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  TUMOR FREE                          35                            99
  WITH TUMOR                          12                            29
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  4(2P24.3) MUTATED       17      3       0      3       3
  AMP PEAK  4(2P24.3) WILD-TYPE     36      2       1      8       4
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK  4(2P24.3) MUTATED              50       3
  AMP PEAK  4(2P24.3) WILD-TYPE           151      11
D4V14, multiclass
               clus
vv              AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  BRAZIL                                 17                            36
  CANADA                                  3                             2
  NIGERIA                                 0                             1
  RUSSIA                                  3                             8
  UKRAINE                                 3                             4
  UNITED STATES                          50                           151
  VIETNAM                                 3                            11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  4(2P24.3) MUTATED    3 30 37  0  6
  AMP PEAK  4(2P24.3) WILD-TYPE 15 99 76  1 18
D4V15, multiclass
    clus
vv   AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  G1                           3                            15
  G2                          30                            99
  G3                          37                            76
  G4                           0                             1
  GX                           6                            18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V16, continuous
D4V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  4(2P24.3) MUTATED                                            10
  AMP PEAK  4(2P24.3) WILD-TYPE                                          27
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  4(2P24.3) MUTATED                                        1
  AMP PEAK  4(2P24.3) WILD-TYPE                                      8
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  4(2P24.3) MUTATED                                                 1
  AMP PEAK  4(2P24.3) WILD-TYPE                                               2
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  4(2P24.3) MUTATED               15                  41
  AMP PEAK  4(2P24.3) WILD-TYPE             47                 101
D4V18, multiclass
                                                 clus
vv                                                AMP PEAK  4(2P24.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           15
  LIFELONG NON-SMOKER                                                      41
                                                 clus
vv                                                AMP PEAK  4(2P24.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             47
  LIFELONG NON-SMOKER                                                       101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V19, continuous
D4V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  4(2P24.3) MUTATED             3       33             2        7
  AMP PEAK  4(2P24.3) WILD-TYPE          16       69            10       18
D4V21, multiclass
               clus
vv              AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  COMBINATION                             3                            16
  EXTERNAL                               33                            69
  EXTERNAL BEAM                           2                            10
  INTERNAL                                7                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V22, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED    5  0
  AMP PEAK  4(2P24.3) WILD-TYPE 20  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      5    0
  AMP PEAK  4(2P24.3) WILD-TYPE   20    3
                         clus
vv                        AMP PEAK  4(2P24.3) MUTATED
  COMPLETED AS PLANNED                              5
  TREATMENT NOT COMPLETED                           0
                         clus
vv                        AMP PEAK  4(2P24.3) WILD-TYPE
  COMPLETED AS PLANNED                               20
  TREATMENT NOT COMPLETED                             3
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  4(2P24.3) MUTATED                    0                0
  AMP PEAK  4(2P24.3) WILD-TYPE                  2                2
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  4(2P24.3) MUTATED                    15             9
  AMP PEAK  4(2P24.3) WILD-TYPE                  21            24
D4V23, multiclass
                     clus
vv                    AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              0                             2
  PRIMARY TUMOR FIELD                          15                            21
  REGIONAL SITE                                 9                            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V24, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   18  2
  AMP PEAK  4(2P24.3) WILD-TYPE 38  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     18    2
  AMP PEAK  4(2P24.3) WILD-TYPE   38    3
     clus
vv    AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  CGY                          18                            38
  GY                            2                             3
[1] 2 2
[1] FALSE
D4V25, continuous
D4V26, continuous
D4V27, continuous
D4V28, continuous
D4V29, continuous
D4V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  4(2P24.3) MUTATED                                     0
  AMP PEAK  4(2P24.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  4(2P24.3) MUTATED                                     2
  AMP PEAK  4(2P24.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  4(2P24.3) MUTATED                         8                       0
  AMP PEAK  4(2P24.3) WILD-TYPE                      27                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  4(2P24.3) MUTATED                         1
  AMP PEAK  4(2P24.3) WILD-TYPE                       7
D4V31, multiclass
                                     clus
vv                                    AMP PEAK  4(2P24.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  OTHER LOCATION, SPECIFY                                       8
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    AMP PEAK  4(2P24.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                        27
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  4(2P24.3) MUTATED                                               0
  AMP PEAK  4(2P24.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  4(2P24.3) MUTATED                                                6
  AMP PEAK  4(2P24.3) WILD-TYPE                                             19
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  4(2P24.3) MUTATED                                                                                  22
  AMP PEAK  4(2P24.3) WILD-TYPE                                                                                59
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  4(2P24.3) MUTATED                                                                                             32
  AMP PEAK  4(2P24.3) WILD-TYPE                                                                                           88
D4V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  4(2P24.3) 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)                                     22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          32
                                                                                              clus
vv                                                                                             AMP PEAK  4(2P24.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       59
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V33, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   20 18
  AMP PEAK  4(2P24.3) WILD-TYPE 50 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     20   18
  AMP PEAK  4(2P24.3) WILD-TYPE   50   55
         clus
vv        AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  ABSENT                           20                            50
  PRESENT                          18                            55
[1] 2 2
[1] FALSE
D4V34, continuous
D4V35, continuous
D4V36, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   11 29
  AMP PEAK  4(2P24.3) WILD-TYPE 37 87
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     11   29
  AMP PEAK  4(2P24.3) WILD-TYPE   37   87
                                          clus
vv                                         AMP PEAK  4(2P24.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          29
                                          clus
vv                                         AMP PEAK  4(2P24.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            87
[1] 2 2
[1] FALSE
D4V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  4(2P24.3) MUTATED              6          18         24
  AMP PEAK  4(2P24.3) WILD-TYPE            9          35         60
D4V38, multiclass
              clus
vv             AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  CURRENT USER                           6                             9
  FORMER USER                           18                            35
  NEVER USED                            24                            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"
D4V39, continuous
D4V40, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   22  6
  AMP PEAK  4(2P24.3) WILD-TYPE 70 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     22    6
  AMP PEAK  4(2P24.3) WILD-TYPE   70   11
         clus
vv        AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  ABSENT                           22                            70
  PRESENT                           6                            11
[1] 2 2
[1] FALSE
D4V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  4(2P24.3) MUTATED      0   6   22    5  2   4    4    2  11  0   1
  AMP PEAK  4(2P24.3) WILD-TYPE    1  28   47   25  4   6    3    7  25  2   1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK  4(2P24.3) MUTATED     4  2   1  3
  AMP PEAK  4(2P24.3) WILD-TYPE  13  6   0 13
D4V42, multiclass
      clus
vv     AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  T1A1                           0                             1
  T1B                            6                            28
  T1B1                          22                            47
  T1B2                           5                            25
  T2                             2                             4
  T2A                            4                             6
  T2A1                           4                             3
  T2A2                           2                             7
  T2B                           11                            25
  T3                             0                             2
  T3A                            1                             1
  T3B                            4                            13
  T4                             2                             6
  TIS                            1                             0
  TX                             3                            13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  4(2P24.3) MUTATED         0        0         0         0        5
  AMP PEAK  4(2P24.3) WILD-TYPE       5        1         1         1       28
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  4(2P24.3) MUTATED          24         8        2         3
  AMP PEAK  4(2P24.3) WILD-TYPE        53        28        2         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  4(2P24.3) MUTATED            3          1        15         0
  AMP PEAK  4(2P24.3) WILD-TYPE          2          6        28         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  4(2P24.3) MUTATED            1         10         0         3
  AMP PEAK  4(2P24.3) WILD-TYPE          2         32         7         9
D4V44, multiclass
            clus
vv           AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             5                            28
  STAGE IB1                           24                            53
  STAGE IB2                            8                            28
  STAGE II                             2                             2
  STAGE IIA                            3                             5
  STAGE IIA1                           3                             2
  STAGE IIA2                           1                             6
  STAGE IIB                           15                            28
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          10                            32
  STAGE IVA                            0                             7
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(2Q33.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(2Q33.1) MUTATED    30  10
  AMP PEAK  5(2Q33.1) WILD-TYPE 183  55
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           40                           238 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           10                            55 
$`AMP PEAK  5(2Q33.1) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LY TCGA-C5-A2M2 
       57.04        31.40        35.61         0.46        78.35        33.24 
TCGA-C5-A3HD TCGA-C5-A7CK TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK 
       52.01       134.33       131.11         2.73        45.83        99.91 
TCGA-DG-A2KJ TCGA-DS-A7WI TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5ZF TCGA-EA-A6QX 
       58.88         8.28        14.50        26.01        14.96        13.58 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RM 
       12.59        45.96        26.27        19.27         0.59         2.24 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-HG-A9SC TCGA-JW-A5VL TCGA-LP-A4AX TCGA-LP-A5U2 
        1.45         1.35        10.82        15.58        12.49         0.30 
TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8QF 
       19.36        11.67        93.99        10.03        18.05        57.93 
TCGA-VS-A959 TCGA-VS-A9UD TCGA-VS-A9UO TCGA-ZJ-A8QQ 
       45.34        19.69        41.42        67.59 

$`AMP PEAK  5(2Q33.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        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-A1M9 TCGA-C5-A1ME 
       19.86        67.46        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05       100.14        38.43 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ 
        9.34        13.61        50.99         8.35       146.86        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52        20.81        20.91        11.87         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18        17.52 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        12.36        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S 
       13.05        25.02        14.50        26.40        24.56        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         7.46        14.89        26.79        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       14.99        13.48         0.36         6.64         1.51         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        0.03         0.36         1.18        47.77         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17        31.36        36.26         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       20.48        28.37         8.28        18.15        21.11       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-LP-A7HU 
       30.31         7.99        11.28         0.89         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        20.28        17.82        19.56         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        13.87        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       20.84         5.49         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC 
       15.39        19.59         3.88        12.16        66.05        40.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       37.78        26.43        19.96        59.51        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        11.51        39.78        31.27        36.26        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
        4.73        24.39        39.78        50.86        15.68        50.63 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       48.07        50.14        44.94        43.40        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       21.30        22.72        46.92        40.96         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV 
       27.25        43.27        35.97        20.09        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        14.04        14.89 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
        4.34        16.24        15.42        26.01        29.26        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                         0.30                          0.03 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                       134.33                        210.67 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                       19.525                        19.910 
[1] "0.3 - 134.3 (19.5)" "0.0 - 210.7 (19.9)"
[1] "hr=" "1"  
D5V2, continuous
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  5(2Q33.1) MUTATED    16   8   3   0
  AMP PEAK  5(2Q33.1) WILD-TYPE 118  60  18   8
D5V3, multiclass
    clus
vv   AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  T1                          16                           118
  T2                           8                            60
  T3                           3                            18
  T4                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED    11  10
  AMP PEAK  5(2Q33.1) WILD-TYPE 116  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     11   10
  AMP PEAK  5(2Q33.1) WILD-TYPE  116   45
   clus
vv  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  0                          11                           116
  1                          10                            45
[1] 2 2
[1] FALSE
D5V5, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED   14  1
  AMP PEAK  5(2Q33.1) WILD-TYPE 93  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     14    1
  AMP PEAK  5(2Q33.1) WILD-TYPE   93    9
   clus
vv  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  0                          14                            93
  1                           1                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(2Q33.1) MUTATED               2                               32
  AMP PEAK  5(2Q33.1) WILD-TYPE             3                              209
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  5(2Q33.1) MUTATED                                               1
  AMP PEAK  5(2Q33.1) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  5(2Q33.1) MUTATED                                     4
  AMP PEAK  5(2Q33.1) WILD-TYPE                                  18
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  5(2Q33.1) MUTATED                                           0
  AMP PEAK  5(2Q33.1) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  5(2Q33.1) MUTATED                                              2
  AMP PEAK  5(2Q33.1) WILD-TYPE                                           13
D5V6, multiclass
                                               clus
vv                                              AMP PEAK  5(2Q33.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       32
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              AMP PEAK  5(2Q33.1) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        209
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED     5  36
  AMP PEAK  5(2Q33.1) WILD-TYPE  25 226
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      5   36
  AMP PEAK  5(2Q33.1) WILD-TYPE   25  226
     clus
vv    AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  NO                            5                            25
  YES                          36                           226
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(2Q33.1) MUTATED                                  2     5
  AMP PEAK  5(2Q33.1) WILD-TYPE                                6    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(2Q33.1) MUTATED                           2
  AMP PEAK  5(2Q33.1) WILD-TYPE                        26
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  5(2Q33.1) MUTATED                                           0    29
  AMP PEAK  5(2Q33.1) WILD-TYPE                                         2   172
D5V10, multiclass
                                           clus
vv                                          AMP PEAK  5(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              29
                                           clus
vv                                          AMP PEAK  5(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               172
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED     2  22
  AMP PEAK  5(2Q33.1) WILD-TYPE  21 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      2   22
  AMP PEAK  5(2Q33.1) WILD-TYPE   21  139
                        clus
vv                       AMP PEAK  5(2Q33.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       AMP PEAK  5(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           139
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED    19   5
  AMP PEAK  5(2Q33.1) WILD-TYPE 115  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     19    5
  AMP PEAK  5(2Q33.1) WILD-TYPE  115   36
            clus
vv           AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  TUMOR FREE                          19                           115
  WITH TUMOR                           5                            36
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  5(2Q33.1) MUTATED        6      1       0      0       1
  AMP PEAK  5(2Q33.1) WILD-TYPE     47      4       1     11       6
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK  5(2Q33.1) MUTATED              28       5
  AMP PEAK  5(2Q33.1) WILD-TYPE           173       9
D5V14, multiclass
               clus
vv              AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  BRAZIL                                  6                            47
  CANADA                                  1                             4
  NIGERIA                                 0                             1
  RUSSIA                                  0                            11
  UKRAINE                                 1                             6
  UNITED STATES                          28                           173
  VIETNAM                                 5                             9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             G1  G2  G3  G4  GX
  AMP PEAK  5(2Q33.1) MUTATED     1  20  16   0   3
  AMP PEAK  5(2Q33.1) WILD-TYPE  17 109  97   1  21
D5V15, multiclass
    clus
vv   AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  G1                           1                            17
  G2                          20                           109
  G3                          16                            97
  G4                           0                             1
  GX                           3                            21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V16, continuous
D5V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  5(2Q33.1) MUTATED                                             5
  AMP PEAK  5(2Q33.1) WILD-TYPE                                          32
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  5(2Q33.1) MUTATED                                        0
  AMP PEAK  5(2Q33.1) WILD-TYPE                                      9
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  5(2Q33.1) MUTATED                                                 1
  AMP PEAK  5(2Q33.1) WILD-TYPE                                               2
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  5(2Q33.1) MUTATED                8                  19
  AMP PEAK  5(2Q33.1) WILD-TYPE             54                 123
D5V18, multiclass
                                                 clus
vv                                                AMP PEAK  5(2Q33.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                            8
  LIFELONG NON-SMOKER                                                      19
                                                 clus
vv                                                AMP PEAK  5(2Q33.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             54
  LIFELONG NON-SMOKER                                                       123
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V19, continuous
D5V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  5(2Q33.1) MUTATED             4       14             1        3
  AMP PEAK  5(2Q33.1) WILD-TYPE          15       88            11       22
D5V21, multiclass
               clus
vv              AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  COMBINATION                             4                            15
  EXTERNAL                               14                            88
  EXTERNAL BEAM                           1                            11
  INTERNAL                                3                            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"
D5V22, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    4  1
  AMP PEAK  5(2Q33.1) WILD-TYPE 21  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      4    1
  AMP PEAK  5(2Q33.1) WILD-TYPE   21    2
                         clus
vv                        AMP PEAK  5(2Q33.1) MUTATED
  COMPLETED AS PLANNED                              4
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        AMP PEAK  5(2Q33.1) WILD-TYPE
  COMPLETED AS PLANNED                               21
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  5(2Q33.1) MUTATED                    0                0
  AMP PEAK  5(2Q33.1) WILD-TYPE                  2                2
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  5(2Q33.1) MUTATED                     5             4
  AMP PEAK  5(2Q33.1) WILD-TYPE                  31            29
D5V23, multiclass
                     clus
vv                    AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              0                             2
  PRIMARY TUMOR FIELD                           5                            31
  REGIONAL SITE                                 4                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V24, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    5  1
  AMP PEAK  5(2Q33.1) WILD-TYPE 51  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      5    1
  AMP PEAK  5(2Q33.1) WILD-TYPE   51    4
     clus
vv    AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  CGY                           5                            51
  GY                            1                             4
[1] 2 2
[1] FALSE
D5V25, continuous
D5V26, continuous
D5V27, continuous
D5V28, continuous
D5V29, continuous
D5V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  5(2Q33.1) MUTATED                                     0
  AMP PEAK  5(2Q33.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  5(2Q33.1) MUTATED                                     0
  AMP PEAK  5(2Q33.1) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  5(2Q33.1) MUTATED                         4                       0
  AMP PEAK  5(2Q33.1) WILD-TYPE                      31                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  5(2Q33.1) MUTATED                         0
  AMP PEAK  5(2Q33.1) WILD-TYPE                       8
D5V31, multiclass
                                     clus
vv                                    AMP PEAK  5(2Q33.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       4
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    AMP PEAK  5(2Q33.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        31
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  5(2Q33.1) MUTATED                                               0
  AMP PEAK  5(2Q33.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  5(2Q33.1) MUTATED                                                5
  AMP PEAK  5(2Q33.1) WILD-TYPE                                             20
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  5(2Q33.1) MUTATED                                                                                   9
  AMP PEAK  5(2Q33.1) WILD-TYPE                                                                                72
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  5(2Q33.1) MUTATED                                                                                             18
  AMP PEAK  5(2Q33.1) WILD-TYPE                                                                                          102
D5V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  5(2Q33.1) 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)                                      9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          18
                                                                                              clus
vv                                                                                             AMP PEAK  5(2Q33.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       72
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V33, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    5 14
  AMP PEAK  5(2Q33.1) WILD-TYPE 65 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      5   14
  AMP PEAK  5(2Q33.1) WILD-TYPE   65   59
         clus
vv        AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  ABSENT                            5                            65
  PRESENT                          14                            59
[1] 2 2
[1] FALSE
D5V34, continuous
D5V35, continuous
D5V36, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED     7  13
  AMP PEAK  5(2Q33.1) WILD-TYPE  41 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      7   13
  AMP PEAK  5(2Q33.1) WILD-TYPE   41  103
                                          clus
vv                                         AMP PEAK  5(2Q33.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          13
                                          clus
vv                                         AMP PEAK  5(2Q33.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           103
[1] 2 2
[1] FALSE
D5V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  5(2Q33.1) MUTATED              0           9          9
  AMP PEAK  5(2Q33.1) WILD-TYPE           15          44         75
D5V38, multiclass
              clus
vv             AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  CURRENT USER                           0                            15
  FORMER USER                            9                            44
  NEVER USED                             9                            75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V39, continuous
D5V40, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    9  3
  AMP PEAK  5(2Q33.1) WILD-TYPE 83 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      9    3
  AMP PEAK  5(2Q33.1) WILD-TYPE   83   14
         clus
vv        AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  ABSENT                            9                            83
  PRESENT                           3                            14
[1] 2 2
[1] FALSE
D5V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  5(2Q33.1) MUTATED      0   2   12    2  0   2    2    1   3  0   1
  AMP PEAK  5(2Q33.1) WILD-TYPE    1  32   57   28  6   8    5    8  33  2   1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK  5(2Q33.1) MUTATED     2  0   0  1
  AMP PEAK  5(2Q33.1) WILD-TYPE  15  8   1 15
D5V42, multiclass
      clus
vv     AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  T1A1                           0                             1
  T1B                            2                            32
  T1B1                          12                            57
  T1B2                           2                            28
  T2                             0                             6
  T2A                            2                             8
  T2A1                           2                             5
  T2A2                           1                             8
  T2B                            3                            33
  T3                             0                             2
  T3A                            1                             1
  T3B                            2                            15
  T4                             0                             8
  TIS                            0                             1
  TX                             1                            15
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  5(2Q33.1) MUTATED         0        0         0         0        3
  AMP PEAK  5(2Q33.1) WILD-TYPE       5        1         1         1       30
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  5(2Q33.1) MUTATED          11         3        0         1
  AMP PEAK  5(2Q33.1) WILD-TYPE        66        33        4         7
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  5(2Q33.1) MUTATED            1          1        10         0
  AMP PEAK  5(2Q33.1) WILD-TYPE          4          6        33         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  5(2Q33.1) MUTATED            1          8         1         0
  AMP PEAK  5(2Q33.1) WILD-TYPE          2         34         6        12
D5V44, multiclass
            clus
vv           AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             3                            30
  STAGE IB1                           11                            66
  STAGE IB2                            3                            33
  STAGE II                             0                             4
  STAGE IIA                            1                             7
  STAGE IIA1                           1                             4
  STAGE IIA2                           1                             6
  STAGE IIB                           10                            33
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                           8                            34
  STAGE IVA                            1                             6
  STAGE IVB                            0                            12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(3Q26.31) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(3Q26.31) MUTATED   166  51
  AMP PEAK  6(3Q26.31) WILD-TYPE  47  14
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                           217                             61 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            51                             14 
$`AMP PEAK  6(3Q26.31) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
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-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14        33.24        18.02        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
      155.77       131.11        94.95         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KH 
       50.99        45.83         8.35        23.51        20.91         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK 
       58.88        50.76        44.94        40.04        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        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        12.36        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E 
       31.36        13.05        24.56        14.50        12.66         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        13.91        15.02        14.99        14.96 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI 
       13.48         0.36        12.59        26.27         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.07         4.04         0.03        47.77         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M 
        0.07         0.03        20.35         6.94        19.79         8.32 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       23.84         1.45         1.48         0.82         3.52         1.35 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.97         9.01        25.41        10.82        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
       14.93         9.44       137.16       117.40        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
       36.36        21.44        20.48        15.58         8.28        18.15 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
      195.85        30.31         7.99        11.28         0.89         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        13.35        22.52        20.28        19.56         9.17 
TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.52        13.87        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       20.84         5.49         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
        9.04        17.56        14.07         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB 
       19.59         3.88        11.67        93.99        12.16        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       40.50        37.78        26.43        18.05        19.96        59.51 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       32.15        46.03        36.13        11.51        57.93        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 
       36.26        16.64         4.73        24.39        39.78        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       50.63        48.07        45.34        44.94        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       25.74        21.30        22.72        19.69        46.92        40.96 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU 
       14.53        27.25        41.42        43.27        35.97        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        14.04 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       15.42        26.01        29.26        19.13         0.69         1.41 
TCGA-ZJ-AAXU 
        0.16 

$`AMP PEAK  6(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       210.67        17.19 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DR-A0ZM 
      146.86        99.91        27.52        20.81        11.87        58.88 
TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA 
       16.18        25.02        14.50        26.40        26.01        12.82 
TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A3GJ 
       13.58        45.96         6.64         0.36         1.18         0.10 
TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
        0.10         7.92        14.70        15.55         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-FU-A770 
        2.17        31.36        36.26         1.58         1.32         1.12 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH 
      147.39        66.81        96.95        29.85        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MA-AA43 
       24.56        28.37        21.11        12.49        17.82        11.38 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-UC-A7PI TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A958 
       16.14        15.88        66.05        39.78        50.86        50.14 
TCGA-VS-A9UJ TCGA-VS-A9UR TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-ZJ-A8QQ 
        1.71        20.09        14.89         4.34        16.24        67.59 
TCGA-ZX-AA5X 
        3.91 

  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                        195.85                         210.67 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                         20.28                          17.82 
[1] "0.0 - 195.8 (20.3)" "0.1 - 210.7 (17.8)"
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  6(3Q26.31) MUTATED   99 53 19  5
  AMP PEAK  6(3Q26.31) WILD-TYPE 35 15  2  3
D6V3, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  T1                           99                             35
  T2                           53                             15
  T3                           19                              2
  T4                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   90 48
  AMP PEAK  6(3Q26.31) WILD-TYPE 37  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     90   48
  AMP PEAK  6(3Q26.31) WILD-TYPE   37    7
   clus
vv  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  0                           90                             37
  1                           48                              7
[1] 2 2
[1] FALSE
D6V5, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   84  8
  AMP PEAK  6(3Q26.31) WILD-TYPE 23  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     84    8
  AMP PEAK  6(3Q26.31) WILD-TYPE   23    2
   clus
vv  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  0                           84                             23
  1                            8                              2
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(3Q26.31) MUTATED               4                              195
  AMP PEAK  6(3Q26.31) WILD-TYPE             1                               46
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  6(3Q26.31) MUTATED                                               4
  AMP PEAK  6(3Q26.31) WILD-TYPE                                             2
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  6(3Q26.31) MUTATED                                    12
  AMP PEAK  6(3Q26.31) WILD-TYPE                                  10
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  6(3Q26.31) MUTATED                                           2
  AMP PEAK  6(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  6(3Q26.31) MUTATED                                              9
  AMP PEAK  6(3Q26.31) WILD-TYPE                                            6
D6V6, multiclass
                                               clus
vv                                              AMP PEAK  6(3Q26.31) MUTATED
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       195
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             9
                                               clus
vv                                              AMP PEAK  6(3Q26.31) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                          46
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    26 200
  AMP PEAK  6(3Q26.31) WILD-TYPE   4  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     26  200
  AMP PEAK  6(3Q26.31) WILD-TYPE    4   62
     clus
vv    AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  NO                            26                              4
  YES                          200                             62
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(3Q26.31) MUTATED                                  5    15
  AMP PEAK  6(3Q26.31) WILD-TYPE                                3     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(3Q26.31) MUTATED                          27
  AMP PEAK  6(3Q26.31) WILD-TYPE                         1
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  6(3Q26.31) MUTATED                                           1
  AMP PEAK  6(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK  6(3Q26.31) MUTATED     146
  AMP PEAK  6(3Q26.31) WILD-TYPE    55
D6V10, multiclass
                                           clus
vv                                          AMP PEAK  6(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                           27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              146
                                           clus
vv                                          AMP PEAK  6(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                  3
  BLACK OR AFRICAN AMERICAN                                              1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    16 124
  AMP PEAK  6(3Q26.31) WILD-TYPE   7  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     16  124
  AMP PEAK  6(3Q26.31) WILD-TYPE    7   37
                        clus
vv                       AMP PEAK  6(3Q26.31) MUTATED
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          124
                        clus
vv                       AMP PEAK  6(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             37
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED   106  32
  AMP PEAK  6(3Q26.31) WILD-TYPE  28   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED    106   32
  AMP PEAK  6(3Q26.31) WILD-TYPE   28    9
            clus
vv           AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  TUMOR FREE                          106                             28
  WITH TUMOR                           32                              9
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  6(3Q26.31) MUTATED       45      5       1      9       4
  AMP PEAK  6(3Q26.31) WILD-TYPE      8      0       0      2       3
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK  6(3Q26.31) MUTATED             150      12
  AMP PEAK  6(3Q26.31) WILD-TYPE            51       2
D6V14, multiclass
               clus
vv              AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  BRAZIL                                  45                              8
  CANADA                                   5                              0
  NIGERIA                                  1                              0
  RUSSIA                                   9                              2
  UKRAINE                                  4                              3
  UNITED STATES                          150                             51
  VIETNAM                                 12                              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK  6(3Q26.31) MUTATED    13 101  86   1  20
  AMP PEAK  6(3Q26.31) WILD-TYPE   5  28  27   0   4
D6V15, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  G1                           13                              5
  G2                          101                             28
  G3                           86                             27
  G4                            1                              0
  GX                           20                              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"
D6V16, continuous
D6V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  6(3Q26.31) MUTATED                                            29
  AMP PEAK  6(3Q26.31) WILD-TYPE                                           8
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  6(3Q26.31) MUTATED                                        8
  AMP PEAK  6(3Q26.31) WILD-TYPE                                      1
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  6(3Q26.31) MUTATED                                                 3
  AMP PEAK  6(3Q26.31) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  6(3Q26.31) MUTATED               51                 108
  AMP PEAK  6(3Q26.31) WILD-TYPE             11                  34
D6V18, multiclass
                                                 clus
vv                                                AMP PEAK  6(3Q26.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            3
  CURRENT SMOKER                                                            51
  LIFELONG NON-SMOKER                                                      108
                                                 clus
vv                                                AMP PEAK  6(3Q26.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                              11
  LIFELONG NON-SMOKER                                                         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"
D6V19, continuous
D6V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  6(3Q26.31) MUTATED            17       77            10       22
  AMP PEAK  6(3Q26.31) WILD-TYPE           2       25             2        3
D6V21, multiclass
               clus
vv              AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  COMBINATION                             17                              2
  EXTERNAL                                77                             25
  EXTERNAL BEAM                           10                              2
  INTERNAL                                22                              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"
D6V22, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   22  2
  AMP PEAK  6(3Q26.31) WILD-TYPE  3  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     22    2
  AMP PEAK  6(3Q26.31) WILD-TYPE    3    1
                         clus
vv                        AMP PEAK  6(3Q26.31) MUTATED
  COMPLETED AS PLANNED                              22
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        AMP PEAK  6(3Q26.31) WILD-TYPE
  COMPLETED AS PLANNED                                 3
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  6(3Q26.31) MUTATED                    0                2
  AMP PEAK  6(3Q26.31) WILD-TYPE                  2                0
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  6(3Q26.31) MUTATED                    26            29
  AMP PEAK  6(3Q26.31) WILD-TYPE                  10             4
D6V23, multiclass
                     clus
vv                    AMP PEAK  6(3Q26.31) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                           26
  REGIONAL SITE                                 29
                     clus
vv                    AMP PEAK  6(3Q26.31) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             10
  REGIONAL SITE                                    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"
D6V24, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   45  4
  AMP PEAK  6(3Q26.31) WILD-TYPE 11  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     45    4
  AMP PEAK  6(3Q26.31) WILD-TYPE   11    1
     clus
vv    AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  CGY                           45                             11
  GY                             4                              1
[1] 2 2
[1] FALSE
D6V25, continuous
D6V26, continuous
D6V27, continuous
D6V28, continuous
D6V29, continuous
D6V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  6(3Q26.31) MUTATED                                     1
  AMP PEAK  6(3Q26.31) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  6(3Q26.31) MUTATED                                     6
  AMP PEAK  6(3Q26.31) WILD-TYPE                                   1
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  6(3Q26.31) MUTATED                        31
  AMP PEAK  6(3Q26.31) WILD-TYPE                       4
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK  6(3Q26.31) MUTATED                         1
  AMP PEAK  6(3Q26.31) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK  6(3Q26.31) MUTATED                         7
  AMP PEAK  6(3Q26.31) WILD-TYPE                       1
D6V31, multiclass
                                     clus
vv                                    AMP PEAK  6(3Q26.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            6
  OTHER LOCATION, SPECIFY                                       31
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        7
                                     clus
vv                                    AMP PEAK  6(3Q26.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  OTHER LOCATION, SPECIFY                                          4
  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(3Q26.31) MUTATED                                               2
  AMP PEAK  6(3Q26.31) WILD-TYPE                                             0
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  6(3Q26.31) MUTATED                                               21
  AMP PEAK  6(3Q26.31) WILD-TYPE                                              4
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  6(3Q26.31) MUTATED                                                                                  67
  AMP PEAK  6(3Q26.31) WILD-TYPE                                                                                14
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  6(3Q26.31) MUTATED                                                                                             91
  AMP PEAK  6(3Q26.31) WILD-TYPE                                                                                           29
D6V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  6(3Q26.31) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           91
                                                                                              clus
vv                                                                                             AMP PEAK  6(3Q26.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V33, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   50 59
  AMP PEAK  6(3Q26.31) WILD-TYPE 20 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     50   59
  AMP PEAK  6(3Q26.31) WILD-TYPE   20   14
         clus
vv        AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  ABSENT                            50                             20
  PRESENT                           59                             14
[1] 2 2
[1] FALSE
D6V34, continuous
D6V35, continuous
D6V36, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   38 89
  AMP PEAK  6(3Q26.31) WILD-TYPE 10 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     38   89
  AMP PEAK  6(3Q26.31) WILD-TYPE   10   27
                                          clus
vv                                         AMP PEAK  6(3Q26.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           89
                                          clus
vv                                         AMP PEAK  6(3Q26.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             27
[1] 2 2
[1] FALSE
D6V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  6(3Q26.31) MUTATED             11          40         64
  AMP PEAK  6(3Q26.31) WILD-TYPE            4          13         20
D6V38, multiclass
              clus
vv             AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  CURRENT USER                           11                              4
  FORMER USER                            40                             13
  NEVER USED                             64                             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"
D6V39, continuous
D6V40, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   69 14
  AMP PEAK  6(3Q26.31) WILD-TYPE 23  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     69   14
  AMP PEAK  6(3Q26.31) WILD-TYPE   23    3
         clus
vv        AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  ABSENT                            69                             23
  PRESENT                           14                              3
[1] 2 2
[1] FALSE
D6V41, continuous
[1] "Remove cluster labels:"         "AMP PEAK  6(3Q26.31) WILD-TYPE"
clus
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            16                              1 
                  TCGA-C5-A1BN                   TCGA-C5-A1MH 
"AMP PEAK  6(3Q26.31) MUTATED" "AMP PEAK  6(3Q26.31) MUTATED" 
                  TCGA-C5-A1ML                   TCGA-C5-A1MN 
"AMP PEAK  6(3Q26.31) MUTATED" "AMP PEAK  6(3Q26.31) MUTATED" 
                  TCGA-C5-A1MP                   TCGA-EK-A2RO 
"AMP PEAK  6(3Q26.31) MUTATED" "AMP PEAK  6(3Q26.31) MUTATED" 
                  TCGA-GH-A9DA                   TCGA-HM-A3JK 
"AMP PEAK  6(3Q26.31) MUTATED" "AMP PEAK  6(3Q26.31) MUTATED" 
                  TCGA-JW-A852                   TCGA-JX-A3Q8 
"AMP PEAK  6(3Q26.31) MUTATED" "AMP PEAK  6(3Q26.31) MUTATED" 
                  TCGA-MA-AA3W                   TCGA-MA-AA3Z 
"AMP PEAK  6(3Q26.31) MUTATED" "AMP PEAK  6(3Q26.31) MUTATED" 
                  TCGA-MA-AA42                   TCGA-MU-A51Y 
"AMP PEAK  6(3Q26.31) MUTATED" "AMP PEAK  6(3Q26.31) MUTATED" 
                  TCGA-MU-A8JM                   TCGA-MY-A913 
"AMP PEAK  6(3Q26.31) MUTATED" "AMP PEAK  6(3Q26.31) MUTATED" 
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  6(3Q26.31) MUTATED      1  26   51   21  6   8    6    5  28  2   2
  AMP PEAK  6(3Q26.31) WILD-TYPE    0   8   18    9  0   2    1    4   8  0   0
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK  6(3Q26.31) MUTATED    15  5   1 13
  AMP PEAK  6(3Q26.31) WILD-TYPE   2  3   0  3
D6V42, multiclass
      clus
vv     AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  T1A1                            1                              0
  T1B                            26                              8
  T1B1                           51                             18
  T1B2                           21                              9
  T2                              6                              0
  T2A                             8                              2
  T2A1                            6                              1
  T2A2                            5                              4
  T2B                            28                              8
  T3                              2                              0
  T3A                             2                              0
  T3B                            15                              2
  T4                              5                              3
  TIS                             1                              0
  TX                             13                              3
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  6(3Q26.31) MUTATED         5        1         1         0       25
  AMP PEAK  6(3Q26.31) WILD-TYPE       0        0         0         1        8
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  6(3Q26.31) MUTATED          57        27        4         5
  AMP PEAK  6(3Q26.31) WILD-TYPE        20         9        0         3
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  6(3Q26.31) MUTATED            5          5        34         1
  AMP PEAK  6(3Q26.31) WILD-TYPE          0          2         9         0
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  6(3Q26.31) MUTATED            3         33         6         9
  AMP PEAK  6(3Q26.31) WILD-TYPE          0          9         1         3
D6V44, multiclass
            clus
vv           AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  STAGE I                               5                              0
  STAGE IA                              1                              0
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                             25                              8
  STAGE IB1                            57                             20
  STAGE IB2                            27                              9
  STAGE II                              4                              0
  STAGE IIA                             5                              3
  STAGE IIA1                            5                              0
  STAGE IIA2                            5                              2
  STAGE IIB                            34                              9
  STAGE III                             1                              0
  STAGE IIIA                            3                              0
  STAGE IIIB                           33                              9
  STAGE IVA                             6                              1
  STAGE IVB                             9                              3
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(3Q28) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(3Q28) MUTATED   164  49
  AMP PEAK  7(3Q28) WILD-TYPE  49  16
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                        213                          65 
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                         49                          16 
$`AMP PEAK  7(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-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
      100.14        33.24        18.02        17.85        20.42       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE 
      101.82       134.33        15.48        20.35       147.35       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ 
       45.83         8.35        23.51        20.91         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL 
       50.76        44.94        40.04        87.75        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99       118.65        22.98        16.83        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        12.36        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 
       13.05        24.56        14.50        12.66         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R 
       26.79        13.91        15.02        14.99        14.96        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
        0.36        12.59        26.27         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        4.04         0.03        47.77         2.24         0.10         0.07 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L 
        0.03        20.35         6.94        19.79         8.32        23.84 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV 
        1.45         1.48         0.82         3.52         1.35         1.97 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA 
        9.01        25.41        10.82        20.78        14.93       137.16 
TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ 
      117.40        78.71        81.96        36.36        27.42        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       20.48        15.58         8.28        18.15       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
        7.99        11.28         0.89         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y 
       22.52        20.28        19.56         9.17         8.52        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       34.62         5.42        54.81        35.05        20.84         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
        2.96        15.58        16.41        15.95         9.04        17.56 
TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07         9.34        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        93.99        12.16        10.03        40.50        37.78 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       26.43        18.05        59.51        32.15        46.03        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        57.93        31.27        36.26        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 
       24.39        39.78        15.68        50.63        48.07        45.34 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UD 
       44.94        43.40        42.41        25.74        21.30        19.69 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       46.92        40.96        14.53        27.25        41.42        43.27 
TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       35.97        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
        5.16        14.04        15.42        26.01        29.26        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        0.69         1.41         0.16 

$`AMP PEAK  7(3Q28) WILD-TYPE`
TCGA-4J-AA1J TCGA-C5-A1BF TCGA-C5-A1BQ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A7CG 
       12.39        18.74        19.86        38.43        52.01       210.67 
TCGA-C5-A7UC TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 
       17.19       146.86        99.91        27.52        20.81        11.87 
TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B 
       58.88        16.18        25.02        14.50        26.40        26.01 
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-EX-A8YF TCGA-FU-A23K 
        0.10         0.10         7.92        14.70        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G 
        0.92         2.17        31.36        36.26         1.58         1.32 
TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF 
        1.12        21.67         9.44       147.39        66.81        96.95 
TCGA-IR-A3LK TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AX 
       29.85         3.29        24.56        28.37        21.11        12.49 
TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-UC-A7PI TCGA-VS-A8EJ 
       17.82        11.38        16.14        15.88        66.05        19.96 
TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A958 TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UR 
       39.78        50.86        50.14        22.72         1.71        20.09 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-ZJ-A8QQ TCGA-ZX-AA5X 
       14.89         4.34        16.24        67.59         3.91 

  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                     195.85                      210.67 
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                      20.35                       17.82 
[1] "0.0 - 195.8 (20.4)" "0.1 - 210.7 (17.8)"
[1] "hr=" "1.2"
D7V2, continuous
                             vv
clus                          T1 T2 T3 T4
  AMP PEAK  7(3Q28) MUTATED   98 51 19  5
  AMP PEAK  7(3Q28) WILD-TYPE 36 17  2  3
D7V3, multiclass
    clus
vv   AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  T1                        98                          36
  T2                        51                          17
  T3                        19                           2
  T4                         5                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   89 47
  AMP PEAK  7(3Q28) WILD-TYPE 38  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     89   47
  AMP PEAK  7(3Q28) WILD-TYPE   38    8
   clus
vv  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  0                        89                          38
  1                        47                           8
[1] 2 2
[1] FALSE
D7V5, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   83  6
  AMP PEAK  7(3Q28) WILD-TYPE 24  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     83    6
  AMP PEAK  7(3Q28) WILD-TYPE   24    4
   clus
vv  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  0                        83                          24
  1                         6                           4
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(3Q28) MUTATED               3                              193
  AMP PEAK  7(3Q28) WILD-TYPE             2                               48
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  7(3Q28) MUTATED                                               4
  AMP PEAK  7(3Q28) WILD-TYPE                                             2
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  7(3Q28) MUTATED                                    12
  AMP PEAK  7(3Q28) WILD-TYPE                                  10
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  7(3Q28) MUTATED                                           2
  AMP PEAK  7(3Q28) WILD-TYPE                                         1
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  7(3Q28) MUTATED                                              9
  AMP PEAK  7(3Q28) WILD-TYPE                                            6
D7V6, multiclass
                                               clus
vv                                              AMP PEAK  7(3Q28) MUTATED
  ADENOSQUAMOUS                                                         3
  CERVICAL SQUAMOUS CELL CARCINOMA                                    193
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                  12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          9
                                               clus
vv                                              AMP PEAK  7(3Q28) WILD-TYPE
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       48
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(3Q28) MUTATED    25 198
  AMP PEAK  7(3Q28) WILD-TYPE   5  64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     25  198
  AMP PEAK  7(3Q28) WILD-TYPE    5   64
     clus
vv    AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  NO                         25                           5
  YES                       198                          64
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(3Q28) MUTATED                                  6    15
  AMP PEAK  7(3Q28) WILD-TYPE                                2     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(3Q28) MUTATED                          25
  AMP PEAK  7(3Q28) WILD-TYPE                         3
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(3Q28) MUTATED                                           1   145
  AMP PEAK  7(3Q28) WILD-TYPE                                         1    56
D7V10, multiclass
                                           clus
vv                                          AMP PEAK  7(3Q28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  6
  ASIAN                                                            15
  BLACK OR AFRICAN AMERICAN                                        25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                           145
                                           clus
vv                                          AMP PEAK  7(3Q28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              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"
D7V11, binary
                             cls
clus                            0   1
  AMP PEAK  7(3Q28) MUTATED    17 122
  AMP PEAK  7(3Q28) WILD-TYPE   6  39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     17  122
  AMP PEAK  7(3Q28) WILD-TYPE    6   39
                        clus
vv                       AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  HISPANIC OR LATINO                            17                           6
  NOT HISPANIC OR LATINO                       122                          39
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                             cls
clus                            0   1
  AMP PEAK  7(3Q28) MUTATED   105  30
  AMP PEAK  7(3Q28) WILD-TYPE  29  11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED    105   30
  AMP PEAK  7(3Q28) WILD-TYPE   29   11
            clus
vv           AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  TUMOR FREE                       105                          29
  WITH TUMOR                        30                          11
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  7(3Q28) MUTATED       43      5       1      8       4
  AMP PEAK  7(3Q28) WILD-TYPE     10      0       0      3       3
                             vv
clus                          UNITED STATES VIETNAM
  AMP PEAK  7(3Q28) MUTATED             150      12
  AMP PEAK  7(3Q28) WILD-TYPE            51       2
D7V14, multiclass
               clus
vv              AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  BRAZIL                               43                          10
  CANADA                                5                           0
  NIGERIA                               1                           0
  RUSSIA                                8                           3
  UKRAINE                               4                           3
  UNITED STATES                       150                          51
  VIETNAM                              12                           2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           G1  G2  G3  G4  GX
  AMP PEAK  7(3Q28) MUTATED    13 100  84   1  20
  AMP PEAK  7(3Q28) WILD-TYPE   5  29  29   0   4
D7V15, multiclass
    clus
vv   AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  G1                        13                           5
  G2                       100                          29
  G3                        84                          29
  G4                         1                           0
  GX                        20                           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"
D7V16, continuous
D7V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  7(3Q28) MUTATED                                            29
  AMP PEAK  7(3Q28) WILD-TYPE                                           8
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  7(3Q28) MUTATED                                        8
  AMP PEAK  7(3Q28) WILD-TYPE                                      1
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  7(3Q28) MUTATED                                                 3
  AMP PEAK  7(3Q28) WILD-TYPE                                               0
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  7(3Q28) MUTATED               50                 106
  AMP PEAK  7(3Q28) WILD-TYPE             12                  36
D7V18, multiclass
                                                 clus
vv                                                AMP PEAK  7(3Q28) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                            29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         3
  CURRENT SMOKER                                                         50
  LIFELONG NON-SMOKER                                                   106
                                                 clus
vv                                                AMP PEAK  7(3Q28) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           12
  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"
D7V19, continuous
D7V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  7(3Q28) MUTATED            17       75             9       21
  AMP PEAK  7(3Q28) WILD-TYPE           2       27             3        4
D7V21, multiclass
               clus
vv              AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  COMBINATION                          17                           2
  EXTERNAL                             75                          27
  EXTERNAL BEAM                         9                           3
  INTERNAL                             21                           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"
D7V22, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   21  2
  AMP PEAK  7(3Q28) WILD-TYPE  4  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     21    2
  AMP PEAK  7(3Q28) WILD-TYPE    4    1
                         clus
vv                        AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  COMPLETED AS PLANNED                           21                           4
  TREATMENT NOT COMPLETED                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                          DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  7(3Q28) MUTATED                    0                1
  AMP PEAK  7(3Q28) WILD-TYPE                  2                1
                             vv
clus                          PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  7(3Q28) MUTATED                    27            29
  AMP PEAK  7(3Q28) WILD-TYPE                   9             4
D7V23, multiclass
                     clus
vv                    AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  DISTANT RECURRENCE                          0                           2
  LOCAL RECURRENCE                            1                           1
  PRIMARY TUMOR FIELD                        27                           9
  REGIONAL SITE                              29                           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"
D7V24, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   45  4
  AMP PEAK  7(3Q28) WILD-TYPE 11  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     45    4
  AMP PEAK  7(3Q28) WILD-TYPE   11    1
     clus
vv    AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  CGY                        45                          11
  GY                          4                           1
[1] 2 2
[1] FALSE
D7V25, continuous
D7V26, continuous
D7V27, continuous
D7V28, continuous
D7V29, continuous
D7V30, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  7(3Q28) MUTATED                                     1
  AMP PEAK  7(3Q28) WILD-TYPE                                   1
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  7(3Q28) MUTATED                                     6
  AMP PEAK  7(3Q28) WILD-TYPE                                   1
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  7(3Q28) MUTATED                        31                       1
  AMP PEAK  7(3Q28) WILD-TYPE                       4                       0
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  7(3Q28) MUTATED                         7
  AMP PEAK  7(3Q28) WILD-TYPE                       1
D7V31, multiclass
                                     clus
vv                                    AMP PEAK  7(3Q28) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         6
  OTHER LOCATION, SPECIFY                                    31
  POSITIVE BLADDER MARGIN                                     1
  POSITIVE VAGINAL MARGIN                                     7
                                     clus
vv                                    AMP PEAK  7(3Q28) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                       4
  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  7(3Q28) MUTATED                                               2
  AMP PEAK  7(3Q28) WILD-TYPE                                             0
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  7(3Q28) MUTATED                                               20
  AMP PEAK  7(3Q28) WILD-TYPE                                              5
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  7(3Q28) MUTATED                                                                                  67
  AMP PEAK  7(3Q28) WILD-TYPE                                                                                14
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  7(3Q28) MUTATED                                                                                             89
  AMP PEAK  7(3Q28) WILD-TYPE                                                                                           31
D7V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  7(3Q28) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                      20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        89
                                                                                              clus
vv                                                                                             AMP PEAK  7(3Q28) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V33, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   51 56
  AMP PEAK  7(3Q28) WILD-TYPE 19 17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     51   56
  AMP PEAK  7(3Q28) WILD-TYPE   19   17
         clus
vv        AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  ABSENT                         51                          19
  PRESENT                        56                          17
[1] 2 2
[1] FALSE
D7V34, continuous
D7V35, continuous
D7V36, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   38 89
  AMP PEAK  7(3Q28) WILD-TYPE 10 27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     38   89
  AMP PEAK  7(3Q28) WILD-TYPE   10   27
                                          clus
vv                                         AMP PEAK  7(3Q28) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        89
                                          clus
vv                                         AMP PEAK  7(3Q28) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          27
[1] 2 2
[1] FALSE
D7V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  7(3Q28) MUTATED             11          38         63
  AMP PEAK  7(3Q28) WILD-TYPE            4          15         21
D7V38, multiclass
              clus
vv             AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  CURRENT USER                        11                           4
  FORMER USER                         38                          15
  NEVER USED                          63                          21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V39, continuous
D7V40, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   68 14
  AMP PEAK  7(3Q28) WILD-TYPE 24  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     68   14
  AMP PEAK  7(3Q28) WILD-TYPE   24    3
         clus
vv        AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  ABSENT                         68                          24
  PRESENT                        14                           3
[1] 2 2
[1] FALSE
D7V41, continuous
[1] "Remove cluster labels:"      "AMP PEAK  7(3Q28) WILD-TYPE"
clus
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                         16                           1 
               TCGA-C5-A1BN                TCGA-C5-A1MH 
"AMP PEAK  7(3Q28) MUTATED" "AMP PEAK  7(3Q28) MUTATED" 
               TCGA-C5-A1ML                TCGA-C5-A1MN 
"AMP PEAK  7(3Q28) MUTATED" "AMP PEAK  7(3Q28) MUTATED" 
               TCGA-C5-A1MP                TCGA-EK-A2RO 
"AMP PEAK  7(3Q28) MUTATED" "AMP PEAK  7(3Q28) MUTATED" 
               TCGA-GH-A9DA                TCGA-HM-A3JK 
"AMP PEAK  7(3Q28) MUTATED" "AMP PEAK  7(3Q28) MUTATED" 
               TCGA-JW-A852                TCGA-JX-A3Q8 
"AMP PEAK  7(3Q28) MUTATED" "AMP PEAK  7(3Q28) MUTATED" 
               TCGA-MA-AA3W                TCGA-MA-AA3Z 
"AMP PEAK  7(3Q28) MUTATED" "AMP PEAK  7(3Q28) MUTATED" 
               TCGA-MA-AA42                TCGA-MU-A51Y 
"AMP PEAK  7(3Q28) MUTATED" "AMP PEAK  7(3Q28) MUTATED" 
               TCGA-MU-A8JM                TCGA-MY-A913 
"AMP PEAK  7(3Q28) MUTATED" "AMP PEAK  7(3Q28) MUTATED" 
                             vv
clus                          T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  7(3Q28) MUTATED      1  26   51   20  6   8    6    5  26  2   2
  AMP PEAK  7(3Q28) WILD-TYPE    0   8   18   10  0   2    1    4  10  0   0
                             vv
clus                          T3B T4 TIS TX
  AMP PEAK  7(3Q28) MUTATED    15  5   1 13
  AMP PEAK  7(3Q28) WILD-TYPE   2  3   0  3
D7V42, multiclass
      clus
vv     AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  T1A1                         1                           0
  T1B                         26                           8
  T1B1                        51                          18
  T1B2                        20                          10
  T2                           6                           0
  T2A                          8                           2
  T2A1                         6                           1
  T2A2                         5                           4
  T2B                         26                          10
  T3                           2                           0
  T3A                          2                           0
  T3B                         15                           2
  T4                           5                           3
  TIS                          1                           0
  TX                          13                           3
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  7(3Q28) MUTATED         5        1         1         1       25
  AMP PEAK  7(3Q28) WILD-TYPE       0        0         0         0        8
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK  7(3Q28) MUTATED          56        26        4         6          5
  AMP PEAK  7(3Q28) WILD-TYPE        21        10        0         2          0
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  AMP PEAK  7(3Q28) MUTATED            5        32         1          3
  AMP PEAK  7(3Q28) WILD-TYPE          2        11         0          0
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  7(3Q28) MUTATED           33         6         8
  AMP PEAK  7(3Q28) WILD-TYPE          9         1         4
D7V44, multiclass
            clus
vv           AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  STAGE I                            5                           0
  STAGE IA                           1                           0
  STAGE IA1                          1                           0
  STAGE IA2                          1                           0
  STAGE IB                          25                           8
  STAGE IB1                         56                          21
  STAGE IB2                         26                          10
  STAGE II                           4                           0
  STAGE IIA                          6                           2
  STAGE IIA1                         5                           0
  STAGE IIA2                         5                           2
  STAGE IIB                         32                          11
  STAGE III                          1                           0
  STAGE IIIA                         3                           0
  STAGE IIIB                        33                           9
  STAGE IVA                          6                           1
  STAGE IVB                          8                           4
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(4Q12) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  8(4Q12) MUTATED    17   2
  AMP PEAK  8(4Q12) WILD-TYPE 196  63
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                         19                         259 
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                          2                          63 
$`AMP PEAK  8(4Q12) MUTATED`
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A8XI TCGA-C5-A907 
       35.01        53.16        40.93         3.58         8.35        11.87 
TCGA-DS-A3LQ TCGA-EK-A2GZ TCGA-EK-A2PI TCGA-EK-A3GK TCGA-FU-A23K TCGA-IR-A3LF 
       22.98        12.59        19.27         0.10         1.22        96.95 
TCGA-IR-A3LH TCGA-JX-A3Q8 TCGA-MA-AA41 TCGA-MY-A5BF TCGA-VS-A8EC TCGA-VS-A950 
       78.71        30.31         9.17        20.84        40.50        39.78 
TCGA-ZJ-AAX4 
        0.69 

$`AMP PEAK  8(4Q12) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       57.73        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61         2.73        50.99        45.83       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ 
       23.51        27.52        20.81        20.91         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99       118.65        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        12.36        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50        26.01        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48         0.36        45.96        26.27         6.64         1.51 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.10         0.07         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        7.92         6.94        14.70        19.79         8.32        15.55 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41        10.82        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       18.15        21.11       195.85         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       12.49         0.30         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       17.82        19.56         8.52        11.38        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        54.81        35.05         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       11.67        93.99        12.16        66.05        10.03        37.78 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       26.43        18.05        19.96        59.51        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       36.13        11.51        57.93        39.78        31.27        36.26 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       16.64         4.73        24.39        50.86        15.68        50.63 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       48.07        50.14        45.34        44.94        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       25.74        21.30        22.72        19.69        46.92        40.96 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        41.42        43.27        35.97 
TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       20.09        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
        5.16        14.04        14.89         4.34        16.24        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       26.01        29.26        67.59        19.13         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                       0.10                        0.03 
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                      96.95                      210.67 
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                      20.84                       19.79 
[1] "0.1 - 97.0 (20.8)"  "0.0 - 210.7 (19.8)"
[1] "hr=" "2.2"
D8V2, continuous
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  8(4Q12) MUTATED     7   4   5   0
  AMP PEAK  8(4Q12) WILD-TYPE 127  64  16   8
D8V3, multiclass
    clus
vv   AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  T1                         7                         127
  T2                         4                          64
  T3                         5                          16
  T4                         0                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                             cls
clus                            0   1
  AMP PEAK  8(4Q12) MUTATED     8   6
  AMP PEAK  8(4Q12) WILD-TYPE 119  49
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      8    6
  AMP PEAK  8(4Q12) WILD-TYPE  119   49
   clus
vv  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  0                         8                         119
  1                         6                          49
[1] 2 2
[1] FALSE
D8V5, binary
                             cls
clus                            0   1
  AMP PEAK  8(4Q12) MUTATED     7   1
  AMP PEAK  8(4Q12) WILD-TYPE 100   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      7    1
  AMP PEAK  8(4Q12) WILD-TYPE  100    9
   clus
vv  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  0                         7                         100
  1                         1                           9
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(4Q12) MUTATED               0                               17
  AMP PEAK  8(4Q12) WILD-TYPE             5                              224
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  8(4Q12) MUTATED                                               1
  AMP PEAK  8(4Q12) WILD-TYPE                                             5
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  8(4Q12) MUTATED                                     3
  AMP PEAK  8(4Q12) WILD-TYPE                                  19
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  8(4Q12) MUTATED                                           0
  AMP PEAK  8(4Q12) WILD-TYPE                                         3
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  8(4Q12) MUTATED                                              0
  AMP PEAK  8(4Q12) WILD-TYPE                                           15
D8V6, multiclass
                                               clus
vv                                              AMP PEAK  8(4Q12) MUTATED
  ADENOSQUAMOUS                                                         0
  CERVICAL SQUAMOUS CELL CARCINOMA                                     17
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          0
                                               clus
vv                                              AMP PEAK  8(4Q12) WILD-TYPE
  ADENOSQUAMOUS                                                           5
  CERVICAL SQUAMOUS CELL CARCINOMA                                      224
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                             cls
clus                            0   1
  AMP PEAK  8(4Q12) MUTATED     4  17
  AMP PEAK  8(4Q12) WILD-TYPE  26 245
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      4   17
  AMP PEAK  8(4Q12) WILD-TYPE   26  245
     clus
vv    AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  NO                          4                          26
  YES                        17                         245
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(4Q12) MUTATED                                  0     1
  AMP PEAK  8(4Q12) WILD-TYPE                                8    17
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(4Q12) MUTATED                           4
  AMP PEAK  8(4Q12) WILD-TYPE                        24
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(4Q12) MUTATED                                           0    12
  AMP PEAK  8(4Q12) WILD-TYPE                                         2   189
D8V10, multiclass
                                           clus
vv                                          AMP PEAK  8(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  0
  ASIAN                                                             1
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            12
                                           clus
vv                                          AMP PEAK  8(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    8
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                          24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                             189
[1] 5 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(4Q12) MUTATED     1  10
  AMP PEAK  8(4Q12) WILD-TYPE  22 151
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      1   10
  AMP PEAK  8(4Q12) WILD-TYPE   22  151
                        clus
vv                       AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                          22
  NOT HISPANIC OR LATINO                        10                         151
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                             cls
clus                            0   1
  AMP PEAK  8(4Q12) MUTATED     8   4
  AMP PEAK  8(4Q12) WILD-TYPE 126  37
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      8    4
  AMP PEAK  8(4Q12) WILD-TYPE  126   37
            clus
vv           AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  TUMOR FREE                         8                         126
  WITH TUMOR                         4                          37
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  8(4Q12) MUTATED        2      0       0      0       0
  AMP PEAK  8(4Q12) WILD-TYPE     51      5       1     11       7
                             vv
clus                          UNITED STATES VIETNAM
  AMP PEAK  8(4Q12) MUTATED              19       0
  AMP PEAK  8(4Q12) WILD-TYPE           182      14
D8V14, multiclass
               clus
vv              AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  BRAZIL                                2                          51
  CANADA                                0                           5
  NIGERIA                               0                           1
  RUSSIA                                0                          11
  UKRAINE                               0                           7
  UNITED STATES                        19                         182
  VIETNAM                               0                          14
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           G1  G2  G3  G4  GX
  AMP PEAK  8(4Q12) MUTATED     1   8   9   1   0
  AMP PEAK  8(4Q12) WILD-TYPE  17 121 104   0  24
D8V15, multiclass
    clus
vv   AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  G1                         1                          17
  G2                         8                         121
  G3                         9                         104
  G4                         1                           0
  GX                         0                          24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V16, continuous
D8V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  8(4Q12) MUTATED                                             4
  AMP PEAK  8(4Q12) WILD-TYPE                                          33
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  8(4Q12) MUTATED                                        1
  AMP PEAK  8(4Q12) WILD-TYPE                                      8
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  8(4Q12) MUTATED                                                 0
  AMP PEAK  8(4Q12) WILD-TYPE                                               3
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  8(4Q12) MUTATED                3                   7
  AMP PEAK  8(4Q12) WILD-TYPE             59                 135
D8V18, multiclass
                                                 clus
vv                                                AMP PEAK  8(4Q12) 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                                                          3
  LIFELONG NON-SMOKER                                                     7
                                                 clus
vv                                                AMP PEAK  8(4Q12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           3
  CURRENT SMOKER                                                           59
  LIFELONG NON-SMOKER                                                     135
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V19, continuous
D8V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  8(4Q12) MUTATED             2        6             2        1
  AMP PEAK  8(4Q12) WILD-TYPE          17       96            10       24
D8V21, multiclass
               clus
vv              AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  COMBINATION                           2                          17
  EXTERNAL                              6                          96
  EXTERNAL BEAM                         2                          10
  INTERNAL                              1                          24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V22, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    4  0
  AMP PEAK  8(4Q12) WILD-TYPE 21  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      4    0
  AMP PEAK  8(4Q12) WILD-TYPE   21    3
                         clus
vv                        AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  COMPLETED AS PLANNED                            4                          21
  TREATMENT NOT COMPLETED                         0                           3
[1] 2 2
[1] FALSE
                             vv
clus                          DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  8(4Q12) MUTATED                    0                0
  AMP PEAK  8(4Q12) WILD-TYPE                  2                2
                             vv
clus                          PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  8(4Q12) MUTATED                     3             2
  AMP PEAK  8(4Q12) WILD-TYPE                  33            31
D8V23, multiclass
                     clus
vv                    AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  DISTANT RECURRENCE                          0                           2
  LOCAL RECURRENCE                            0                           2
  PRIMARY TUMOR FIELD                         3                          33
  REGIONAL SITE                               2                          31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V24, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    5  0
  AMP PEAK  8(4Q12) WILD-TYPE 51  5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      5    0
  AMP PEAK  8(4Q12) WILD-TYPE   51    5
     clus
vv    AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  CGY                         5                          51
  GY                          0                           5
[1] 2 2
[1] FALSE
D8V25, continuous
D8V26, continuous
D8V27, continuous
D8V28, continuous
D8V29, continuous
D8V30, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  8(4Q12) MUTATED                                     0
  AMP PEAK  8(4Q12) WILD-TYPE                                   2
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  8(4Q12) MUTATED                                     0
  AMP PEAK  8(4Q12) WILD-TYPE                                   7
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  8(4Q12) MUTATED                         5                       0
  AMP PEAK  8(4Q12) WILD-TYPE                      30                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  8(4Q12) MUTATED                         2
  AMP PEAK  8(4Q12) WILD-TYPE                       6
D8V31, multiclass
                                     clus
vv                                    AMP PEAK  8(4Q12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  OTHER LOCATION, SPECIFY                                     5
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     2
                                     clus
vv                                    AMP PEAK  8(4Q12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           7
  OTHER LOCATION, SPECIFY                                      30
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  8(4Q12) MUTATED                                               0
  AMP PEAK  8(4Q12) WILD-TYPE                                             2
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  8(4Q12) MUTATED                                                1
  AMP PEAK  8(4Q12) WILD-TYPE                                             24
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  8(4Q12) MUTATED                                                                                   4
  AMP PEAK  8(4Q12) WILD-TYPE                                                                                77
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  8(4Q12) MUTATED                                                                                             10
  AMP PEAK  8(4Q12) WILD-TYPE                                                                                          110
D8V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  8(4Q12) 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)                        10
                                                                                              clus
vv                                                                                             AMP PEAK  8(4Q12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     77
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V33, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    3  8
  AMP PEAK  8(4Q12) WILD-TYPE 67 65
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      3    8
  AMP PEAK  8(4Q12) WILD-TYPE   67   65
         clus
vv        AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  ABSENT                          3                          67
  PRESENT                         8                          65
[1] 2 2
[1] FALSE
D8V34, continuous
D8V35, continuous
D8V36, binary
                             cls
clus                            0   1
  AMP PEAK  8(4Q12) MUTATED     2   8
  AMP PEAK  8(4Q12) WILD-TYPE  46 108
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      2    8
  AMP PEAK  8(4Q12) WILD-TYPE   46  108
                                          clus
vv                                         AMP PEAK  8(4Q12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         8
                                          clus
vv                                         AMP PEAK  8(4Q12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              46
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         108
[1] 2 2
[1] FALSE
D8V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  8(4Q12) MUTATED              1           8          3
  AMP PEAK  8(4Q12) WILD-TYPE           14          45         81
D8V38, multiclass
              clus
vv             AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  CURRENT USER                         1                          14
  FORMER USER                          8                          45
  NEVER USED                           3                          81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V39, continuous
D8V40, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    6  0
  AMP PEAK  8(4Q12) WILD-TYPE 86 17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      6    0
  AMP PEAK  8(4Q12) WILD-TYPE   86   17
         clus
vv        AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  ABSENT                          6                          86
  PRESENT                         0                          17
[1] 2 2
[1] FALSE
D8V41, continuous
                             vv
clus                          T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  8(4Q12) MUTATED      0   0    4    3  2   0    1    1   0  0   1
  AMP PEAK  8(4Q12) WILD-TYPE    1  34   65   27  4  10    6    8  36  2   1
                             vv
clus                          T3B T4 TIS TX
  AMP PEAK  8(4Q12) MUTATED     4  0   0  0
  AMP PEAK  8(4Q12) WILD-TYPE  13  8   1 16
D8V42, multiclass
      clus
vv     AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  T1A1                         0                           1
  T1B                          0                          34
  T1B1                         4                          65
  T1B2                         3                          27
  T2                           2                           4
  T2A                          0                          10
  T2A1                         1                           6
  T2A2                         1                           8
  T2B                          0                          36
  T3                           0                           2
  T3A                          1                           1
  T3B                          4                          13
  T4                           0                           8
  TIS                          0                           1
  TX                           0                          16
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  8(4Q12) MUTATED         0        0         0         0        0
  AMP PEAK  8(4Q12) WILD-TYPE       5        1         1         1       33
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK  8(4Q12) MUTATED           4         4        1         0          1
  AMP PEAK  8(4Q12) WILD-TYPE        73        32        3         8          4
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  AMP PEAK  8(4Q12) MUTATED            1         1         0          1
  AMP PEAK  8(4Q12) WILD-TYPE          6        42         1          2
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  8(4Q12) MUTATED            7         0         0
  AMP PEAK  8(4Q12) WILD-TYPE         35         7        12
D8V44, multiclass
            clus
vv           AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  STAGE I                            0                           5
  STAGE IA                           0                           1
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           0                          33
  STAGE IB1                          4                          73
  STAGE IB2                          4                          32
  STAGE II                           1                           3
  STAGE IIA                          0                           8
  STAGE IIA1                         1                           4
  STAGE IIA2                         1                           6
  STAGE IIB                          1                          42
  STAGE III                          0                           1
  STAGE IIIA                         1                           2
  STAGE IIIB                         7                          35
  STAGE IVA                          0                           7
  STAGE IVB                          0                          12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(5P15.33) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(5P15.33) MUTATED    99  27
  AMP PEAK  9(5P15.33) WILD-TYPE 114  38
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           126                            152 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                            27                             38 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BL 
       12.39        49.48        57.04        11.44       144.16       173.29 
TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A1MN 
       19.86        31.40        46.32        57.73        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE 
        3.58        73.18       100.14        38.43        52.01        18.02 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34         2.73        50.99        45.83       146.86        99.91 
TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VL 
       27.52        11.87         1.12        58.88        44.94         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3Y4 TCGA-EA-A439 
      117.99        22.98        39.55        30.90        14.50        14.50 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 
       26.01        14.89        13.91        14.96        13.48        45.96 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA 
        1.51        19.27         0.43         0.59         0.59        16.08 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        1.18         2.24         0.10         0.10         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI 
        6.94        19.79        15.55        23.84        31.36         1.45 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH 
        1.97         9.01        25.41        10.82        21.67        78.71 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A852 TCGA-JW-AAVH 
       29.85        36.36        27.42        24.56         8.28        18.15 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        7.99         0.89         0.82        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 
       19.56         8.52        11.38        35.05         2.96        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI 
       15.95         9.04        17.56        11.67        12.16        66.05 
TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QC 
       10.03        26.43        18.05        19.96        59.51        11.51 
TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A958 
       57.93        16.64         4.73        39.78        15.68        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       45.34        44.94        25.74        21.30        22.72        19.69 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UY TCGA-VS-A9V0 
       46.92        40.96        14.53        43.27        18.25        18.84 
TCGA-VS-A9V4 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        4.34        26.01        29.26        67.59         1.41         0.16 

$`AMP PEAK  9(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        33.24        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A8XI TCGA-C5-A8YQ 
      101.82       134.33        94.95        13.61         8.35        23.51 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       20.81        20.91        50.76        40.04        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        17.52         8.28 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       26.40        24.56        12.66        12.82         7.46        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 
       15.02        14.99        13.58         0.36        12.59        26.27 
TCGA-EK-A2IP TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        6.64         1.45         0.13         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A449 
        0.36        47.77         0.07         0.10         7.92        14.70 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ 
        8.32         1.22         0.92         2.17        36.26         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-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
      117.40        96.95        81.96         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
       15.58        28.37        21.11       195.85        30.31        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA41 TCGA-MU-A51Y TCGA-MU-A5YI 
       12.49         0.30        13.35         9.17        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A6DV 
        5.42        54.81        20.84         5.49        15.58        16.14 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        15.39        19.36        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8Q8 TCGA-VS-A8Q9 
        3.88        93.99        40.50        37.78        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A952 
       36.13        39.78        31.27        36.26        24.39        50.86 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UJ TCGA-VS-A9UM 
       50.63        48.07        43.40        42.41         1.71        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ 
       41.42        35.97        20.09        14.53         3.42        67.20 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QR 
        5.16        14.04        14.89        16.24        15.42        19.13 
TCGA-ZJ-AAX4 TCGA-ZX-AA5X 
        0.69         3.91 

  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                        173.29                         210.67 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                        19.740                         20.255 
[1] "0.0 - 173.3 (19.7)" "0.0 - 210.7 (20.3)"
[1] "hr=" "1.1"
D9V2, continuous
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  9(5P15.33) MUTATED   56 32 14  3
  AMP PEAK  9(5P15.33) WILD-TYPE 78 36  7  5
D9V3, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T1                           56                             78
  T2                           32                             36
  T3                           14                              7
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   53 23
  AMP PEAK  9(5P15.33) WILD-TYPE 74 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     53   23
  AMP PEAK  9(5P15.33) WILD-TYPE   74   32
   clus
vv  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  0                           53                             74
  1                           23                             32
[1] 2 2
[1] FALSE
D9V5, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   56  2
  AMP PEAK  9(5P15.33) WILD-TYPE 51  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     56    2
  AMP PEAK  9(5P15.33) WILD-TYPE   51    8
   clus
vv  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  0                           56                             51
  1                            2                              8
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(5P15.33) MUTATED               2                              123
  AMP PEAK  9(5P15.33) WILD-TYPE             3                              118
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  9(5P15.33) MUTATED                                               2
  AMP PEAK  9(5P15.33) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  9(5P15.33) MUTATED                                     4
  AMP PEAK  9(5P15.33) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  9(5P15.33) MUTATED                                           2
  AMP PEAK  9(5P15.33) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  9(5P15.33) MUTATED                                              4
  AMP PEAK  9(5P15.33) WILD-TYPE                                           11
D9V6, multiclass
                                               clus
vv                                              AMP PEAK  9(5P15.33) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              AMP PEAK  9(5P15.33) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         118
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED    12 125
  AMP PEAK  9(5P15.33) WILD-TYPE  18 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     12  125
  AMP PEAK  9(5P15.33) WILD-TYPE   18  137
     clus
vv    AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  NO                            12                             18
  YES                          125                            137
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(5P15.33) MUTATED                                  3     7
  AMP PEAK  9(5P15.33) WILD-TYPE                                5    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(5P15.33) MUTATED                          14
  AMP PEAK  9(5P15.33) WILD-TYPE                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  9(5P15.33) MUTATED                                           0
  AMP PEAK  9(5P15.33) WILD-TYPE                                         2
                                vv
clus                             WHITE
  AMP PEAK  9(5P15.33) MUTATED      95
  AMP PEAK  9(5P15.33) WILD-TYPE   106
D9V10, multiclass
                                           clus
vv                                          AMP PEAK  9(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               95
                                           clus
vv                                          AMP PEAK  9(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  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"
D9V11, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   13 70
  AMP PEAK  9(5P15.33) WILD-TYPE 10 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     13   70
  AMP PEAK  9(5P15.33) WILD-TYPE   10   91
                        clus
vv                       AMP PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       AMP PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             91
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   63 18
  AMP PEAK  9(5P15.33) WILD-TYPE 71 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     63   18
  AMP PEAK  9(5P15.33) WILD-TYPE   71   23
            clus
vv           AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  TUMOR FREE                           63                             71
  WITH TUMOR                           18                             23
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  9(5P15.33) MUTATED       26      3       1      4       3
  AMP PEAK  9(5P15.33) WILD-TYPE     27      2       0      7       4
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK  9(5P15.33) MUTATED              94       6
  AMP PEAK  9(5P15.33) WILD-TYPE           107       8
D9V14, multiclass
               clus
vv              AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  BRAZIL                                  26                             27
  CANADA                                   3                              2
  NIGERIA                                  1                              0
  RUSSIA                                   4                              7
  UKRAINE                                  3                              4
  UNITED STATES                           94                            107
  VIETNAM                                  6                              8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK  9(5P15.33) MUTATED    5 51 63  1 11
  AMP PEAK  9(5P15.33) WILD-TYPE 13 78 50  0 13
D9V15, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  G1                            5                             13
  G2                           51                             78
  G3                           63                             50
  G4                            1                              0
  GX                           11                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V16, continuous
D9V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  9(5P15.33) MUTATED                                            19
  AMP PEAK  9(5P15.33) WILD-TYPE                                          18
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  9(5P15.33) MUTATED                                        3
  AMP PEAK  9(5P15.33) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  9(5P15.33) MUTATED                                                 1
  AMP PEAK  9(5P15.33) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  9(5P15.33) MUTATED               32                  60
  AMP PEAK  9(5P15.33) WILD-TYPE             30                  82
D9V18, multiclass
                                                 clus
vv                                                AMP PEAK  9(5P15.33) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            32
  LIFELONG NON-SMOKER                                                       60
                                                 clus
vv                                                AMP PEAK  9(5P15.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              30
  LIFELONG NON-SMOKER                                                         82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V19, continuous
D9V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  9(5P15.33) MUTATED             6       52             5       13
  AMP PEAK  9(5P15.33) WILD-TYPE          13       50             7       12
D9V21, multiclass
               clus
vv              AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  COMBINATION                              6                             13
  EXTERNAL                                52                             50
  EXTERNAL BEAM                            5                              7
  INTERNAL                                13                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V22, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   10  2
  AMP PEAK  9(5P15.33) WILD-TYPE 15  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     10    2
  AMP PEAK  9(5P15.33) WILD-TYPE   15    1
                         clus
vv                        AMP PEAK  9(5P15.33) MUTATED
  COMPLETED AS PLANNED                              10
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        AMP PEAK  9(5P15.33) WILD-TYPE
  COMPLETED AS PLANNED                                15
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK  9(5P15.33) MUTATED                    0                2
  AMP PEAK  9(5P15.33) WILD-TYPE                  2                0
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK  9(5P15.33) MUTATED                    24            16
  AMP PEAK  9(5P15.33) WILD-TYPE                  12            17
D9V23, multiclass
                     clus
vv                    AMP PEAK  9(5P15.33) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                           24
  REGIONAL SITE                                 16
                     clus
vv                    AMP PEAK  9(5P15.33) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             12
  REGIONAL SITE                                   17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V24, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   32  2
  AMP PEAK  9(5P15.33) WILD-TYPE 24  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     32    2
  AMP PEAK  9(5P15.33) WILD-TYPE   24    3
     clus
vv    AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  CGY                           32                             24
  GY                             2                              3
[1] 2 2
[1] FALSE
D9V25, continuous
D9V26, continuous
D9V27, continuous
D9V28, continuous
D9V29, continuous
D9V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  9(5P15.33) MUTATED                                     0
  AMP PEAK  9(5P15.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  9(5P15.33) MUTATED                                     4
  AMP PEAK  9(5P15.33) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  9(5P15.33) MUTATED                        16
  AMP PEAK  9(5P15.33) WILD-TYPE                      19
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK  9(5P15.33) MUTATED                         0
  AMP PEAK  9(5P15.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK  9(5P15.33) MUTATED                         2
  AMP PEAK  9(5P15.33) WILD-TYPE                       6
D9V31, multiclass
                                     clus
vv                                    AMP PEAK  9(5P15.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                       16
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK  9(5P15.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              3
  OTHER LOCATION, SPECIFY                                         19
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  9(5P15.33) MUTATED                                               0
  AMP PEAK  9(5P15.33) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  9(5P15.33) MUTATED                                                9
  AMP PEAK  9(5P15.33) WILD-TYPE                                             16
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  9(5P15.33) MUTATED                                                                                  36
  AMP PEAK  9(5P15.33) WILD-TYPE                                                                                45
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  9(5P15.33) MUTATED                                                                                             54
  AMP PEAK  9(5P15.33) WILD-TYPE                                                                                           66
D9V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  9(5P15.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      36
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           54
                                                                                              clus
vv                                                                                             AMP PEAK  9(5P15.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V33, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   25 31
  AMP PEAK  9(5P15.33) WILD-TYPE 45 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     25   31
  AMP PEAK  9(5P15.33) WILD-TYPE   45   42
         clus
vv        AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  ABSENT                            25                             45
  PRESENT                           31                             42
[1] 2 2
[1] FALSE
D9V34, continuous
D9V35, continuous
D9V36, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   18 62
  AMP PEAK  9(5P15.33) WILD-TYPE 30 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     18   62
  AMP PEAK  9(5P15.33) WILD-TYPE   30   54
                                          clus
vv                                         AMP PEAK  9(5P15.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           62
                                          clus
vv                                         AMP PEAK  9(5P15.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             54
[1] 2 2
[1] FALSE
D9V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  9(5P15.33) MUTATED              5          23         37
  AMP PEAK  9(5P15.33) WILD-TYPE           10          30         47
D9V38, multiclass
              clus
vv             AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  CURRENT USER                            5                             10
  FORMER USER                            23                             30
  NEVER USED                             37                             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"
D9V39, continuous
D9V40, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   34  6
  AMP PEAK  9(5P15.33) WILD-TYPE 58 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     34    6
  AMP PEAK  9(5P15.33) WILD-TYPE   58   11
         clus
vv        AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  ABSENT                            34                             58
  PRESENT                            6                             11
[1] 2 2
[1] FALSE
D9V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK  9(5P15.33) MUTATED      0  14   28   14  0   5    5    1  21  1   2
  AMP PEAK  9(5P15.33) WILD-TYPE    1  20   41   16  6   5    2    8  15  1   0
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK  9(5P15.33) MUTATED    11  3   0  7
  AMP PEAK  9(5P15.33) WILD-TYPE   6  5   1  9
D9V42, multiclass
      clus
vv     AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T1A1                            0                              1
  T1B                            14                             20
  T1B1                           28                             41
  T1B2                           14                             16
  T2                              0                              6
  T2A                             5                              5
  T2A1                            5                              2
  T2A2                            1                              8
  T2B                            21                             15
  T3                              1                              1
  T3A                             2                              0
  T3B                            11                              6
  T4                              3                              5
  TIS                             0                              1
  TX                              7                              9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  9(5P15.33) MUTATED         2        1         0         1       15
  AMP PEAK  9(5P15.33) WILD-TYPE       3        0         1         0       18
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  9(5P15.33) MUTATED          30        16        1         4
  AMP PEAK  9(5P15.33) WILD-TYPE        47        20        3         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  9(5P15.33) MUTATED            4          1        27         0
  AMP PEAK  9(5P15.33) WILD-TYPE          1          6        16         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  9(5P15.33) MUTATED            3         22         4         1
  AMP PEAK  9(5P15.33) WILD-TYPE          0         20         3        11
D9V44, multiclass
            clus
vv           AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             15                             18
  STAGE IB1                            30                             47
  STAGE IB2                            16                             20
  STAGE II                              1                              3
  STAGE IIA                             4                              4
  STAGE IIA1                            4                              1
  STAGE IIA2                            1                              6
  STAGE IIB                            27                             16
  STAGE III                             0                              1
  STAGE IIIA                            3                              0
  STAGE IIIB                           22                             20
  STAGE IVA                             4                              3
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(6P21.33) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(6P21.33) MUTATED    57  23
  AMP PEAK 10(6P21.33) WILD-TYPE 156  42
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                            80                            198 
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                            23                             42 
$`AMP PEAK 10(6P21.33) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 
       12.39        49.48        57.04        11.44         5.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LY 
       46.32        35.01        38.99        35.61        20.91        78.35 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7UE TCGA-C5-A7UH 
       52.01        18.02        17.85       154.32       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VM 
       94.95         2.73        45.83        58.88        44.94       117.99 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 
       17.52         8.28        39.55        14.50        26.01        14.89 
TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RA 
       13.91        14.96         0.36        19.27         0.59        16.08 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        1.18         2.24         0.10         8.32         1.22        23.84 
TCGA-FU-A57G TCGA-HG-A2PA TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-JX-A3Q8 
        1.32        25.41        96.95        78.71        21.11        30.31 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MY-A5BD 
       11.28        12.49        17.82        11.38        34.62        54.81 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EI 
        5.49         2.96        16.41        11.67        93.99        18.05 
TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A959 
       19.96        11.51        39.78        50.86        15.68        45.34 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       44.94        43.40        42.41        21.30        22.72        19.69 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UY TCGA-VS-A9V2 
       46.92        40.96        14.53        41.42        18.25        14.04 
TCGA-VS-AA62 TCGA-ZJ-AAXA 
       15.42         1.41 

$`AMP PEAK 10(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        33.24 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       210.67       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI 
      147.35        17.19         9.34        13.61        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
      146.86        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       11.87         1.12        50.76        40.04        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        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA 
       25.02        14.50        26.40        24.56        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        7.46        26.79        15.02        14.99        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       12.59        45.96        26.27         6.64         1.51         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         1.45         0.13         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
        0.36        47.77         0.10         0.07         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF 
       20.35         7.92         6.94        14.70        19.79        15.55 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.35         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        9.01        10.82        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK 
      147.39       137.16        66.81       117.40        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58        28.37         8.28        18.15       195.85         7.99 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89         0.30         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BE 
       19.56         9.17         8.52        13.87         5.42        35.05 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84        15.58        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        15.39        19.36        19.59 
TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        3.88        12.16        66.05        10.03        40.50        37.78 
TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF 
       26.43        59.51        32.15        46.03        36.13        57.93 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        36.26        16.64         4.73        24.39        39.78 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9UA TCGA-VS-A9UJ TCGA-VS-A9UM 
       50.63        48.07        50.14        25.74         1.71        27.25 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ 
       43.27        35.97        20.09        14.53         3.42        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-WL-A834 
       18.84         5.16        14.89         4.34        16.24        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        67.59        19.13         0.69         0.16         3.91 

  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                        155.77                         210.67 
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                        20.435                         19.690 
[1] "0.1 - 155.8 (20.4)" "0.0 - 210.7 (19.7)"
[1] "hr=" "1.2"
D10V2, continuous
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 10(6P21.33) MUTATED   37 20  5  3
  AMP PEAK 10(6P21.33) WILD-TYPE 97 48 16  5
D10V3, multiclass
    clus
vv   AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  T1                           37                             97
  T2                           20                             48
  T3                            5                             16
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   37 13
  AMP PEAK 10(6P21.33) WILD-TYPE 90 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     37   13
  AMP PEAK 10(6P21.33) WILD-TYPE   90   42
   clus
vv  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  0                           37                             90
  1                           13                             42
[1] 2 2
[1] FALSE
D10V5, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   32  3
  AMP PEAK 10(6P21.33) WILD-TYPE 75  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     32    3
  AMP PEAK 10(6P21.33) WILD-TYPE   75    7
   clus
vv  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  0                           32                             75
  1                            3                              7
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(6P21.33) MUTATED               0                               71
  AMP PEAK 10(6P21.33) WILD-TYPE             5                              170
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 10(6P21.33) MUTATED                                               1
  AMP PEAK 10(6P21.33) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 10(6P21.33) MUTATED                                     4
  AMP PEAK 10(6P21.33) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 10(6P21.33) MUTATED                                           1
  AMP PEAK 10(6P21.33) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 10(6P21.33) MUTATED                                              5
  AMP PEAK 10(6P21.33) WILD-TYPE                                           10
D10V6, multiclass
                                               clus
vv                                              AMP PEAK 10(6P21.33) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        71
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             5
                                               clus
vv                                              AMP PEAK 10(6P21.33) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         170
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              10
[1] 6 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(6P21.33) MUTATED    10  72
  AMP PEAK 10(6P21.33) WILD-TYPE  20 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     10   72
  AMP PEAK 10(6P21.33) WILD-TYPE   20  190
     clus
vv    AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  NO                            10                             20
  YES                           72                            190
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(6P21.33) MUTATED                                  1     5
  AMP PEAK 10(6P21.33) WILD-TYPE                                7    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(6P21.33) MUTATED                           7
  AMP PEAK 10(6P21.33) WILD-TYPE                        21
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 10(6P21.33) MUTATED                                           1
  AMP PEAK 10(6P21.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 10(6P21.33) MUTATED      59
  AMP PEAK 10(6P21.33) WILD-TYPE   142
D10V10, multiclass
                                           clus
vv                                          AMP PEAK 10(6P21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               59
                                           clus
vv                                          AMP PEAK 10(6P21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                142
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                                cls
clus                               0   1
  AMP PEAK 10(6P21.33) MUTATED     5  41
  AMP PEAK 10(6P21.33) WILD-TYPE  18 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED      5   41
  AMP PEAK 10(6P21.33) WILD-TYPE   18  120
                        clus
vv                       AMP PEAK 10(6P21.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       AMP PEAK 10(6P21.33) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            120
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   38 16
  AMP PEAK 10(6P21.33) WILD-TYPE 96 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     38   16
  AMP PEAK 10(6P21.33) WILD-TYPE   96   25
            clus
vv           AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  TUMOR FREE                           38                             96
  WITH TUMOR                           16                             25
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 10(6P21.33) MUTATED       20      2       1      3       3
  AMP PEAK 10(6P21.33) WILD-TYPE     33      3       0      8       4
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 10(6P21.33) MUTATED              49       4
  AMP PEAK 10(6P21.33) WILD-TYPE           152      10
D10V14, multiclass
               clus
vv              AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  BRAZIL                                  20                             33
  CANADA                                   2                              3
  NIGERIA                                  1                              0
  RUSSIA                                   3                              8
  UKRAINE                                  3                              4
  UNITED STATES                           49                            152
  VIETNAM                                  4                             10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 10(6P21.33) MUTATED    2 33 39  1  5
  AMP PEAK 10(6P21.33) WILD-TYPE 16 96 74  0 19
D10V15, multiclass
    clus
vv   AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  G1                            2                             16
  G2                           33                             96
  G3                           39                             74
  G4                            1                              0
  GX                            5                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V16, continuous
D10V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 10(6P21.33) MUTATED                                             8
  AMP PEAK 10(6P21.33) WILD-TYPE                                          29
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 10(6P21.33) MUTATED                                        3
  AMP PEAK 10(6P21.33) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 10(6P21.33) MUTATED                                                 1
  AMP PEAK 10(6P21.33) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 10(6P21.33) MUTATED               15                  47
  AMP PEAK 10(6P21.33) WILD-TYPE             47                  95
D10V18, multiclass
                                                 clus
vv                                                AMP PEAK 10(6P21.33) 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                                                            15
  LIFELONG NON-SMOKER                                                       47
                                                 clus
vv                                                AMP PEAK 10(6P21.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              47
  LIFELONG NON-SMOKER                                                         95
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V19, continuous
D10V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 10(6P21.33) MUTATED             8       31             2        9
  AMP PEAK 10(6P21.33) WILD-TYPE          11       71            10       16
D10V21, multiclass
               clus
vv              AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  COMBINATION                              8                             11
  EXTERNAL                                31                             71
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 9                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V22, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED    9  1
  AMP PEAK 10(6P21.33) WILD-TYPE 16  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED      9    1
  AMP PEAK 10(6P21.33) WILD-TYPE   16    2
                         clus
vv                        AMP PEAK 10(6P21.33) MUTATED
  COMPLETED AS PLANNED                               9
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 10(6P21.33) WILD-TYPE
  COMPLETED AS PLANNED                                16
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 10(6P21.33) MUTATED                    0                1
  AMP PEAK 10(6P21.33) WILD-TYPE                  2                1
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 10(6P21.33) MUTATED                    11            12
  AMP PEAK 10(6P21.33) WILD-TYPE                  25            21
D10V23, multiclass
                     clus
vv                    AMP PEAK 10(6P21.33) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                           11
  REGIONAL SITE                                 12
                     clus
vv                    AMP PEAK 10(6P21.33) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             25
  REGIONAL SITE                                   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"
D10V24, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   20  2
  AMP PEAK 10(6P21.33) WILD-TYPE 36  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     20    2
  AMP PEAK 10(6P21.33) WILD-TYPE   36    3
     clus
vv    AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  CGY                           20                             36
  GY                             2                              3
[1] 2 2
[1] FALSE
D10V25, continuous
D10V26, continuous
D10V27, continuous
D10V28, continuous
D10V29, continuous
D10V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 10(6P21.33) MUTATED                                     0
  AMP PEAK 10(6P21.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 10(6P21.33) MUTATED                                     1
  AMP PEAK 10(6P21.33) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 10(6P21.33) MUTATED                         9
  AMP PEAK 10(6P21.33) WILD-TYPE                      26
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 10(6P21.33) MUTATED                         0
  AMP PEAK 10(6P21.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 10(6P21.33) MUTATED                         2
  AMP PEAK 10(6P21.33) WILD-TYPE                       6
D10V31, multiclass
                                     clus
vv                                    AMP PEAK 10(6P21.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        9
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK 10(6P21.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         26
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 10(6P21.33) MUTATED                                               0
  AMP PEAK 10(6P21.33) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 10(6P21.33) MUTATED                                               10
  AMP PEAK 10(6P21.33) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 10(6P21.33) MUTATED                                                                                  23
  AMP PEAK 10(6P21.33) WILD-TYPE                                                                                58
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 10(6P21.33) MUTATED                                                                                             30
  AMP PEAK 10(6P21.33) WILD-TYPE                                                                                           90
D10V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 10(6P21.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           30
                                                                                              clus
vv                                                                                             AMP PEAK 10(6P21.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        58
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V33, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   16 20
  AMP PEAK 10(6P21.33) WILD-TYPE 54 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     16   20
  AMP PEAK 10(6P21.33) WILD-TYPE   54   53
         clus
vv        AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  ABSENT                            16                             54
  PRESENT                           20                             53
[1] 2 2
[1] FALSE
D10V34, continuous
D10V35, continuous
D10V36, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   13 29
  AMP PEAK 10(6P21.33) WILD-TYPE 35 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     13   29
  AMP PEAK 10(6P21.33) WILD-TYPE   35   87
                                          clus
vv                                         AMP PEAK 10(6P21.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           29
                                          clus
vv                                         AMP PEAK 10(6P21.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             87
[1] 2 2
[1] FALSE
D10V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 10(6P21.33) MUTATED              2          14         29
  AMP PEAK 10(6P21.33) WILD-TYPE           13          39         55
D10V38, multiclass
              clus
vv             AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                            14                             39
  NEVER USED                             29                             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"
D10V39, continuous
D10V40, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   21  7
  AMP PEAK 10(6P21.33) WILD-TYPE 71 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     21    7
  AMP PEAK 10(6P21.33) WILD-TYPE   71   10
         clus
vv        AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  ABSENT                            21                             71
  PRESENT                            7                             10
[1] 2 2
[1] FALSE
D10V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 10(6P21.33) MUTATED      1   9   18    9  1   2    3    2  12  0   1
  AMP PEAK 10(6P21.33) WILD-TYPE    0  25   51   21  5   8    4    7  24  2   1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 10(6P21.33) MUTATED     4  3   1  3
  AMP PEAK 10(6P21.33) WILD-TYPE  13  5   0 13
D10V42, multiclass
      clus
vv     AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  T1A1                            1                              0
  T1B                             9                             25
  T1B1                           18                             51
  T1B2                            9                             21
  T2                              1                              5
  T2A                             2                              8
  T2A1                            3                              4
  T2A2                            2                              7
  T2B                            12                             24
  T3                              0                              2
  T3A                             1                              1
  T3B                             4                             13
  T4                              3                              5
  TIS                             1                              0
  TX                              3                             13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 10(6P21.33) MUTATED         0        0         1         0        6
  AMP PEAK 10(6P21.33) WILD-TYPE       5        1         0         1       27
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 10(6P21.33) MUTATED          24        12        0         2
  AMP PEAK 10(6P21.33) WILD-TYPE        53        24        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 10(6P21.33) MUTATED            3          2        16         0
  AMP PEAK 10(6P21.33) WILD-TYPE          2          5        27         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 10(6P21.33) MUTATED            1          9         3         2
  AMP PEAK 10(6P21.33) WILD-TYPE          2         33         4        10
D10V44, multiclass
            clus
vv           AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                              6                             27
  STAGE IB1                            24                             53
  STAGE IB2                            12                             24
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            3                              2
  STAGE IIA2                            2                              5
  STAGE IIB                            16                             27
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                            9                             33
  STAGE IVA                             3                              4
  STAGE IVB                             2                             10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7P11.2) MUTATED    33  18
  AMP PEAK 11(7P11.2) WILD-TYPE 180  47
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           51                           227 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           18                            47 
$`AMP PEAK 11(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-C5-A8XH TCGA-C5-A8YQ 
      100.14       154.32       147.35       131.11        45.83        23.51 
TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A50E 
       58.88        87.75        36.76        22.98         8.28         7.46 
TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM 
       12.59         1.51         0.07         0.36         1.18         2.24 
TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A40J TCGA-HM-A3JJ TCGA-IR-A3LH 
        6.94        15.55        23.84         1.35        21.67        78.71 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ TCGA-MA-AA41 
       36.36        21.44        20.48        28.37        21.11         9.17 
TCGA-MY-A913 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8EJ 
        5.49         9.04        19.59        12.16        18.05        19.96 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A953 TCGA-VS-A9U5 TCGA-VS-A9UB TCGA-VS-A9UD 
       11.51        57.93        15.68        44.94        21.30        19.69 
TCGA-VS-A9UH TCGA-VS-A9UY TCGA-VS-A9V4 
       46.92        18.25         4.34 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        57.04        23.67        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MP 
       53.16        38.99        35.61         0.46        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       44.22        73.45        83.05        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       15.48        20.35        17.19       155.77        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61         2.73        50.99         8.35       146.86        99.91 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52        20.81        20.91        11.87         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       44.94        40.04        58.88         2.66       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18        17.52        39.55        12.36        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        14.50        26.01        12.66        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48         0.36        45.96        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
       16.08         4.04         0.03        47.77         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-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       19.79         8.32         1.22         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41        10.82 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        96.95        81.96        29.85        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       24.56        15.58         8.28        18.15       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 
       13.35        22.52        20.28        17.82        19.56         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        13.87        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
       20.84         2.96        15.58        16.41        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
        3.88        11.67        93.99        66.05        10.03        40.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       37.78        26.43        59.51        32.15        46.03        36.13 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        36.26        16.64         4.73        24.39 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       39.78        50.86        50.63        48.07        50.14        45.34 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ 
       43.40        42.41        25.74        22.72        40.96         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        41.42        43.27        35.97        20.09 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
       14.53         3.42        67.20        18.84         5.16        14.04 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       14.89        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         1.41         0.16         3.91 

  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                       173.29                        210.67 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                        20.48                         19.56 
[1] "0.1 - 173.3 (20.5)" "0.0 - 210.7 (19.6)"
[1] "hr=" "1.6"
D11V2, continuous
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(7P11.2) MUTATED    15  12   5   4
  AMP PEAK 11(7P11.2) WILD-TYPE 119  56  16   4
D11V3, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1                          15                           119
  T2                          12                            56
  T3                           5                            16
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED    15  11
  AMP PEAK 11(7P11.2) WILD-TYPE 112  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     15   11
  AMP PEAK 11(7P11.2) WILD-TYPE  112   44
   clus
vv  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  0                          15                           112
  1                          11                            44
[1] 2 2
[1] FALSE
D11V5, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   15  3
  AMP PEAK 11(7P11.2) WILD-TYPE 92  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     15    3
  AMP PEAK 11(7P11.2) WILD-TYPE   92    7
   clus
vv  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  0                          15                            92
  1                           3                             7
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(7P11.2) MUTATED               0                               49
  AMP PEAK 11(7P11.2) WILD-TYPE             5                              192
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 11(7P11.2) MUTATED                                               0
  AMP PEAK 11(7P11.2) WILD-TYPE                                             6
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 11(7P11.2) MUTATED                                     2
  AMP PEAK 11(7P11.2) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 11(7P11.2) MUTATED                                           0
  AMP PEAK 11(7P11.2) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 11(7P11.2) MUTATED                                              1
  AMP PEAK 11(7P11.2) WILD-TYPE                                           14
D11V6, multiclass
                                               clus
vv                                              AMP PEAK 11(7P11.2) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              AMP PEAK 11(7P11.2) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED     8  44
  AMP PEAK 11(7P11.2) WILD-TYPE  22 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      8   44
  AMP PEAK 11(7P11.2) WILD-TYPE   22  218
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  NO                            8                            22
  YES                          44                           218
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(7P11.2) MUTATED                                  1     2
  AMP PEAK 11(7P11.2) WILD-TYPE                                7    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(7P11.2) MUTATED                           8
  AMP PEAK 11(7P11.2) WILD-TYPE                        20
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(7P11.2) MUTATED                                           0    35
  AMP PEAK 11(7P11.2) WILD-TYPE                                         2   166
D11V10, multiclass
                                           clus
vv                                          AMP PEAK 11(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              35
                                           clus
vv                                          AMP PEAK 11(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               166
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED     4  27
  AMP PEAK 11(7P11.2) WILD-TYPE  19 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      4   27
  AMP PEAK 11(7P11.2) WILD-TYPE   19  134
                        clus
vv                       AMP PEAK 11(7P11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          27
                        clus
vv                       AMP PEAK 11(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           134
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED    19  11
  AMP PEAK 11(7P11.2) WILD-TYPE 115  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     19   11
  AMP PEAK 11(7P11.2) WILD-TYPE  115   30
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  TUMOR FREE                          19                           115
  WITH TUMOR                          11                            30
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 11(7P11.2) MUTATED       11      1       0      0       0
  AMP PEAK 11(7P11.2) WILD-TYPE     42      4       1     11       7
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK 11(7P11.2) MUTATED              39       1
  AMP PEAK 11(7P11.2) WILD-TYPE           162      13
D11V14, multiclass
               clus
vv              AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  BRAZIL                                 11                            42
  CANADA                                  1                             4
  NIGERIA                                 0                             1
  RUSSIA                                  0                            11
  UKRAINE                                 0                             7
  UNITED STATES                          39                           162
  VIETNAM                                 1                            13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             G1  G2  G3  G4  GX
  AMP PEAK 11(7P11.2) MUTATED     1  19  24   1   5
  AMP PEAK 11(7P11.2) WILD-TYPE  17 110  89   0  19
D11V15, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  G1                           1                            17
  G2                          19                           110
  G3                          24                            89
  G4                           1                             0
  GX                           5                            19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V16, continuous
D11V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 11(7P11.2) MUTATED                                             6
  AMP PEAK 11(7P11.2) WILD-TYPE                                          31
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 11(7P11.2) MUTATED                                        3
  AMP PEAK 11(7P11.2) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 11(7P11.2) MUTATED                                                 1
  AMP PEAK 11(7P11.2) WILD-TYPE                                               2
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 11(7P11.2) MUTATED                8                  26
  AMP PEAK 11(7P11.2) WILD-TYPE             54                 116
D11V18, multiclass
                                                 clus
vv                                                AMP PEAK 11(7P11.2) 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                                                            8
  LIFELONG NON-SMOKER                                                      26
                                                 clus
vv                                                AMP PEAK 11(7P11.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             54
  LIFELONG NON-SMOKER                                                       116
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V19, continuous
D11V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 11(7P11.2) MUTATED             4       19             5        5
  AMP PEAK 11(7P11.2) WILD-TYPE          15       83             7       20
D11V21, multiclass
               clus
vv              AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  COMBINATION                             4                            15
  EXTERNAL                               19                            83
  EXTERNAL BEAM                           5                             7
  INTERNAL                                5                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V22, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED    6  2
  AMP PEAK 11(7P11.2) WILD-TYPE 19  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      6    2
  AMP PEAK 11(7P11.2) WILD-TYPE   19    1
                         clus
vv                        AMP PEAK 11(7P11.2) MUTATED
  COMPLETED AS PLANNED                              6
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        AMP PEAK 11(7P11.2) WILD-TYPE
  COMPLETED AS PLANNED                               19
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 11(7P11.2) MUTATED                    0                2
  AMP PEAK 11(7P11.2) WILD-TYPE                  2                0
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 11(7P11.2) MUTATED                    11             7
  AMP PEAK 11(7P11.2) WILD-TYPE                  25            26
D11V23, multiclass
                     clus
vv                    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              2                             0
  PRIMARY TUMOR FIELD                          11                            25
  REGIONAL SITE                                 7                            26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V24, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   16  2
  AMP PEAK 11(7P11.2) WILD-TYPE 40  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     16    2
  AMP PEAK 11(7P11.2) WILD-TYPE   40    3
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  CGY                          16                            40
  GY                            2                             3
[1] 2 2
[1] FALSE
D11V25, continuous
D11V26, continuous
D11V27, continuous
D11V28, continuous
D11V29, continuous
D11V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 11(7P11.2) MUTATED                                     0
  AMP PEAK 11(7P11.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 11(7P11.2) MUTATED                                     1
  AMP PEAK 11(7P11.2) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 11(7P11.2) MUTATED                         3                       1
  AMP PEAK 11(7P11.2) WILD-TYPE                      32                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK 11(7P11.2) MUTATED                         2
  AMP PEAK 11(7P11.2) WILD-TYPE                       6
D11V31, multiclass
                                     clus
vv                                    AMP PEAK 11(7P11.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                       3
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    AMP PEAK 11(7P11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                        32
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 11(7P11.2) MUTATED                                               0
  AMP PEAK 11(7P11.2) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 11(7P11.2) MUTATED                                                3
  AMP PEAK 11(7P11.2) WILD-TYPE                                             22
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 11(7P11.2) MUTATED                                                                                  16
  AMP PEAK 11(7P11.2) WILD-TYPE                                                                                65
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 11(7P11.2) MUTATED                                                                                             23
  AMP PEAK 11(7P11.2) WILD-TYPE                                                                                           97
D11V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 11(7P11.2) 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)                          23
                                                                                              clus
vv                                                                                             AMP PEAK 11(7P11.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V33, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED    6 16
  AMP PEAK 11(7P11.2) WILD-TYPE 64 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      6   16
  AMP PEAK 11(7P11.2) WILD-TYPE   64   57
         clus
vv        AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  ABSENT                            6                            64
  PRESENT                          16                            57
[1] 2 2
[1] FALSE
D11V34, continuous
D11V35, continuous
D11V36, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   11 20
  AMP PEAK 11(7P11.2) WILD-TYPE 37 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     11   20
  AMP PEAK 11(7P11.2) WILD-TYPE   37   96
                                          clus
vv                                         AMP PEAK 11(7P11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          20
                                          clus
vv                                         AMP PEAK 11(7P11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            96
[1] 2 2
[1] FALSE
D11V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK 11(7P11.2) MUTATED              2           8         14
  AMP PEAK 11(7P11.2) WILD-TYPE           13          45         70
D11V38, multiclass
              clus
vv             AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  CURRENT USER                           2                            13
  FORMER USER                            8                            45
  NEVER USED                            14                            70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V39, continuous
D11V40, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   14  2
  AMP PEAK 11(7P11.2) WILD-TYPE 78 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     14    2
  AMP PEAK 11(7P11.2) WILD-TYPE   78   15
         clus
vv        AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  ABSENT                           14                            78
  PRESENT                           2                            15
[1] 2 2
[1] FALSE
D11V41, continuous
[1] "Remove cluster labels:"      "AMP PEAK 11(7P11.2) MUTATED"
clus
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                            2                            15 
                   TCGA-C5-A1BN                    TCGA-C5-A1MH 
"AMP PEAK 11(7P11.2) WILD-TYPE" "AMP PEAK 11(7P11.2) WILD-TYPE" 
                   TCGA-C5-A1ML                    TCGA-C5-A1MP 
"AMP PEAK 11(7P11.2) WILD-TYPE" "AMP PEAK 11(7P11.2) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-GH-A9DA 
"AMP PEAK 11(7P11.2) WILD-TYPE" "AMP PEAK 11(7P11.2) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-JW-A852 
"AMP PEAK 11(7P11.2) WILD-TYPE" "AMP PEAK 11(7P11.2) WILD-TYPE" 
                   TCGA-JX-A3Q8                    TCGA-MA-AA3W 
"AMP PEAK 11(7P11.2) WILD-TYPE" "AMP PEAK 11(7P11.2) WILD-TYPE" 
                   TCGA-MA-AA3Z                    TCGA-MA-AA42 
"AMP PEAK 11(7P11.2) WILD-TYPE" "AMP PEAK 11(7P11.2) WILD-TYPE" 
                   TCGA-MU-A51Y                    TCGA-MU-A8JM 
"AMP PEAK 11(7P11.2) WILD-TYPE" "AMP PEAK 11(7P11.2) WILD-TYPE" 
                   TCGA-ZX-AA5X 
"AMP PEAK 11(7P11.2) WILD-TYPE" 
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 11(7P11.2) MUTATED      0   5    6    4  1   0    5    2   4  0   1
  AMP PEAK 11(7P11.2) WILD-TYPE    1  29   63   26  5  10    2    7  32  2   1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK 11(7P11.2) MUTATED     4  4   1  3
  AMP PEAK 11(7P11.2) WILD-TYPE  13  4   0 13
D11V42, multiclass
      clus
vv     AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1A1                           0                             1
  T1B                            5                            29
  T1B1                           6                            63
  T1B2                           4                            26
  T2                             1                             5
  T2A                            0                            10
  T2A1                           5                             2
  T2A2                           2                             7
  T2B                            4                            32
  T3                             0                             2
  T3A                            1                             1
  T3B                            4                            13
  T4                             4                             4
  TIS                            1                             0
  TX                             3                            13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 11(7P11.2) MUTATED         1        0         0         0        7
  AMP PEAK 11(7P11.2) WILD-TYPE       4        1         1         1       26
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 11(7P11.2) MUTATED           6         5        0         2
  AMP PEAK 11(7P11.2) WILD-TYPE        71        31        4         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 11(7P11.2) MUTATED            3          1         8         0
  AMP PEAK 11(7P11.2) WILD-TYPE          2          6        35         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 11(7P11.2) MUTATED            1         10         5         2
  AMP PEAK 11(7P11.2) WILD-TYPE          2         32         2        10
D11V44, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             7                            26
  STAGE IB1                            6                            71
  STAGE IB2                            5                            31
  STAGE II                             0                             4
  STAGE IIA                            2                             6
  STAGE IIA1                           3                             2
  STAGE IIA2                           1                             6
  STAGE IIB                            8                            35
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          10                            32
  STAGE IVA                            5                             2
  STAGE IVB                            2                            10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED    90  27
  AMP PEAK 12(8Q24.21) WILD-TYPE 123  38
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           117                            161 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            27                             38 
$`AMP PEAK 12(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-C5-A7XC TCGA-C5-A8XI 
      210.67       154.32       131.11        13.61        50.99         8.35 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DR-A0ZL 
       23.51        27.52        20.91         1.12        58.88        87.75 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3QD 
        2.66       117.99        22.98        12.36        37.35        13.05 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 
       14.50        24.56        12.82         7.46        14.89        13.91 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RN 
        0.36        45.96         6.64         1.51         0.59         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A69M TCGA-EX-A8YF 
        0.07         0.10         0.10         0.03         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A40J 
        1.22        23.84        31.36         1.45         3.52         1.35 
TCGA-FU-A57G TCGA-HG-A9SC TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LK TCGA-IR-A3LL 
        1.32        10.82         9.44       137.16        29.85        36.36 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
       21.44        15.58         8.28        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA3Y 
       12.49         0.30         0.82        13.35        20.28        17.82 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MY-A5BF TCGA-MY-A913 
        9.17         8.52        11.38        34.62        20.84         5.49 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V 
       16.41         9.04        17.56         9.34        19.36        19.59 
TCGA-RA-A741 TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A94X 
        3.88        12.16        10.03        26.43        19.96        16.64 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 
       39.78        15.68        50.63        50.14        44.94        43.40 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UM TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV 
       21.30        22.72        27.25        35.97        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-WL-A834 
       18.25        18.84        14.04        14.89         4.34        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       29.26        67.59         1.41 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M7 TCGA-C5-A1M8 
       36.56       144.16       173.29         5.46        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
       57.73         0.46        20.91        40.93        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       83.05        78.35        33.24        20.42       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT 
        9.34         2.73        45.83       146.86        99.91        20.81 
TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK 
       11.87        50.76        44.94        40.04        58.88        36.76 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
      118.65        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 
       30.90        31.53        31.36        25.02        26.40        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       26.01        12.66        26.79        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PL 
       13.58        13.48        12.59        26.27        19.27         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EX-A1H5 
        0.03         0.36         1.18        47.77         2.24        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92         6.94        14.70        19.79         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A5XV TCGA-FU-A770 
       36.26         1.58         1.48         0.82         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 
        9.01        25.41        21.67        20.78        14.93       147.39 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VG 
       66.81       117.40        96.95        78.71        81.96        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ 
        3.29        24.56        20.48        28.37        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-MA-AA3W TCGA-MA-AA3Z TCGA-MU-A51Y TCGA-MU-A8JM 
      195.85         7.99        22.52        19.56        13.87         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
       54.81        35.05         2.96        15.58        15.95        16.14 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       14.07        15.88        15.39        11.67        93.99        66.05 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       40.50        37.78        18.05        59.51        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       36.13        11.51        57.93        39.78        31.27        36.26 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U7 
        4.73        24.39        50.86        48.07        45.34        42.41 
TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       25.74        19.69        46.92        40.96         1.71        14.53 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V5 
       41.42        43.27        20.09        67.20         5.16        16.24 
TCGA-VS-AA62 TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        19.13         0.69         0.16         3.91 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        210.67                         195.85 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         17.82                          20.81 
[1] "0.0 - 210.7 (17.8)" "0.0 - 195.8 (20.8)"
[1] "hr=" "1.2"
D12V2, continuous
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 12(8Q24.21) MUTATED   57 25 13  6
  AMP PEAK 12(8Q24.21) WILD-TYPE 77 43  8  2
D12V3, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  T1                           57                             77
  T2                           25                             43
  T3                           13                              8
  T4                            6                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   52 27
  AMP PEAK 12(8Q24.21) WILD-TYPE 75 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     52   27
  AMP PEAK 12(8Q24.21) WILD-TYPE   75   28
   clus
vv  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  0                           52                             75
  1                           27                             28
[1] 2 2
[1] FALSE
D12V5, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   44  6
  AMP PEAK 12(8Q24.21) WILD-TYPE 63  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     44    6
  AMP PEAK 12(8Q24.21) WILD-TYPE   63    4
   clus
vv  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  0                           44                             63
  1                            6                              4
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8Q24.21) MUTATED               4                              107
  AMP PEAK 12(8Q24.21) WILD-TYPE             1                              134
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 12(8Q24.21) MUTATED                                               1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 12(8Q24.21) MUTATED                                     8
  AMP PEAK 12(8Q24.21) WILD-TYPE                                  14
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 12(8Q24.21) MUTATED                                           2
  AMP PEAK 12(8Q24.21) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 12(8Q24.21) MUTATED                                              4
  AMP PEAK 12(8Q24.21) WILD-TYPE                                           11
D12V6, multiclass
                                               clus
vv                                              AMP PEAK 12(8Q24.21) MUTATED
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       107
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              AMP PEAK 12(8Q24.21) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         134
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    11 115
  AMP PEAK 12(8Q24.21) WILD-TYPE  19 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     11  115
  AMP PEAK 12(8Q24.21) WILD-TYPE   19  147
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            11                             19
  YES                          115                            147
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(8Q24.21) MUTATED                                  3     9
  AMP PEAK 12(8Q24.21) WILD-TYPE                                5     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(8Q24.21) MUTATED                          14
  AMP PEAK 12(8Q24.21) WILD-TYPE                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 12(8Q24.21) MUTATED                                           1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 12(8Q24.21) MUTATED      81
  AMP PEAK 12(8Q24.21) WILD-TYPE   120
D12V10, multiclass
                                           clus
vv                                          AMP PEAK 12(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               81
                                           clus
vv                                          AMP PEAK 12(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   10 70
  AMP PEAK 12(8Q24.21) WILD-TYPE 13 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     10   70
  AMP PEAK 12(8Q24.21) WILD-TYPE   13   91
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                             91
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   52 22
  AMP PEAK 12(8Q24.21) WILD-TYPE 82 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     52   22
  AMP PEAK 12(8Q24.21) WILD-TYPE   82   19
            clus
vv           AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  TUMOR FREE                           52                             82
  WITH TUMOR                           22                             19
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 12(8Q24.21) MUTATED       22      2       0      4       4
  AMP PEAK 12(8Q24.21) WILD-TYPE     31      3       1      7       3
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 12(8Q24.21) MUTATED              87       7
  AMP PEAK 12(8Q24.21) WILD-TYPE           114       7
D12V14, multiclass
               clus
vv              AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  BRAZIL                                  22                             31
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   4                              7
  UKRAINE                                  4                              3
  UNITED STATES                           87                            114
  VIETNAM                                  7                              7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 12(8Q24.21) MUTATED    7 47 58  0 10
  AMP PEAK 12(8Q24.21) WILD-TYPE 11 82 55  1 14
D12V15, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  G1                            7                             11
  G2                           47                             82
  G3                           58                             55
  G4                            0                              1
  GX                           10                             14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V16, continuous
D12V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 12(8Q24.21) MUTATED                                            15
  AMP PEAK 12(8Q24.21) WILD-TYPE                                          22
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 12(8Q24.21) MUTATED                                        4
  AMP PEAK 12(8Q24.21) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 12(8Q24.21) MUTATED                                                 2
  AMP PEAK 12(8Q24.21) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 12(8Q24.21) MUTATED               23                  65
  AMP PEAK 12(8Q24.21) WILD-TYPE             39                  77
D12V18, multiclass
                                                 clus
vv                                                AMP PEAK 12(8Q24.21) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            23
  LIFELONG NON-SMOKER                                                       65
                                                 clus
vv                                                AMP PEAK 12(8Q24.21) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              39
  LIFELONG NON-SMOKER                                                         77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V19, continuous
D12V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 12(8Q24.21) MUTATED             9       44             3       12
  AMP PEAK 12(8Q24.21) WILD-TYPE          10       58             9       13
D12V21, multiclass
               clus
vv              AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  COMBINATION                              9                             10
  EXTERNAL                                44                             58
  EXTERNAL BEAM                            3                              9
  INTERNAL                                12                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V22, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED    9  2
  AMP PEAK 12(8Q24.21) WILD-TYPE 16  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      9    2
  AMP PEAK 12(8Q24.21) WILD-TYPE   16    1
                         clus
vv                        AMP PEAK 12(8Q24.21) MUTATED
  COMPLETED AS PLANNED                               9
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        AMP PEAK 12(8Q24.21) WILD-TYPE
  COMPLETED AS PLANNED                                16
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 12(8Q24.21) MUTATED                    0                0
  AMP PEAK 12(8Q24.21) WILD-TYPE                  2                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 12(8Q24.21) MUTATED                    12            14
  AMP PEAK 12(8Q24.21) WILD-TYPE                  24            19
D12V23, multiclass
                     clus
vv                    AMP PEAK 12(8Q24.21) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                           12
  REGIONAL SITE                                 14
                     clus
vv                    AMP PEAK 12(8Q24.21) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             24
  REGIONAL SITE                                   19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V24, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   18  2
  AMP PEAK 12(8Q24.21) WILD-TYPE 38  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     18    2
  AMP PEAK 12(8Q24.21) WILD-TYPE   38    3
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  CGY                           18                             38
  GY                             2                              3
[1] 2 2
[1] FALSE
D12V25, continuous
D12V26, continuous
D12V27, continuous
D12V28, continuous
D12V29, continuous
D12V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 12(8Q24.21) MUTATED                                     1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 12(8Q24.21) MUTATED                                     2
  AMP PEAK 12(8Q24.21) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 12(8Q24.21) MUTATED                        18
  AMP PEAK 12(8Q24.21) WILD-TYPE                      17
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 12(8Q24.21) MUTATED                         1
  AMP PEAK 12(8Q24.21) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 12(8Q24.21) MUTATED                         1
  AMP PEAK 12(8Q24.21) WILD-TYPE                       7
D12V31, multiclass
                                     clus
vv                                    AMP PEAK 12(8Q24.21) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       18
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 12(8Q24.21) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         17
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 12(8Q24.21) MUTATED                                               1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 12(8Q24.21) MUTATED                                               11
  AMP PEAK 12(8Q24.21) WILD-TYPE                                             14
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 12(8Q24.21) MUTATED                                                                                  39
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                                                42
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 12(8Q24.21) MUTATED                                                                                             50
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                                                           70
D12V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 12(8Q24.21) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      39
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           50
                                                                                              clus
vv                                                                                             AMP PEAK 12(8Q24.21) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        42
  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"
D12V33, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   23 30
  AMP PEAK 12(8Q24.21) WILD-TYPE 47 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     23   30
  AMP PEAK 12(8Q24.21) WILD-TYPE   47   43
         clus
vv        AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  ABSENT                            23                             47
  PRESENT                           30                             43
[1] 2 2
[1] FALSE
D12V34, continuous
D12V35, continuous
D12V36, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   21 55
  AMP PEAK 12(8Q24.21) WILD-TYPE 27 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     21   55
  AMP PEAK 12(8Q24.21) WILD-TYPE   27   61
                                          clus
vv                                         AMP PEAK 12(8Q24.21) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           55
                                          clus
vv                                         AMP PEAK 12(8Q24.21) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             61
[1] 2 2
[1] FALSE
D12V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 12(8Q24.21) MUTATED              3          23         35
  AMP PEAK 12(8Q24.21) WILD-TYPE           12          30         49
D12V38, multiclass
              clus
vv             AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                            23                             30
  NEVER USED                             35                             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"
D12V39, continuous
D12V40, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   36  4
  AMP PEAK 12(8Q24.21) WILD-TYPE 56 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     36    4
  AMP PEAK 12(8Q24.21) WILD-TYPE   56   13
         clus
vv        AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  ABSENT                            36                             56
  PRESENT                            4                             13
[1] 2 2
[1] FALSE
D12V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 12(8Q24.21) MUTATED      1  15   26   15  4   3    3    1  14  0   1
  AMP PEAK 12(8Q24.21) WILD-TYPE    0  19   43   15  2   7    4    8  22  2   1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 12(8Q24.21) MUTATED    12  6   1  5
  AMP PEAK 12(8Q24.21) WILD-TYPE   5  2   0 11
D12V42, multiclass
      clus
vv     AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  T1A1                            1                              0
  T1B                            15                             19
  T1B1                           26                             43
  T1B2                           15                             15
  T2                              4                              2
  T2A                             3                              7
  T2A1                            3                              4
  T2A2                            1                              8
  T2B                            14                             22
  T3                              0                              2
  T3A                             1                              1
  T3B                            12                              5
  T4                              6                              2
  TIS                             1                              0
  TX                              5                             11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 12(8Q24.21) MUTATED         3        1         1         1       15
  AMP PEAK 12(8Q24.21) WILD-TYPE       2        0         0         0       18
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 12(8Q24.21) MUTATED          26        14        2         1
  AMP PEAK 12(8Q24.21) WILD-TYPE        51        22        2         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 12(8Q24.21) MUTATED            1          1        23         0
  AMP PEAK 12(8Q24.21) WILD-TYPE          4          6        20         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 12(8Q24.21) MUTATED            1         22         4         6
  AMP PEAK 12(8Q24.21) WILD-TYPE          2         20         3         6
D12V44, multiclass
            clus
vv           AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                              1                              0
  STAGE IA1                             1                              0
  STAGE IA2                             1                              0
  STAGE IB                             15                             18
  STAGE IB1                            26                             51
  STAGE IB2                            14                             22
  STAGE II                              2                              2
  STAGE IIA                             1                              7
  STAGE IIA1                            1                              4
  STAGE IIA2                            1                              6
  STAGE IIB                            23                             20
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                           22                             20
  STAGE IVA                             4                              3
  STAGE IVB                             6                              6
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(9P24.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(9P24.1) MUTATED    45  12
  AMP PEAK 13(9P24.1) WILD-TYPE 168  53
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           57                           221 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           12                            53 
$`AMP PEAK 13(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 
       33.24        52.01       210.67       134.33        15.48       147.35 
TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VM 
      155.77         2.73       146.86        44.94        40.04       117.99 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EK-A2H1 
       22.98        16.83        13.05        13.91        14.99        26.27 
TCGA-EK-A2PG TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A40J 
        1.51         2.24         0.10         6.94         1.22         1.35 
TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q8 
       78.71        36.36        15.58        28.37        21.11        30.31 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 
       11.28         0.30        35.05         5.49         2.96        16.41 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC 
       11.67        93.99        12.16        59.51        32.15        11.51 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A9U5 TCGA-VS-A9UB TCGA-VS-A9UH 
       36.26        16.64        39.78        44.94        21.30        46.92 
TCGA-VS-A9UU TCGA-VS-A9V4 TCGA-ZJ-A8QR 
       14.53         4.34        19.13 

$`AMP PEAK 13(9P24.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HE 
       40.93        44.22        78.35       100.14        38.43        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC 
       17.85        20.42       154.32       101.82        20.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
      131.11        94.95         9.34        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM 
       11.87         1.12        58.88        50.76        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       36.76         2.66       118.65        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        12.36        37.35        30.90        31.53        31.36 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       12.66        12.82         7.46        14.89        26.79        15.02 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64        19.27         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        1.18        47.77         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
       20.35         7.92        14.70        19.79         8.32        15.55 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41        10.82        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       96.95        81.96        29.85        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       21.44        20.48         8.28        18.15       195.85         7.99 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89        12.49         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         9.17         8.52        11.38        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       34.62         5.42        54.81        20.84        15.58        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PI TCGA-VS-A8EB 
       15.39        19.36        19.59         3.88        66.05        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 
       40.50        37.78        26.43        18.05        19.96        46.03 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z 
       36.13        57.93        39.78        31.27         4.73        24.39 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       50.86        15.68        50.63        48.07        50.14        45.34 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI 
       43.40        42.41        25.74        22.72        19.69        40.96 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        41.42        43.27        35.97 
TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       20.09         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       14.04        14.89        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59         0.69         1.41         0.16         3.91 

  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                       210.67                        195.85 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                        22.98                         19.59 
[1] "0.1 - 210.7 (23.0)" "0.0 - 195.8 (19.6)"
[1] "hr=" "1.5"
D13V2, continuous
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 13(9P24.1) MUTATED    21  19   5   2
  AMP PEAK 13(9P24.1) WILD-TYPE 113  49  16   6
D13V3, multiclass
    clus
vv   AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  T1                          21                           113
  T2                          19                            49
  T3                           5                            16
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED    19  19
  AMP PEAK 13(9P24.1) WILD-TYPE 108  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     19   19
  AMP PEAK 13(9P24.1) WILD-TYPE  108   36
   clus
vv  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  0                          19                           108
  1                          19                            36
[1] 2 2
[1] FALSE
D13V5, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   22  1
  AMP PEAK 13(9P24.1) WILD-TYPE 85  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     22    1
  AMP PEAK 13(9P24.1) WILD-TYPE   85    9
   clus
vv  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  0                          22                            85
  1                           1                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(9P24.1) MUTATED               0                               56
  AMP PEAK 13(9P24.1) WILD-TYPE             5                              185
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 13(9P24.1) MUTATED                                               1
  AMP PEAK 13(9P24.1) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 13(9P24.1) MUTATED                                     4
  AMP PEAK 13(9P24.1) WILD-TYPE                                  18
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 13(9P24.1) MUTATED                                           0
  AMP PEAK 13(9P24.1) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 13(9P24.1) MUTATED                                              2
  AMP PEAK 13(9P24.1) WILD-TYPE                                           13
D13V6, multiclass
                                               clus
vv                                              AMP PEAK 13(9P24.1) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       56
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              AMP PEAK 13(9P24.1) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        185
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED     4  59
  AMP PEAK 13(9P24.1) WILD-TYPE  26 203
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED      4   59
  AMP PEAK 13(9P24.1) WILD-TYPE   26  203
     clus
vv    AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  NO                            4                            26
  YES                          59                           203
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(9P24.1) MUTATED                                  2     4
  AMP PEAK 13(9P24.1) WILD-TYPE                                6    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(9P24.1) MUTATED                          11
  AMP PEAK 13(9P24.1) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(9P24.1) MUTATED                                           1    34
  AMP PEAK 13(9P24.1) WILD-TYPE                                         1   167
D13V10, multiclass
                                           clus
vv                                          AMP PEAK 13(9P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              34
                                           clus
vv                                          AMP PEAK 13(9P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               167
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED     3  29
  AMP PEAK 13(9P24.1) WILD-TYPE  20 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED      3   29
  AMP PEAK 13(9P24.1) WILD-TYPE   20  132
                        clus
vv                       AMP PEAK 13(9P24.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          29
                        clus
vv                       AMP PEAK 13(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           132
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED    31   2
  AMP PEAK 13(9P24.1) WILD-TYPE 103  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     31    2
  AMP PEAK 13(9P24.1) WILD-TYPE  103   39
            clus
vv           AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  TUMOR FREE                          31                           103
  WITH TUMOR                           2                            39
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 13(9P24.1) MUTATED       11      2       1      0       1
  AMP PEAK 13(9P24.1) WILD-TYPE     42      3       0     11       6
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK 13(9P24.1) MUTATED              45       3
  AMP PEAK 13(9P24.1) WILD-TYPE           156      11
D13V14, multiclass
               clus
vv              AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  BRAZIL                                 11                            42
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  0                            11
  UKRAINE                                 1                             6
  UNITED STATES                          45                           156
  VIETNAM                                 3                            11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             G1  G2  G3  G4  GX
  AMP PEAK 13(9P24.1) MUTATED     4  25  26   1   3
  AMP PEAK 13(9P24.1) WILD-TYPE  14 104  87   0  21
D13V15, multiclass
    clus
vv   AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  G1                           4                            14
  G2                          25                           104
  G3                          26                            87
  G4                           1                             0
  GX                           3                            21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V16, continuous
D13V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 13(9P24.1) MUTATED                                             6
  AMP PEAK 13(9P24.1) WILD-TYPE                                          31
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 13(9P24.1) MUTATED                                        2
  AMP PEAK 13(9P24.1) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 13(9P24.1) MUTATED                                                 2
  AMP PEAK 13(9P24.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 13(9P24.1) MUTATED               14                  29
  AMP PEAK 13(9P24.1) WILD-TYPE             48                 113
D13V18, multiclass
                                                 clus
vv                                                AMP PEAK 13(9P24.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           14
  LIFELONG NON-SMOKER                                                      29
                                                 clus
vv                                                AMP PEAK 13(9P24.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             48
  LIFELONG NON-SMOKER                                                       113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V19, continuous
D13V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 13(9P24.1) MUTATED             2       22             2        8
  AMP PEAK 13(9P24.1) WILD-TYPE          17       80            10       17
D13V21, multiclass
               clus
vv              AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  COMBINATION                             2                            17
  EXTERNAL                               22                            80
  EXTERNAL BEAM                           2                            10
  INTERNAL                                8                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V22, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED    4  0
  AMP PEAK 13(9P24.1) WILD-TYPE 21  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED      4    0
  AMP PEAK 13(9P24.1) WILD-TYPE   21    3
                         clus
vv                        AMP PEAK 13(9P24.1) MUTATED
  COMPLETED AS PLANNED                              4
  TREATMENT NOT COMPLETED                           0
                         clus
vv                        AMP PEAK 13(9P24.1) WILD-TYPE
  COMPLETED AS PLANNED                               21
  TREATMENT NOT COMPLETED                             3
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 13(9P24.1) MUTATED                    0                0
  AMP PEAK 13(9P24.1) WILD-TYPE                  2                2
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 13(9P24.1) MUTATED                    10             9
  AMP PEAK 13(9P24.1) WILD-TYPE                  26            24
D13V23, multiclass
                     clus
vv                    AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              0                             2
  PRIMARY TUMOR FIELD                          10                            26
  REGIONAL SITE                                 9                            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V24, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   14  2
  AMP PEAK 13(9P24.1) WILD-TYPE 42  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     14    2
  AMP PEAK 13(9P24.1) WILD-TYPE   42    3
     clus
vv    AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  CGY                          14                            42
  GY                            2                             3
[1] 2 2
[1] FALSE
D13V25, continuous
D13V26, continuous
D13V27, continuous
D13V28, continuous
D13V29, continuous
D13V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 13(9P24.1) MUTATED                                     0
  AMP PEAK 13(9P24.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 13(9P24.1) MUTATED                                     0
  AMP PEAK 13(9P24.1) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 13(9P24.1) MUTATED                        10                       0
  AMP PEAK 13(9P24.1) WILD-TYPE                      25                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK 13(9P24.1) MUTATED                         3
  AMP PEAK 13(9P24.1) WILD-TYPE                       5
D13V31, multiclass
                                     clus
vv                                    AMP PEAK 13(9P24.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                      10
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    AMP PEAK 13(9P24.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        25
  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 13(9P24.1) MUTATED                                               0
  AMP PEAK 13(9P24.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 13(9P24.1) MUTATED                                                3
  AMP PEAK 13(9P24.1) WILD-TYPE                                             22
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 13(9P24.1) MUTATED                                                                                  15
  AMP PEAK 13(9P24.1) WILD-TYPE                                                                                66
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 13(9P24.1) MUTATED                                                                                             28
  AMP PEAK 13(9P24.1) WILD-TYPE                                                                                           92
D13V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 13(9P24.1) 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)                                     15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          28
                                                                                              clus
vv                                                                                             AMP PEAK 13(9P24.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       66
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V33, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   12 19
  AMP PEAK 13(9P24.1) WILD-TYPE 58 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     12   19
  AMP PEAK 13(9P24.1) WILD-TYPE   58   54
         clus
vv        AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  ABSENT                           12                            58
  PRESENT                          19                            54
[1] 2 2
[1] FALSE
D13V34, continuous
D13V35, continuous
D13V36, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   13 19
  AMP PEAK 13(9P24.1) WILD-TYPE 35 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     13   19
  AMP PEAK 13(9P24.1) WILD-TYPE   35   97
                                          clus
vv                                         AMP PEAK 13(9P24.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          19
                                          clus
vv                                         AMP PEAK 13(9P24.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            97
[1] 2 2
[1] FALSE
D13V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK 13(9P24.1) MUTATED              3          15         12
  AMP PEAK 13(9P24.1) WILD-TYPE           12          38         72
D13V38, multiclass
              clus
vv             AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           15                            38
  NEVER USED                            12                            72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V39, continuous
D13V40, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   17  2
  AMP PEAK 13(9P24.1) WILD-TYPE 75 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     17    2
  AMP PEAK 13(9P24.1) WILD-TYPE   75   15
         clus
vv        AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  ABSENT                           17                            75
  PRESENT                           2                            15
[1] 2 2
[1] FALSE
D13V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 13(9P24.1) MUTATED      0   7   10    4  2   3    3    0  11  0   1
  AMP PEAK 13(9P24.1) WILD-TYPE    1  27   59   26  4   7    4    9  25  2   1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK 13(9P24.1) MUTATED     4  2   1  3
  AMP PEAK 13(9P24.1) WILD-TYPE  13  6   0 13
D13V42, multiclass
      clus
vv     AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  T1A1                           0                             1
  T1B                            7                            27
  T1B1                          10                            59
  T1B2                           4                            26
  T2                             2                             4
  T2A                            3                             7
  T2A1                           3                             4
  T2A2                           0                             9
  T2B                           11                            25
  T3                             0                             2
  T3A                            1                             1
  T3B                            4                            13
  T4                             2                             6
  TIS                            1                             0
  TX                             3                            13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 13(9P24.1) MUTATED         1        0         0         0       10
  AMP PEAK 13(9P24.1) WILD-TYPE       4        1         1         1       23
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 13(9P24.1) MUTATED          12         7        0         2
  AMP PEAK 13(9P24.1) WILD-TYPE        65        29        4         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 13(9P24.1) MUTATED            2          0        10         0
  AMP PEAK 13(9P24.1) WILD-TYPE          3          7        33         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 13(9P24.1) MUTATED            1         11         4         0
  AMP PEAK 13(9P24.1) WILD-TYPE          2         31         3        12
D13V44, multiclass
            clus
vv           AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            10                            23
  STAGE IB1                           12                            65
  STAGE IB2                            7                            29
  STAGE II                             0                             4
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           10                            33
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          11                            31
  STAGE IVA                            4                             3
  STAGE IVB                            0                            12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(11P12) MUTATION ANALYSIS
D14V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 14(11P12) MUTATED    18   4
  AMP PEAK 14(11P12) WILD-TYPE 195  61
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                          22                          256 
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                           4                           61 
$`AMP PEAK 14(11P12) MUTATED`
TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-DG-A2KM TCGA-EK-A2H0 
        5.46        31.40        35.01        73.18        40.04        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-FU-A40J TCGA-FU-A770 TCGA-JW-A5VI TCGA-JW-A5VJ 
       26.27        19.27         1.35         1.12        24.56        21.44 
TCGA-MA-AA3W TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A6DW TCGA-VS-A8EC TCGA-VS-A8EI 
       22.52         5.49         2.96        17.56        40.50        18.05 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A9V2 TCGA-ZJ-A8QQ 
       32.15        46.03        14.04        67.59 

$`AMP PEAK 14(11P12) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF 
       19.86        67.46        46.32        30.21        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        3.58        44.22        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       13.61         2.73        50.99        45.83         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52        20.81        20.91        11.87 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        58.88        50.76        44.94        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        12.36        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        14.50        26.01        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2IP 
       14.96        13.58        13.48         0.36        12.59         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       47.77         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        8.32        15.55         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        3.52         1.32         1.97         9.01        25.41        10.82 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        27.42         3.29        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       20.28        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87        34.62         5.42        54.81        35.05        20.84 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O 
       15.58        16.41        15.95         9.04        16.14        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       11.67        93.99        12.16        66.05        10.03        37.78 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       26.43        19.96        59.51        36.13        11.51        57.93 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        36.26        16.64         4.73        24.39 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       39.78        50.86        15.68        50.63        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       45.34        44.94        43.40        42.41        25.74        21.30 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       22.72        19.69        46.92        40.96         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU 
       27.25        41.42        43.27        35.97        20.09        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 
        3.42        18.25        67.20        18.84         5.16        14.89 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
        4.34        16.24        15.42        26.01        29.26        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                        1.12                         0.03 
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                       73.18                       210.67 
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                       23.54                        19.64 
[1] "1.1 - 73.2 (23.5)"  "0.0 - 210.7 (19.6)"
[1] "hr=" "1.3"
D14V2, continuous
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 14(11P12) MUTATED     6   5   3   0
  AMP PEAK 14(11P12) WILD-TYPE 128  63  18   8
D14V3, multiclass
    clus
vv   AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  T1                          6                          128
  T2                          5                           63
  T3                          3                           18
  T4                          0                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                              cls
clus                             0   1
  AMP PEAK 14(11P12) MUTATED     6   5
  AMP PEAK 14(11P12) WILD-TYPE 121  50
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      6    5
  AMP PEAK 14(11P12) WILD-TYPE  121   50
   clus
vv  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  0                          6                          121
  1                          5                           50
[1] 2 2
[1] FALSE
D14V5, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    8  1
  AMP PEAK 14(11P12) WILD-TYPE 99  9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      8    1
  AMP PEAK 14(11P12) WILD-TYPE   99    9
   clus
vv  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  0                          8                           99
  1                          1                            9
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(11P12) MUTATED               0                               20
  AMP PEAK 14(11P12) WILD-TYPE             5                              221
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 14(11P12) MUTATED                                               1
  AMP PEAK 14(11P12) WILD-TYPE                                             5
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 14(11P12) MUTATED                                     2
  AMP PEAK 14(11P12) WILD-TYPE                                  20
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 14(11P12) MUTATED                                           0
  AMP PEAK 14(11P12) WILD-TYPE                                         3
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 14(11P12) MUTATED                                              0
  AMP PEAK 14(11P12) WILD-TYPE                                           15
D14V6, multiclass
                                               clus
vv                                              AMP PEAK 14(11P12) MUTATED
  ADENOSQUAMOUS                                                          0
  CERVICAL SQUAMOUS CELL CARCINOMA                                      20
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           0
                                               clus
vv                                              AMP PEAK 14(11P12) WILD-TYPE
  ADENOSQUAMOUS                                                            5
  CERVICAL SQUAMOUS CELL CARCINOMA                                       221
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                              cls
clus                             0   1
  AMP PEAK 14(11P12) MUTATED     5  18
  AMP PEAK 14(11P12) WILD-TYPE  25 244
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      5   18
  AMP PEAK 14(11P12) WILD-TYPE   25  244
     clus
vv    AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  NO                           5                           25
  YES                         18                          244
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(11P12) MUTATED                                  2     0
  AMP PEAK 14(11P12) WILD-TYPE                                6    18
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(11P12) MUTATED                           2
  AMP PEAK 14(11P12) WILD-TYPE                        26
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 14(11P12) MUTATED                                           0    17
  AMP PEAK 14(11P12) WILD-TYPE                                         2   184
D14V10, multiclass
                                           clus
vv                                          AMP PEAK 14(11P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              0
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             17
                                           clus
vv                                          AMP PEAK 14(11P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                              184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                              cls
clus                             0   1
  AMP PEAK 14(11P12) MUTATED     4   8
  AMP PEAK 14(11P12) WILD-TYPE  19 153
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      4    8
  AMP PEAK 14(11P12) WILD-TYPE   19  153
                        clus
vv                       AMP PEAK 14(11P12) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                          8
                        clus
vv                       AMP PEAK 14(11P12) WILD-TYPE
  HISPANIC OR LATINO                               19
  NOT HISPANIC OR LATINO                          153
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                              cls
clus                             0   1
  AMP PEAK 14(11P12) MUTATED     7   6
  AMP PEAK 14(11P12) WILD-TYPE 127  35
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      7    6
  AMP PEAK 14(11P12) WILD-TYPE  127   35
            clus
vv           AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  TUMOR FREE                          7                          127
  WITH TUMOR                          6                           35
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 14(11P12) MUTATED        5      1       1      0       0
  AMP PEAK 14(11P12) WILD-TYPE     48      4       0     11       7
                              vv
clus                           UNITED STATES VIETNAM
  AMP PEAK 14(11P12) MUTATED              16       0
  AMP PEAK 14(11P12) WILD-TYPE           185      14
D14V14, multiclass
               clus
vv              AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  BRAZIL                                 5                           48
  CANADA                                 1                            4
  NIGERIA                                1                            0
  RUSSIA                                 0                           11
  UKRAINE                                0                            7
  UNITED STATES                         16                          185
  VIETNAM                                0                           14
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            G1  G2  G3  G4  GX
  AMP PEAK 14(11P12) MUTATED     0   7  12   0   3
  AMP PEAK 14(11P12) WILD-TYPE  18 122 101   1  21
D14V15, multiclass
    clus
vv   AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  G1                          0                           18
  G2                          7                          122
  G3                         12                          101
  G4                          0                            1
  GX                          3                           21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V16, continuous
[1] "Remove cluster labels:"     "AMP PEAK 14(11P12) MUTATED"
clus
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                           1                           41 
                  TCGA-BI-A0VR                   TCGA-C5-A1BJ 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1BL                   TCGA-C5-A1BQ 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1ME                   TCGA-C5-A1MF 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1MH                   TCGA-C5-A2M2 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A3HD                   TCGA-C5-A7CM 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A7CO                   TCGA-C5-A8XH 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A907                   TCGA-DG-A2KK 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-DS-A3LQ                   TCGA-EK-A2RA 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-EX-A69M                   TCGA-FU-A2QG 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-FU-A3TX                   TCGA-FU-A3WB 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-HM-A3JK                   TCGA-HM-A4S6 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-IR-A3L7                   TCGA-IR-A3LB 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-IR-A3LH                   TCGA-JX-A3Q0 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-MA-AA43                   TCGA-MU-A5YI 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-MU-A8JM                   TCGA-Q1-A73S 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-RA-A741                   TCGA-VS-A8QF 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-VS-A94Z                   TCGA-VS-A9V0 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-VS-A9V4                   TCGA-WL-A834 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-ZJ-A8QR                   TCGA-ZJ-AAX4 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-ZJ-AAXA                   TCGA-ZJ-AAXT 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-ZJ-AB0I 
"AMP PEAK 14(11P12) WILD-TYPE" 
D14V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 14(11P12) MUTATED                                             1
  AMP PEAK 14(11P12) WILD-TYPE                                          36
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 14(11P12) MUTATED                                        0
  AMP PEAK 14(11P12) WILD-TYPE                                      9
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 14(11P12) MUTATED                                                 1
  AMP PEAK 14(11P12) WILD-TYPE                                               2
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 14(11P12) MUTATED                6                   9
  AMP PEAK 14(11P12) WILD-TYPE             56                 133
D14V18, multiclass
                                                 clus
vv                                                AMP PEAK 14(11P12) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          1
  CURRENT SMOKER                                                           6
  LIFELONG NON-SMOKER                                                      9
                                                 clus
vv                                                AMP PEAK 14(11P12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            56
  LIFELONG NON-SMOKER                                                      133
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V19, continuous
D14V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 14(11P12) MUTATED             2       10             3        2
  AMP PEAK 14(11P12) WILD-TYPE          17       92             9       23
D14V21, multiclass
               clus
vv              AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  COMBINATION                            2                           17
  EXTERNAL                              10                           92
  EXTERNAL BEAM                          3                            9
  INTERNAL                               2                           23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V22, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    4  1
  AMP PEAK 14(11P12) WILD-TYPE 21  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      4    1
  AMP PEAK 14(11P12) WILD-TYPE   21    2
                         clus
vv                        AMP PEAK 14(11P12) MUTATED
  COMPLETED AS PLANNED                             4
  TREATMENT NOT COMPLETED                          1
                         clus
vv                        AMP PEAK 14(11P12) WILD-TYPE
  COMPLETED AS PLANNED                              21
  TREATMENT NOT COMPLETED                            2
[1] 2 2
[1] FALSE
                              vv
clus                           DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 14(11P12) MUTATED                    0                0
  AMP PEAK 14(11P12) WILD-TYPE                  2                2
                              vv
clus                           PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 14(11P12) MUTATED                     3             2
  AMP PEAK 14(11P12) WILD-TYPE                  33            31
D14V23, multiclass
                     clus
vv                    AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  DISTANT RECURRENCE                           0                            2
  LOCAL RECURRENCE                             0                            2
  PRIMARY TUMOR FIELD                          3                           33
  REGIONAL SITE                                2                           31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V24, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    4  1
  AMP PEAK 14(11P12) WILD-TYPE 52  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      4    1
  AMP PEAK 14(11P12) WILD-TYPE   52    4
     clus
vv    AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  CGY                          4                           52
  GY                           1                            4
[1] 2 2
[1] FALSE
D14V25, continuous
D14V26, continuous
D14V27, continuous
D14V28, continuous
D14V29, continuous
D14V30, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 14(11P12) MUTATED                                     0
  AMP PEAK 14(11P12) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 14(11P12) MUTATED                                     0
  AMP PEAK 14(11P12) WILD-TYPE                                   7
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 14(11P12) MUTATED                         3                       0
  AMP PEAK 14(11P12) WILD-TYPE                      32                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 14(11P12) MUTATED                         0
  AMP PEAK 14(11P12) WILD-TYPE                       8
D14V31, multiclass
                                     clus
vv                                    AMP PEAK 14(11P12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  OTHER LOCATION, SPECIFY                                      3
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      0
                                     clus
vv                                    AMP PEAK 14(11P12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            7
  OTHER LOCATION, SPECIFY                                       32
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 14(11P12) MUTATED                                               0
  AMP PEAK 14(11P12) WILD-TYPE                                             2
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 14(11P12) MUTATED                                                2
  AMP PEAK 14(11P12) WILD-TYPE                                             23
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 14(11P12) MUTATED                                                                                   5
  AMP PEAK 14(11P12) WILD-TYPE                                                                                76
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 14(11P12) MUTATED                                                                                             13
  AMP PEAK 14(11P12) WILD-TYPE                                                                                          107
D14V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 14(11P12) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         13
                                                                                              clus
vv                                                                                             AMP PEAK 14(11P12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      76
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V33, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    6  3
  AMP PEAK 14(11P12) WILD-TYPE 64 70
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      6    3
  AMP PEAK 14(11P12) WILD-TYPE   64   70
         clus
vv        AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  ABSENT                           6                           64
  PRESENT                          3                           70
[1] 2 2
[1] FALSE
D14V34, continuous
D14V35, continuous
D14V36, binary
                              cls
clus                             0   1
  AMP PEAK 14(11P12) MUTATED     1   9
  AMP PEAK 14(11P12) WILD-TYPE  47 107
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      1    9
  AMP PEAK 14(11P12) WILD-TYPE   47  107
                                          clus
vv                                         AMP PEAK 14(11P12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              1
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          9
                                          clus
vv                                         AMP PEAK 14(11P12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               47
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          107
[1] 2 2
[1] FALSE
D14V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 14(11P12) MUTATED              1           8          5
  AMP PEAK 14(11P12) WILD-TYPE           14          45         79
D14V38, multiclass
              clus
vv             AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  CURRENT USER                          1                           14
  FORMER USER                           8                           45
  NEVER USED                            5                           79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V39, continuous
D14V40, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    6  1
  AMP PEAK 14(11P12) WILD-TYPE 86 16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      6    1
  AMP PEAK 14(11P12) WILD-TYPE   86   16
         clus
vv        AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  ABSENT                           6                           86
  PRESENT                          1                           16
[1] 2 2
[1] FALSE
D14V41, continuous
                              vv
clus                           T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 14(11P12) MUTATED      0   3    2    1  0   0    1    1   3  0   0
  AMP PEAK 14(11P12) WILD-TYPE    1  31   67   29  6  10    6    8  33  2   2
                              vv
clus                           T3B T4 TIS TX
  AMP PEAK 14(11P12) MUTATED     3  0   1  2
  AMP PEAK 14(11P12) WILD-TYPE  14  8   0 14
D14V42, multiclass
      clus
vv     AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  T1A1                          0                            1
  T1B                           3                           31
  T1B1                          2                           67
  T1B2                          1                           29
  T2                            0                            6
  T2A                           0                           10
  T2A1                          1                            6
  T2A2                          1                            8
  T2B                           3                           33
  T3                            0                            2
  T3A                           0                            2
  T3B                           3                           14
  T4                            0                            8
  TIS                           1                            0
  TX                            2                           14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 14(11P12) MUTATED         1        0         0         0        2
  AMP PEAK 14(11P12) WILD-TYPE       4        1         1         1       31
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 14(11P12) MUTATED           5         2        0         1
  AMP PEAK 14(11P12) WILD-TYPE        72        34        4         7
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 14(11P12) MUTATED            0          0         7         0
  AMP PEAK 14(11P12) WILD-TYPE          5          7        36         1
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 14(11P12) MUTATED            0          4         0         0
  AMP PEAK 14(11P12) WILD-TYPE          3         38         7        12
D14V44, multiclass
            clus
vv           AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                            0                            1
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            2                           31
  STAGE IB1                           5                           72
  STAGE IB2                           2                           34
  STAGE II                            0                            4
  STAGE IIA                           1                            7
  STAGE IIA1                          0                            5
  STAGE IIA2                          0                            7
  STAGE IIB                           7                           36
  STAGE III                           0                            1
  STAGE IIIA                          0                            3
  STAGE IIIB                          4                           38
  STAGE IVA                           0                            7
  STAGE IVB                           0                           12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(11Q13.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(11Q13.3) MUTATED    28  10
  AMP PEAK 15(11Q13.3) WILD-TYPE 185  55
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            38                            240 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            10                             55 
$`AMP PEAK 15(11Q13.3) MUTATED`
TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M9 
       12.39        11.44        68.84       144.16         5.46        35.01 
TCGA-C5-A1MF TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A8XJ 
       53.16        73.18        73.45       154.32        17.19       146.86 
TCGA-DG-A2KJ TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       58.88         8.28        12.36        26.27         6.64        19.27 
TCGA-EK-A2RJ TCGA-FU-A40J TCGA-HG-A9SC TCGA-IR-A3LA TCGA-IR-A3LH TCGA-JW-A5VK 
        1.18         1.35        10.82       137.16        78.71        20.48 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EI TCGA-VS-A8EJ 
       12.49         0.82         5.49         9.04        18.05        19.96 
TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A9U5 TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9UY 
       46.03        57.93        44.94        40.96        43.27        18.25 
TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       19.13         3.91 

$`AMP PEAK 15(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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY 
       20.91        40.93         3.58        44.22        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       210.67       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35       155.77       131.11        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99        45.83         8.35        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52        20.81        20.91        11.87         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18        17.52 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         7.46        14.89        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       12.59        45.96         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36        47.77         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         8.32        15.55         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17        31.36        36.26         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81       117.40        96.95        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       11.28         0.89         0.30        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         9.17         8.52        11.38        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62         5.42        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        66.05        10.03        40.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC 
       37.78        26.43        59.51        32.15        36.13        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        36.26        16.64         4.73        24.39 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       39.78        50.86        15.68        50.63        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       45.34        43.40        42.41        25.74        21.30        22.72 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       19.69        46.92         1.71        14.53        27.25        41.42 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 
       35.97        20.09        14.53         3.42        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
        5.16        14.04        14.89         4.34        16.24        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       26.01        29.26        67.59         0.69         1.41         0.16 

  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                          0.82                           0.03 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                        154.32                         210.67 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                        19.615                         19.825 
[1] "0.8 - 154.3 (19.6)" "0.0 - 210.7 (19.8)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 15(11Q13.3) MUTATED    17   9   2   0
  AMP PEAK 15(11Q13.3) WILD-TYPE 117  59  19   8
D15V3, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1                           17                            117
  T2                            9                             59
  T3                            2                             19
  T4                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED    13   8
  AMP PEAK 15(11Q13.3) WILD-TYPE 114  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     13    8
  AMP PEAK 15(11Q13.3) WILD-TYPE  114   47
   clus
vv  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  0                           13                            114
  1                            8                             47
[1] 2 2
[1] FALSE
D15V5, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED   13  2
  AMP PEAK 15(11Q13.3) WILD-TYPE 94  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     13    2
  AMP PEAK 15(11Q13.3) WILD-TYPE   94    8
   clus
vv  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  0                           13                             94
  1                            2                              8
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED               1                               36
  AMP PEAK 15(11Q13.3) WILD-TYPE             4                              205
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 15(11Q13.3) MUTATED                                               0
  AMP PEAK 15(11Q13.3) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                     2
  AMP PEAK 15(11Q13.3) WILD-TYPE                                  20
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 15(11Q13.3) MUTATED                                           1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 15(11Q13.3) MUTATED                                              1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                           14
D15V6, multiclass
                                               clus
vv                                              AMP PEAK 15(11Q13.3) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        36
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 15(11Q13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         205
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     7  34
  AMP PEAK 15(11Q13.3) WILD-TYPE  23 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      7   34
  AMP PEAK 15(11Q13.3) WILD-TYPE   23  228
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  NO                             7                             23
  YES                           34                            228
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(11Q13.3) MUTATED                                  0     2
  AMP PEAK 15(11Q13.3) WILD-TYPE                                8    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(11Q13.3) MUTATED                           5
  AMP PEAK 15(11Q13.3) WILD-TYPE                        23
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 15(11Q13.3) MUTATED                                           1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 15(11Q13.3) MUTATED      28
  AMP PEAK 15(11Q13.3) WILD-TYPE   173
D15V10, multiclass
                                           clus
vv                                          AMP PEAK 15(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               28
                                           clus
vv                                          AMP PEAK 15(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                173
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     1  21
  AMP PEAK 15(11Q13.3) WILD-TYPE  22 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      1   21
  AMP PEAK 15(11Q13.3) WILD-TYPE   22  140
                        clus
vv                       AMP PEAK 15(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       AMP PEAK 15(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            140
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED    17   8
  AMP PEAK 15(11Q13.3) WILD-TYPE 117  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     17    8
  AMP PEAK 15(11Q13.3) WILD-TYPE  117   33
            clus
vv           AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  TUMOR FREE                           17                            117
  WITH TUMOR                            8                             33
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 15(11Q13.3) MUTATED        8      1       0      2       0
  AMP PEAK 15(11Q13.3) WILD-TYPE     45      4       1      9       7
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 15(11Q13.3) MUTATED              28       2
  AMP PEAK 15(11Q13.3) WILD-TYPE           173      12
D15V14, multiclass
               clus
vv              AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  BRAZIL                                   8                             45
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   2                              9
  UKRAINE                                  0                              7
  UNITED STATES                           28                            173
  VIETNAM                                  2                             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 15(11Q13.3) MUTATED     0  12  21   1   4
  AMP PEAK 15(11Q13.3) WILD-TYPE  18 117  92   0  20
D15V15, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  G1                            0                             18
  G2                           12                            117
  G3                           21                             92
  G4                            1                              0
  GX                            4                             20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V16, continuous
D15V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 15(11Q13.3) MUTATED                                             4
  AMP PEAK 15(11Q13.3) WILD-TYPE                                          33
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 15(11Q13.3) MUTATED                                        2
  AMP PEAK 15(11Q13.3) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 15(11Q13.3) MUTATED                                                 1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 15(11Q13.3) MUTATED                6                  20
  AMP PEAK 15(11Q13.3) WILD-TYPE             56                 122
D15V18, multiclass
                                                 clus
vv                                                AMP PEAK 15(11Q13.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             6
  LIFELONG NON-SMOKER                                                       20
                                                 clus
vv                                                AMP PEAK 15(11Q13.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              56
  LIFELONG NON-SMOKER                                                        122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V19, continuous
D15V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 15(11Q13.3) MUTATED             4       13             3        3
  AMP PEAK 15(11Q13.3) WILD-TYPE          15       89             9       22
D15V21, multiclass
               clus
vv              AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                13                             89
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 3                             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"
D15V22, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    6  1
  AMP PEAK 15(11Q13.3) WILD-TYPE 19  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      6    1
  AMP PEAK 15(11Q13.3) WILD-TYPE   19    2
                         clus
vv                        AMP PEAK 15(11Q13.3) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 15(11Q13.3) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 15(11Q13.3) MUTATED                    0                1
  AMP PEAK 15(11Q13.3) WILD-TYPE                  2                1
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 15(11Q13.3) MUTATED                     7             3
  AMP PEAK 15(11Q13.3) WILD-TYPE                  29            30
D15V23, multiclass
                     clus
vv                    AMP PEAK 15(11Q13.3) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            7
  REGIONAL SITE                                  3
                     clus
vv                    AMP PEAK 15(11Q13.3) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             29
  REGIONAL SITE                                   30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V24, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    9  1
  AMP PEAK 15(11Q13.3) WILD-TYPE 47  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      9    1
  AMP PEAK 15(11Q13.3) WILD-TYPE   47    4
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  CGY                            9                             47
  GY                             1                              4
[1] 2 2
[1] FALSE
D15V25, continuous
D15V26, continuous
D15V27, continuous
D15V28, continuous
D15V29, continuous
D15V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 15(11Q13.3) MUTATED                                     0
  AMP PEAK 15(11Q13.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 15(11Q13.3) MUTATED                                     1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 15(11Q13.3) MUTATED                         6
  AMP PEAK 15(11Q13.3) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 15(11Q13.3) MUTATED                         0
  AMP PEAK 15(11Q13.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 15(11Q13.3) MUTATED                         1
  AMP PEAK 15(11Q13.3) WILD-TYPE                       7
D15V31, multiclass
                                     clus
vv                                    AMP PEAK 15(11Q13.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        6
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 15(11Q13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 15(11Q13.3) MUTATED                                               0
  AMP PEAK 15(11Q13.3) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 15(11Q13.3) MUTATED                                                3
  AMP PEAK 15(11Q13.3) WILD-TYPE                                             22
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 15(11Q13.3) MUTATED                                                                                   8
  AMP PEAK 15(11Q13.3) WILD-TYPE                                                                                73
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 15(11Q13.3) MUTATED                                                                                             19
  AMP PEAK 15(11Q13.3) WILD-TYPE                                                                                          101
D15V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 15(11Q13.3) 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)                                       8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           19
                                                                                              clus
vv                                                                                             AMP PEAK 15(11Q13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        73
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V33, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    7 11
  AMP PEAK 15(11Q13.3) WILD-TYPE 63 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      7   11
  AMP PEAK 15(11Q13.3) WILD-TYPE   63   62
         clus
vv        AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  ABSENT                             7                             63
  PRESENT                           11                             62
[1] 2 2
[1] FALSE
D15V34, continuous
D15V35, continuous
D15V36, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    5 18
  AMP PEAK 15(11Q13.3) WILD-TYPE 43 98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      5   18
  AMP PEAK 15(11Q13.3) WILD-TYPE   43   98
                                          clus
vv                                         AMP PEAK 15(11Q13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           18
                                          clus
vv                                         AMP PEAK 15(11Q13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             98
[1] 2 2
[1] FALSE
D15V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 15(11Q13.3) MUTATED              1           4         12
  AMP PEAK 15(11Q13.3) WILD-TYPE           14          49         72
D15V38, multiclass
              clus
vv             AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  CURRENT USER                            1                             14
  FORMER USER                             4                             49
  NEVER USED                             12                             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V39, continuous
D15V40, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED   12  1
  AMP PEAK 15(11Q13.3) WILD-TYPE 80 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     12    1
  AMP PEAK 15(11Q13.3) WILD-TYPE   80   16
         clus
vv        AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  ABSENT                            12                             80
  PRESENT                            1                             16
[1] 2 2
[1] FALSE
D15V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 15(11Q13.3) MUTATED      0   7    4    6  0   1    2    1   5  0   0
  AMP PEAK 15(11Q13.3) WILD-TYPE    1  27   65   24  6   9    5    8  31  2   2
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 15(11Q13.3) MUTATED     2  0   1  5
  AMP PEAK 15(11Q13.3) WILD-TYPE  15  8   0 11
D15V42, multiclass
      clus
vv     AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1A1                            0                              1
  T1B                             7                             27
  T1B1                            4                             65
  T1B2                            6                             24
  T2                              0                              6
  T2A                             1                              9
  T2A1                            2                              5
  T2A2                            1                              8
  T2B                             5                             31
  T3                              0                              2
  T3A                             0                              2
  T3B                             2                             15
  T4                              0                              8
  TIS                             1                              0
  TX                              5                             11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 15(11Q13.3) MUTATED         2        0         0         0        5
  AMP PEAK 15(11Q13.3) WILD-TYPE       3        1         1         1       28
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 15(11Q13.3) MUTATED           6         9        0         2
  AMP PEAK 15(11Q13.3) WILD-TYPE        71        27        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 15(11Q13.3) MUTATED            1          1         9         0
  AMP PEAK 15(11Q13.3) WILD-TYPE          4          6        34         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 15(11Q13.3) MUTATED            0          4         0         1
  AMP PEAK 15(11Q13.3) WILD-TYPE          3         38         7        11
D15V44, multiclass
            clus
vv           AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              5                             28
  STAGE IB1                             6                             71
  STAGE IB2                             9                             27
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            1                              4
  STAGE IIA2                            1                              6
  STAGE IIB                             9                             34
  STAGE III                             0                              1
  STAGE IIIA                            0                              3
  STAGE IIIB                            4                             38
  STAGE IVA                             0                              7
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(11Q22.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(11Q22.1) MUTATED    33  13
  AMP PEAK 16(11Q22.1) WILD-TYPE 180  52
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                            46                            232 
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                            13                             52 
$`AMP PEAK 16(11Q22.1) MUTATED`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BN 
       12.39        23.67        11.44       144.16       177.04         5.46 
TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A7CH TCGA-C5-A7UC 
       35.01        73.18        73.45        78.35       154.32        17.19 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XK TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VK 
       13.61        50.99        99.91        58.88        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A43B TCGA-EA-A5O9 
        2.66         8.28        13.05        25.02        26.01        13.91 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A3L1 
       26.27         6.64         1.18         0.07         0.10         6.94 
TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-LP-A4AX 
        1.35        10.82        21.67        78.71        21.11        12.49 
TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8Q9 TCGA-VS-A8QF 
        5.49         3.88        11.67        10.03        46.03        57.93 
TCGA-VS-A9U5 TCGA-VS-A9UP TCGA-VS-AA62 TCGA-ZJ-A8QR 
       44.94        43.27        15.42        19.13 

$`AMP PEAK 16(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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ 
       20.91        40.93         3.58        44.22        83.05       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      210.67       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8XH 
      155.77       131.11        94.95         9.34         2.73        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35       146.86        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM 
       11.87         1.12        50.76        44.94        40.04        58.88 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18        17.52 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        12.36        37.35        30.90        31.53        31.36 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA 
       14.50        26.40        24.56        14.50        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
        7.46        14.89        26.79        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG 
       13.58        13.48         0.36        12.59        45.96         1.51 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       16.08         0.07         4.04         0.03         0.36        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        2.24         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        9.01        25.41        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81       117.40        96.95        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       15.58        28.37         8.28        18.15       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
        7.99        11.28         0.89         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        20.28        17.82        19.56         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        13.87        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC 
       19.36        19.59        93.99        12.16        66.05        40.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       37.78        26.43        18.05        19.96        59.51        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        11.51        39.78        31.27        36.26        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
        4.73        24.39        39.78        50.86        15.68        50.63 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       48.07        50.14        45.34        43.40        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       21.30        22.72        19.69        46.92        40.96         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU 
       14.53        27.25        41.42        35.97        20.09        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        14.04 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       14.89         4.34        16.24        26.01        29.26        67.59 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                        177.04                         210.67 
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                        20.120                         19.825 
[1] "0.1 - 177.0 (20.1)" "0.0 - 210.7 (19.8)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 16(11Q22.1) MUTATED    25   8   2   0
  AMP PEAK 16(11Q22.1) WILD-TYPE 109  60  19   8
D16V3, multiclass
    clus
vv   AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  T1                           25                            109
  T2                            8                             60
  T3                            2                             19
  T4                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q22.1) MUTATED    22  10
  AMP PEAK 16(11Q22.1) WILD-TYPE 105  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     22   10
  AMP PEAK 16(11Q22.1) WILD-TYPE  105   45
   clus
vv  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  0                           22                            105
  1                           10                             45
[1] 2 2
[1] FALSE
D16V5, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   21  2
  AMP PEAK 16(11Q22.1) WILD-TYPE 86  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     21    2
  AMP PEAK 16(11Q22.1) WILD-TYPE   86    8
   clus
vv  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  0                           21                             86
  1                            2                              8
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(11Q22.1) MUTATED               1                               43
  AMP PEAK 16(11Q22.1) WILD-TYPE             4                              198
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 16(11Q22.1) MUTATED                                               0
  AMP PEAK 16(11Q22.1) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 16(11Q22.1) MUTATED                                     2
  AMP PEAK 16(11Q22.1) WILD-TYPE                                  20
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 16(11Q22.1) MUTATED                                           0
  AMP PEAK 16(11Q22.1) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 16(11Q22.1) MUTATED                                              1
  AMP PEAK 16(11Q22.1) WILD-TYPE                                           14
D16V6, multiclass
                                               clus
vv                                              AMP PEAK 16(11Q22.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        43
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 16(11Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         198
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q22.1) MUTATED     7  40
  AMP PEAK 16(11Q22.1) WILD-TYPE  23 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED      7   40
  AMP PEAK 16(11Q22.1) WILD-TYPE   23  222
     clus
vv    AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  NO                             7                             23
  YES                           40                            222
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(11Q22.1) MUTATED                                  2     2
  AMP PEAK 16(11Q22.1) WILD-TYPE                                6    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(11Q22.1) MUTATED                           8
  AMP PEAK 16(11Q22.1) WILD-TYPE                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 16(11Q22.1) MUTATED                                           2
  AMP PEAK 16(11Q22.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 16(11Q22.1) MUTATED      31
  AMP PEAK 16(11Q22.1) WILD-TYPE   170
D16V10, multiclass
                                           clus
vv                                          AMP PEAK 16(11Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               31
                                           clus
vv                                          AMP PEAK 16(11Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q22.1) MUTATED     2  28
  AMP PEAK 16(11Q22.1) WILD-TYPE  21 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED      2   28
  AMP PEAK 16(11Q22.1) WILD-TYPE   21  133
                        clus
vv                       AMP PEAK 16(11Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       AMP PEAK 16(11Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            133
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q22.1) MUTATED    19   6
  AMP PEAK 16(11Q22.1) WILD-TYPE 115  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     19    6
  AMP PEAK 16(11Q22.1) WILD-TYPE  115   35
            clus
vv           AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  TUMOR FREE                           19                            115
  WITH TUMOR                            6                             35
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 16(11Q22.1) MUTATED        6      1       0      2       2
  AMP PEAK 16(11Q22.1) WILD-TYPE     47      4       1      9       5
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 16(11Q22.1) MUTATED              35       1
  AMP PEAK 16(11Q22.1) WILD-TYPE           166      13
D16V14, multiclass
               clus
vv              AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  BRAZIL                                   6                             47
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   2                              9
  UKRAINE                                  2                              5
  UNITED STATES                           35                            166
  VIETNAM                                  1                             13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 16(11Q22.1) MUTATED     1  15  26   1   3
  AMP PEAK 16(11Q22.1) WILD-TYPE  17 114  87   0  21
D16V15, multiclass
    clus
vv   AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  G1                            1                             17
  G2                           15                            114
  G3                           26                             87
  G4                            1                              0
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V16, continuous
D16V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 16(11Q22.1) MUTATED                                             5
  AMP PEAK 16(11Q22.1) WILD-TYPE                                          32
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 16(11Q22.1) MUTATED                                        0
  AMP PEAK 16(11Q22.1) WILD-TYPE                                      9
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 16(11Q22.1) MUTATED                                                 1
  AMP PEAK 16(11Q22.1) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 16(11Q22.1) MUTATED                9                  21
  AMP PEAK 16(11Q22.1) WILD-TYPE             53                 121
D16V18, multiclass
                                                 clus
vv                                                AMP PEAK 16(11Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             9
  LIFELONG NON-SMOKER                                                       21
                                                 clus
vv                                                AMP PEAK 16(11Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              53
  LIFELONG NON-SMOKER                                                        121
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V19, continuous
D16V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 16(11Q22.1) MUTATED             3       16             5        4
  AMP PEAK 16(11Q22.1) WILD-TYPE          16       86             7       21
D16V21, multiclass
               clus
vv              AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  COMBINATION                              3                             16
  EXTERNAL                                16                             86
  EXTERNAL BEAM                            5                              7
  INTERNAL                                 4                             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"
D16V22, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED    6  1
  AMP PEAK 16(11Q22.1) WILD-TYPE 19  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED      6    1
  AMP PEAK 16(11Q22.1) WILD-TYPE   19    2
                         clus
vv                        AMP PEAK 16(11Q22.1) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 16(11Q22.1) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 16(11Q22.1) MUTATED                    0                2
  AMP PEAK 16(11Q22.1) WILD-TYPE                  2                0
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 16(11Q22.1) MUTATED                     9             2
  AMP PEAK 16(11Q22.1) WILD-TYPE                  27            31
D16V23, multiclass
                     clus
vv                    AMP PEAK 16(11Q22.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                            9
  REGIONAL SITE                                  2
                     clus
vv                    AMP PEAK 16(11Q22.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             27
  REGIONAL SITE                                   31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V24, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED    9  2
  AMP PEAK 16(11Q22.1) WILD-TYPE 47  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED      9    2
  AMP PEAK 16(11Q22.1) WILD-TYPE   47    3
     clus
vv    AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  CGY                            9                             47
  GY                             2                              3
[1] 2 2
[1] FALSE
D16V25, continuous
D16V26, continuous
D16V27, continuous
D16V28, continuous
D16V29, continuous
D16V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 16(11Q22.1) MUTATED                                     1
  AMP PEAK 16(11Q22.1) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 16(11Q22.1) MUTATED                                     2
  AMP PEAK 16(11Q22.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 16(11Q22.1) MUTATED                         8
  AMP PEAK 16(11Q22.1) WILD-TYPE                      27
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 16(11Q22.1) MUTATED                         0
  AMP PEAK 16(11Q22.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 16(11Q22.1) MUTATED                         2
  AMP PEAK 16(11Q22.1) WILD-TYPE                       6
D16V31, multiclass
                                     clus
vv                                    AMP PEAK 16(11Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        8
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK 16(11Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         27
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 16(11Q22.1) MUTATED                                               0
  AMP PEAK 16(11Q22.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 16(11Q22.1) MUTATED                                                4
  AMP PEAK 16(11Q22.1) WILD-TYPE                                             21
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 16(11Q22.1) MUTATED                                                                                   4
  AMP PEAK 16(11Q22.1) WILD-TYPE                                                                                77
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 16(11Q22.1) MUTATED                                                                                             28
  AMP PEAK 16(11Q22.1) WILD-TYPE                                                                                           92
D16V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 16(11Q22.1) 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)                                       4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           28
                                                                                              clus
vv                                                                                             AMP PEAK 16(11Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        77
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V33, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   11 15
  AMP PEAK 16(11Q22.1) WILD-TYPE 59 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     11   15
  AMP PEAK 16(11Q22.1) WILD-TYPE   59   58
         clus
vv        AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  ABSENT                            11                             59
  PRESENT                           15                             58
[1] 2 2
[1] FALSE
D16V34, continuous
D16V35, continuous
D16V36, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   12 19
  AMP PEAK 16(11Q22.1) WILD-TYPE 36 97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     12   19
  AMP PEAK 16(11Q22.1) WILD-TYPE   36   97
                                          clus
vv                                         AMP PEAK 16(11Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           19
                                          clus
vv                                         AMP PEAK 16(11Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             97
[1] 2 2
[1] FALSE
D16V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 16(11Q22.1) MUTATED              3           7         14
  AMP PEAK 16(11Q22.1) WILD-TYPE           12          46         70
D16V38, multiclass
              clus
vv             AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                             7                             46
  NEVER USED                             14                             70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V39, continuous
D16V40, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   18  1
  AMP PEAK 16(11Q22.1) WILD-TYPE 74 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     18    1
  AMP PEAK 16(11Q22.1) WILD-TYPE   74   16
         clus
vv        AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  ABSENT                            18                             74
  PRESENT                            1                             16
[1] 2 2
[1] FALSE
D16V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 16(11Q22.1) MUTATED      0  10   11    4  0   1    3    1   3  0   0
  AMP PEAK 16(11Q22.1) WILD-TYPE    1  24   58   26  6   9    4    8  33  2   2
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 16(11Q22.1) MUTATED     2  0   1  3
  AMP PEAK 16(11Q22.1) WILD-TYPE  15  8   0 13
D16V42, multiclass
      clus
vv     AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  T1A1                            0                              1
  T1B                            10                             24
  T1B1                           11                             58
  T1B2                            4                             26
  T2                              0                              6
  T2A                             1                              9
  T2A1                            3                              4
  T2A2                            1                              8
  T2B                             3                             33
  T3                              0                              2
  T3A                             0                              2
  T3B                             2                             15
  T4                              0                              8
  TIS                             1                              0
  TX                              3                             13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 16(11Q22.1) MUTATED         1        0         0         0       10
  AMP PEAK 16(11Q22.1) WILD-TYPE       4        1         1         1       23
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 16(11Q22.1) MUTATED          10         7        0         2
  AMP PEAK 16(11Q22.1) WILD-TYPE        67        29        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 16(11Q22.1) MUTATED            2          1         8         0
  AMP PEAK 16(11Q22.1) WILD-TYPE          3          6        35         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 16(11Q22.1) MUTATED            0          4         0         1
  AMP PEAK 16(11Q22.1) WILD-TYPE          3         38         7        11
D16V44, multiclass
            clus
vv           AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             10                             23
  STAGE IB1                            10                             67
  STAGE IB2                             7                             29
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            2                              3
  STAGE IIA2                            1                              6
  STAGE IIB                             8                             35
  STAGE III                             0                              1
  STAGE IIIA                            0                              3
  STAGE IIIB                            4                             38
  STAGE IVA                             0                              7
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(13Q22.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(13Q22.1) MUTATED    46  18
  AMP PEAK 17(13Q22.1) WILD-TYPE 167  47
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                            64                            214 
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                            18                             47 
$`AMP PEAK 17(13Q22.1) MUTATED`
TCGA-4J-AA1J TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MP 
       12.39        82.85         5.46        35.01         0.46         3.58 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH 
      100.14        38.43        52.01        17.85       210.67       154.32 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DS-A0VM 
       13.61         2.73        50.99        27.52         1.12       117.99 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZF 
       31.36        13.05        12.66         7.46        13.91        14.96 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM 
        0.36        45.96         1.51         0.36         1.18         2.24 
TCGA-EK-A3GN TCGA-EX-A8YF TCGA-FU-A3HY TCGA-FU-A40J TCGA-FU-A5XV TCGA-IR-A3L7 
        0.03        15.55        31.36         1.35         1.97       147.39 
TCGA-IR-A3LB TCGA-IR-A3LK TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       66.81        29.85        21.44        21.11       195.85         7.99 
TCGA-LP-A4AW TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73R 
        0.89        35.05         2.96        16.41         9.04        15.39 
TCGA-VS-A8EC TCGA-VS-A8Q8 TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A950 TCGA-VS-A954 
       40.50        32.15        57.93        39.78        39.78        50.63 
TCGA-VS-A959 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UQ TCGA-VS-A9UV TCGA-VS-A9V2 
       45.34        25.74        22.72        35.97         3.42        14.04 
TCGA-VS-A9V4 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
        4.34        26.01        67.59        19.13 

$`AMP PEAK 17(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-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
       35.61         2.43        20.91        40.93        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL 
       73.45        83.05        78.35        33.24        18.02        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-C5-A8XI 
      155.77       131.11        94.95         9.34        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        23.51        20.81        20.91        11.87 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       58.88        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28        39.55        12.36        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       31.53        25.02        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       26.01        12.82        14.89        26.79        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       13.58        13.48        12.59        26.27         6.64        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        0.07         4.04         0.03        47.77         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.10        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 
       19.79         8.32         1.22        23.84         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.32         1.12         9.01        25.41        10.82        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF 
       20.78        14.93         9.44       137.16       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 
       20.48        15.58        28.37         8.28        18.15        30.31 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       11.28        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       20.28        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       13.87        34.62         5.42        54.81        20.84         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        9.34        19.36        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       12.16        66.05        10.03        37.78        26.43        18.05 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM 
       19.96        59.51        46.03        36.13        11.51        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 
       36.26        16.64         4.73        24.39        50.86        15.68 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB 
       48.07        50.14        44.94        43.40        42.41        21.30 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       19.69        46.92        40.96         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.42        43.27        20.09        14.53        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ 
       18.84         5.16        14.89        16.24        15.42        29.26 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                        210.67                         177.04 
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                        20.120                         19.825 
[1] "0.0 - 210.7 (20.1)" "0.0 - 177.0 (19.8)"
[1] "hr=" "1.2"
D17V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 17(13Q22.1) MUTATED    29  10   7   3
  AMP PEAK 17(13Q22.1) WILD-TYPE 105  58  14   5
D17V3, multiclass
    clus
vv   AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  T1                           29                            105
  T2                           10                             58
  T3                            7                             14
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                                cls
clus                               0   1
  AMP PEAK 17(13Q22.1) MUTATED    26  13
  AMP PEAK 17(13Q22.1) WILD-TYPE 101  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     26   13
  AMP PEAK 17(13Q22.1) WILD-TYPE  101   42
   clus
vv  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  0                           26                            101
  1                           13                             42
[1] 2 2
[1] FALSE
D17V5, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   26  0
  AMP PEAK 17(13Q22.1) WILD-TYPE 81 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     26    0
  AMP PEAK 17(13Q22.1) WILD-TYPE   81   10
   clus
vv  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  0                           26                             81
  1                            0                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(13Q22.1) MUTATED               1                               53
  AMP PEAK 17(13Q22.1) WILD-TYPE             4                              188
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 17(13Q22.1) MUTATED                                               0
  AMP PEAK 17(13Q22.1) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 17(13Q22.1) MUTATED                                     6
  AMP PEAK 17(13Q22.1) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 17(13Q22.1) MUTATED                                           0
  AMP PEAK 17(13Q22.1) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 17(13Q22.1) MUTATED                                              5
  AMP PEAK 17(13Q22.1) WILD-TYPE                                           10
D17V6, multiclass
                                               clus
vv                                              AMP PEAK 17(13Q22.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        53
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             5
                                               clus
vv                                              AMP PEAK 17(13Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         188
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              10
[1] 6 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(13Q22.1) MUTATED     6  59
  AMP PEAK 17(13Q22.1) WILD-TYPE  24 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED      6   59
  AMP PEAK 17(13Q22.1) WILD-TYPE   24  203
     clus
vv    AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  NO                             6                             24
  YES                           59                            203
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(13Q22.1) MUTATED                                  1     3
  AMP PEAK 17(13Q22.1) WILD-TYPE                                7    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(13Q22.1) MUTATED                           7
  AMP PEAK 17(13Q22.1) WILD-TYPE                        21
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 17(13Q22.1) MUTATED                                           1
  AMP PEAK 17(13Q22.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 17(13Q22.1) MUTATED      45
  AMP PEAK 17(13Q22.1) WILD-TYPE   156
D17V10, multiclass
                                           clus
vv                                          AMP PEAK 17(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               45
                                           clus
vv                                          AMP PEAK 17(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                156
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                                cls
clus                               0   1
  AMP PEAK 17(13Q22.1) MUTATED     1  40
  AMP PEAK 17(13Q22.1) WILD-TYPE  22 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED      1   40
  AMP PEAK 17(13Q22.1) WILD-TYPE   22  121
                        clus
vv                       AMP PEAK 17(13Q22.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       AMP PEAK 17(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            121
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                                cls
clus                               0   1
  AMP PEAK 17(13Q22.1) MUTATED    28  13
  AMP PEAK 17(13Q22.1) WILD-TYPE 106  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     28   13
  AMP PEAK 17(13Q22.1) WILD-TYPE  106   28
            clus
vv           AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  TUMOR FREE                           28                            106
  WITH TUMOR                           13                             28
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 17(13Q22.1) MUTATED       13      1       1      2       3
  AMP PEAK 17(13Q22.1) WILD-TYPE     40      4       0      9       4
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 17(13Q22.1) MUTATED              42       3
  AMP PEAK 17(13Q22.1) WILD-TYPE           159      11
D17V14, multiclass
               clus
vv              AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  BRAZIL                                  13                             40
  CANADA                                   1                              4
  NIGERIA                                  1                              0
  RUSSIA                                   2                              9
  UKRAINE                                  3                              4
  UNITED STATES                           42                            159
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 17(13Q22.1) MUTATED     2  29  28   0   6
  AMP PEAK 17(13Q22.1) WILD-TYPE  16 100  85   1  18
D17V15, multiclass
    clus
vv   AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  G1                            2                             16
  G2                           29                            100
  G3                           28                             85
  G4                            0                              1
  GX                            6                             18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V16, continuous
D17V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 17(13Q22.1) MUTATED                                             8
  AMP PEAK 17(13Q22.1) WILD-TYPE                                          29
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 17(13Q22.1) MUTATED                                        1
  AMP PEAK 17(13Q22.1) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 17(13Q22.1) MUTATED                                                 0
  AMP PEAK 17(13Q22.1) WILD-TYPE                                               3
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 17(13Q22.1) MUTATED                9                  37
  AMP PEAK 17(13Q22.1) WILD-TYPE             53                 105
D17V18, multiclass
                                                 clus
vv                                                AMP PEAK 17(13Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             9
  LIFELONG NON-SMOKER                                                       37
                                                 clus
vv                                                AMP PEAK 17(13Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              3
  CURRENT SMOKER                                                              53
  LIFELONG NON-SMOKER                                                        105
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V19, continuous
D17V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 17(13Q22.1) MUTATED             4       25             2        5
  AMP PEAK 17(13Q22.1) WILD-TYPE          15       77            10       20
D17V21, multiclass
               clus
vv              AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                25                             77
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V22, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED    5  1
  AMP PEAK 17(13Q22.1) WILD-TYPE 20  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED      5    1
  AMP PEAK 17(13Q22.1) WILD-TYPE   20    2
                         clus
vv                        AMP PEAK 17(13Q22.1) MUTATED
  COMPLETED AS PLANNED                               5
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 17(13Q22.1) WILD-TYPE
  COMPLETED AS PLANNED                                20
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 17(13Q22.1) MUTATED                    0                0
  AMP PEAK 17(13Q22.1) WILD-TYPE                  2                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 17(13Q22.1) MUTATED                     7             8
  AMP PEAK 17(13Q22.1) WILD-TYPE                  29            25
D17V23, multiclass
                     clus
vv                    AMP PEAK 17(13Q22.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            7
  REGIONAL SITE                                  8
                     clus
vv                    AMP PEAK 17(13Q22.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             29
  REGIONAL SITE                                   25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V24, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   12  0
  AMP PEAK 17(13Q22.1) WILD-TYPE 44  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     12    0
  AMP PEAK 17(13Q22.1) WILD-TYPE   44    5
     clus
vv    AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  CGY                           12                             44
  GY                             0                              5
[1] 2 2
[1] FALSE
D17V25, continuous
D17V26, continuous
D17V27, continuous
D17V28, continuous
D17V29, continuous
D17V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 17(13Q22.1) MUTATED                                     0
  AMP PEAK 17(13Q22.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 17(13Q22.1) MUTATED                                     2
  AMP PEAK 17(13Q22.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 17(13Q22.1) MUTATED                        10
  AMP PEAK 17(13Q22.1) WILD-TYPE                      25
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 17(13Q22.1) MUTATED                         1
  AMP PEAK 17(13Q22.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 17(13Q22.1) MUTATED                         1
  AMP PEAK 17(13Q22.1) WILD-TYPE                       7
D17V31, multiclass
                                     clus
vv                                    AMP PEAK 17(13Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       10
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 17(13Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         25
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 17(13Q22.1) MUTATED                                               0
  AMP PEAK 17(13Q22.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 17(13Q22.1) MUTATED                                                6
  AMP PEAK 17(13Q22.1) WILD-TYPE                                             19
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 17(13Q22.1) MUTATED                                                                                  21
  AMP PEAK 17(13Q22.1) WILD-TYPE                                                                                60
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 17(13Q22.1) MUTATED                                                                                             27
  AMP PEAK 17(13Q22.1) WILD-TYPE                                                                                           93
D17V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 17(13Q22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           27
                                                                                              clus
vv                                                                                             AMP PEAK 17(13Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V33, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   11 21
  AMP PEAK 17(13Q22.1) WILD-TYPE 59 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     11   21
  AMP PEAK 17(13Q22.1) WILD-TYPE   59   52
         clus
vv        AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  ABSENT                            11                             59
  PRESENT                           21                             52
[1] 2 2
[1] FALSE
D17V34, continuous
D17V35, continuous
D17V36, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   11 22
  AMP PEAK 17(13Q22.1) WILD-TYPE 37 94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     11   22
  AMP PEAK 17(13Q22.1) WILD-TYPE   37   94
                                          clus
vv                                         AMP PEAK 17(13Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           22
                                          clus
vv                                         AMP PEAK 17(13Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             94
[1] 2 2
[1] FALSE
D17V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 17(13Q22.1) MUTATED              1          14         21
  AMP PEAK 17(13Q22.1) WILD-TYPE           14          39         63
D17V38, multiclass
              clus
vv             AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  CURRENT USER                            1                             14
  FORMER USER                            14                             39
  NEVER USED                             21                             63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V39, continuous
D17V40, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   19  2
  AMP PEAK 17(13Q22.1) WILD-TYPE 73 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     19    2
  AMP PEAK 17(13Q22.1) WILD-TYPE   73   15
         clus
vv        AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  ABSENT                            19                             73
  PRESENT                            2                             15
[1] 2 2
[1] FALSE
D17V41, continuous
[1] "Remove cluster labels:"       "AMP PEAK 17(13Q22.1) MUTATED"
clus
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1MH                     TCGA-C5-A1ML 
"AMP PEAK 17(13Q22.1) WILD-TYPE" "AMP PEAK 17(13Q22.1) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-EK-A2RO 
"AMP PEAK 17(13Q22.1) WILD-TYPE" "AMP PEAK 17(13Q22.1) WILD-TYPE" 
                    TCGA-GH-A9DA                     TCGA-HM-A3JK 
"AMP PEAK 17(13Q22.1) WILD-TYPE" "AMP PEAK 17(13Q22.1) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-JX-A3Q8 
"AMP PEAK 17(13Q22.1) WILD-TYPE" "AMP PEAK 17(13Q22.1) WILD-TYPE" 
                    TCGA-MA-AA3W                     TCGA-MA-AA3Z 
"AMP PEAK 17(13Q22.1) WILD-TYPE" "AMP PEAK 17(13Q22.1) WILD-TYPE" 
                    TCGA-MA-AA42                     TCGA-MU-A51Y 
"AMP PEAK 17(13Q22.1) WILD-TYPE" "AMP PEAK 17(13Q22.1) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-MY-A913 
"AMP PEAK 17(13Q22.1) WILD-TYPE" "AMP PEAK 17(13Q22.1) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"AMP PEAK 17(13Q22.1) WILD-TYPE" 
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 17(13Q22.1) MUTATED      0   9   11    9  1   1    2    2   4  2   1
  AMP PEAK 17(13Q22.1) WILD-TYPE    1  25   58   21  5   9    5    7  32  0   1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 17(13Q22.1) MUTATED     4  3   0  7
  AMP PEAK 17(13Q22.1) WILD-TYPE  13  5   1  9
D17V42, multiclass
      clus
vv     AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  T1A1                            0                              1
  T1B                             9                             25
  T1B1                           11                             58
  T1B2                            9                             21
  T2                              1                              5
  T2A                             1                              9
  T2A1                            2                              5
  T2A2                            2                              7
  T2B                             4                             32
  T3                              2                              0
  T3A                             1                              1
  T3B                             4                             13
  T4                              3                              5
  TIS                             0                              1
  TX                              7                              9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 17(13Q22.1) MUTATED         3        1         0         0        9
  AMP PEAK 17(13Q22.1) WILD-TYPE       2        0         1         1       24
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 17(13Q22.1) MUTATED          14         9        0         1
  AMP PEAK 17(13Q22.1) WILD-TYPE        63        27        4         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 17(13Q22.1) MUTATED            0          0         9         1
  AMP PEAK 17(13Q22.1) WILD-TYPE          5          7        34         0
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 17(13Q22.1) MUTATED            2          9         3         1
  AMP PEAK 17(13Q22.1) WILD-TYPE          1         33         4        11
D17V44, multiclass
            clus
vv           AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              9                             24
  STAGE IB1                            14                             63
  STAGE IB2                             9                             27
  STAGE II                              0                              4
  STAGE IIA                             1                              7
  STAGE IIA1                            0                              5
  STAGE IIA2                            0                              7
  STAGE IIB                             9                             34
  STAGE III                             1                              0
  STAGE IIIA                            2                              1
  STAGE IIIB                            9                             33
  STAGE IVA                             3                              4
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(13Q34) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(13Q34) MUTATED    50  18
  AMP PEAK 18(13Q34) WILD-TYPE 163  47
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          68                          210 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          18                           47 
$`AMP PEAK 18(13Q34) MUTATED`
TCGA-4J-AA1J TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LZ TCGA-C5-A3HF 
       12.39        35.01         0.46         2.43       100.14        17.85 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      210.67       154.32       131.11        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DS-A0VM TCGA-DS-A7WI 
       45.83        23.51        27.52         1.12       117.99         8.28 
TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
       37.35        31.36        13.05        13.91        14.96         0.36 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM 
       45.96         1.51         0.59         0.36         1.18         2.24 
TCGA-EX-A1H6 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A40J 
        7.92         8.32        15.55        23.84         1.45         1.35 
TCGA-FU-A5XV TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
        1.97       147.39        78.71        81.96        29.85        27.42 
TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3Z 
       21.44        21.11       195.85        11.28         0.89        19.56 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
       35.05         2.96        16.41         9.34        15.39        19.59 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QH TCGA-VS-A954 TCGA-VS-A959 TCGA-VS-A9U7 
       19.96        32.15        39.78        50.63        45.34        42.41 
TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UQ TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-WL-A834 
       25.74        22.72        35.97        14.04         4.34        26.01 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       67.59        19.13 

$`AMP PEAK 18(13Q34) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99        35.61        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       33.24        52.01        18.02        20.42       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ 
        9.34         8.35       146.86        99.91        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       11.87        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52        39.55        12.36        30.90        31.53 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       12.66        12.82         7.46        14.89        26.79        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP 
       14.99        13.58        13.48        12.59        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
       19.27         0.43         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        0.07         4.04         0.03        47.77         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.10         0.03        20.35         6.94        14.70 
TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       19.79         1.22         0.92         2.17        31.36        36.26 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41        10.82        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LL 
        9.44       137.16        66.81       117.40        96.95        36.36 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       18.15        30.31         7.99        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 
       13.35        22.52        20.28        17.82         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
       11.38        13.87        34.62         5.42        54.81        20.84 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        5.49        15.58        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       14.07        15.88        19.36         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        66.05        10.03        40.50        37.78        26.43 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       18.05        59.51        46.03        36.13        11.51        57.93 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        36.26        16.64         4.73        24.39        39.78 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 
       50.86        15.68        48.07        50.14        44.94        43.40 
TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       21.30        19.69        46.92        40.96         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV 
       27.25        41.42        43.27        20.09        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 
       18.25        67.20        18.84         5.16        14.89        16.24 
TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        29.26         0.69         1.41         0.16         3.91 

  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                        0.36                         0.03 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      210.67                       177.04 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      19.775                       19.825 
[1] "0.4 - 210.7 (19.8)" "0.0 - 177.0 (19.8)"
[1] "hr=" "1.2"
D18V2, continuous
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 18(13Q34) MUTATED    31  16   5   1
  AMP PEAK 18(13Q34) WILD-TYPE 103  52  16   7
D18V3, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  T1                         31                          103
  T2                         16                           52
  T3                          5                           16
  T4                          1                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   31 13
  AMP PEAK 18(13Q34) WILD-TYPE 96 42
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     31   13
  AMP PEAK 18(13Q34) WILD-TYPE   96   42
   clus
vv  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  0                         31                           96
  1                         13                           42
[1] 2 2
[1] FALSE
D18V5, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   28  2
  AMP PEAK 18(13Q34) WILD-TYPE 79  8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     28    2
  AMP PEAK 18(13Q34) WILD-TYPE   79    8
   clus
vv  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  0                         28                           79
  1                          2                            8
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(13Q34) MUTATED               1                               57
  AMP PEAK 18(13Q34) WILD-TYPE             4                              184
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 18(13Q34) MUTATED                                               0
  AMP PEAK 18(13Q34) WILD-TYPE                                             6
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 18(13Q34) MUTATED                                     6
  AMP PEAK 18(13Q34) WILD-TYPE                                  16
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 18(13Q34) MUTATED                                           0
  AMP PEAK 18(13Q34) WILD-TYPE                                         3
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 18(13Q34) MUTATED                                              5
  AMP PEAK 18(13Q34) WILD-TYPE                                           10
D18V6, multiclass
                                               clus
vv                                              AMP PEAK 18(13Q34) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      57
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           5
                                               clus
vv                                              AMP PEAK 18(13Q34) WILD-TYPE
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       184
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            10
[1] 6 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(13Q34) MUTATED     4  65
  AMP PEAK 18(13Q34) WILD-TYPE  26 197
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      4   65
  AMP PEAK 18(13Q34) WILD-TYPE   26  197
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  NO                           4                           26
  YES                         65                          197
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(13Q34) MUTATED                                  2     3
  AMP PEAK 18(13Q34) WILD-TYPE                                6    15
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(13Q34) MUTATED                           6
  AMP PEAK 18(13Q34) WILD-TYPE                        22
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 18(13Q34) MUTATED                                           1    51
  AMP PEAK 18(13Q34) WILD-TYPE                                         1   150
D18V10, multiclass
                                           clus
vv                                          AMP PEAK 18(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              3
  BLACK OR AFRICAN AMERICAN                                          6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             51
                                           clus
vv                                          AMP PEAK 18(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                           22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              150
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     3  39
  AMP PEAK 18(13Q34) WILD-TYPE  20 122
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      3   39
  AMP PEAK 18(13Q34) WILD-TYPE   20  122
                        clus
vv                       AMP PEAK 18(13Q34) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         39
                        clus
vv                       AMP PEAK 18(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               20
  NOT HISPANIC OR LATINO                          122
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED    30  12
  AMP PEAK 18(13Q34) WILD-TYPE 104  29
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     30   12
  AMP PEAK 18(13Q34) WILD-TYPE  104   29
            clus
vv           AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  TUMOR FREE                         30                          104
  WITH TUMOR                         12                           29
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 18(13Q34) MUTATED       11      1       1      3       2
  AMP PEAK 18(13Q34) WILD-TYPE     42      4       0      8       5
                              vv
clus                           UNITED STATES VIETNAM
  AMP PEAK 18(13Q34) MUTATED              48       3
  AMP PEAK 18(13Q34) WILD-TYPE           153      11
D18V14, multiclass
               clus
vv              AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  BRAZIL                                11                           42
  CANADA                                 1                            4
  NIGERIA                                1                            0
  RUSSIA                                 3                            8
  UKRAINE                                2                            5
  UNITED STATES                         48                          153
  VIETNAM                                3                           11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            G1  G2  G3  G4  GX
  AMP PEAK 18(13Q34) MUTATED     3  25  32   1   6
  AMP PEAK 18(13Q34) WILD-TYPE  15 104  81   0  18
D18V15, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  G1                          3                           15
  G2                         25                          104
  G3                         32                           81
  G4                          1                            0
  GX                          6                           18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V16, continuous
D18V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 18(13Q34) MUTATED                                             8
  AMP PEAK 18(13Q34) WILD-TYPE                                          29
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 18(13Q34) MUTATED                                        0
  AMP PEAK 18(13Q34) WILD-TYPE                                      9
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 18(13Q34) MUTATED                                                 0
  AMP PEAK 18(13Q34) WILD-TYPE                                               3
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 18(13Q34) MUTATED               10                  42
  AMP PEAK 18(13Q34) WILD-TYPE             52                 100
D18V18, multiclass
                                                 clus
vv                                                AMP PEAK 18(13Q34) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          0
  CURRENT SMOKER                                                          10
  LIFELONG NON-SMOKER                                                     42
                                                 clus
vv                                                AMP PEAK 18(13Q34) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            3
  CURRENT SMOKER                                                            52
  LIFELONG NON-SMOKER                                                      100
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V19, continuous
D18V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 18(13Q34) MUTATED             2       30             2        5
  AMP PEAK 18(13Q34) WILD-TYPE          17       72            10       20
D18V21, multiclass
               clus
vv              AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  COMBINATION                            2                           17
  EXTERNAL                              30                           72
  EXTERNAL BEAM                          2                           10
  INTERNAL                               5                           20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V22, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED    2  2
  AMP PEAK 18(13Q34) WILD-TYPE 23  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      2    2
  AMP PEAK 18(13Q34) WILD-TYPE   23    1
                         clus
vv                        AMP PEAK 18(13Q34) MUTATED
  COMPLETED AS PLANNED                             2
  TREATMENT NOT COMPLETED                          2
                         clus
vv                        AMP PEAK 18(13Q34) WILD-TYPE
  COMPLETED AS PLANNED                              23
  TREATMENT NOT COMPLETED                            1
[1] 2 2
[1] FALSE
                              vv
clus                           DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 18(13Q34) MUTATED                    0                0
  AMP PEAK 18(13Q34) WILD-TYPE                  2                2
                              vv
clus                           PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 18(13Q34) MUTATED                    10             7
  AMP PEAK 18(13Q34) WILD-TYPE                  26            26
D18V23, multiclass
                     clus
vv                    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  DISTANT RECURRENCE                           0                            2
  LOCAL RECURRENCE                             0                            2
  PRIMARY TUMOR FIELD                         10                           26
  REGIONAL SITE                                7                           26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V24, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   12  1
  AMP PEAK 18(13Q34) WILD-TYPE 44  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     12    1
  AMP PEAK 18(13Q34) WILD-TYPE   44    4
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  CGY                         12                           44
  GY                           1                            4
[1] 2 2
[1] FALSE
D18V25, continuous
D18V26, continuous
D18V27, continuous
D18V28, continuous
D18V29, continuous
D18V30, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 18(13Q34) MUTATED                                     0
  AMP PEAK 18(13Q34) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 18(13Q34) MUTATED                                     3
  AMP PEAK 18(13Q34) WILD-TYPE                                   4
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 18(13Q34) MUTATED                         9                       0
  AMP PEAK 18(13Q34) WILD-TYPE                      26                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 18(13Q34) MUTATED                         1
  AMP PEAK 18(13Q34) WILD-TYPE                       7
D18V31, multiclass
                                     clus
vv                                    AMP PEAK 18(13Q34) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          3
  OTHER LOCATION, SPECIFY                                      9
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      1
                                     clus
vv                                    AMP PEAK 18(13Q34) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                       26
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 18(13Q34) MUTATED                                               0
  AMP PEAK 18(13Q34) WILD-TYPE                                             2
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 18(13Q34) MUTATED                                                7
  AMP PEAK 18(13Q34) WILD-TYPE                                             18
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 18(13Q34) MUTATED                                                                                  24
  AMP PEAK 18(13Q34) WILD-TYPE                                                                                57
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 18(13Q34) MUTATED                                                                                             27
  AMP PEAK 18(13Q34) WILD-TYPE                                                                                           93
D18V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 18(13Q34) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    24
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         27
                                                                                              clus
vv                                                                                             AMP PEAK 18(13Q34) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V33, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   11 19
  AMP PEAK 18(13Q34) WILD-TYPE 59 54
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     11   19
  AMP PEAK 18(13Q34) WILD-TYPE   59   54
         clus
vv        AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  ABSENT                          11                           59
  PRESENT                         19                           54
[1] 2 2
[1] FALSE
D18V34, continuous
D18V35, continuous
D18V36, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   15 23
  AMP PEAK 18(13Q34) WILD-TYPE 33 93
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     15   23
  AMP PEAK 18(13Q34) WILD-TYPE   33   93
                                          clus
vv                                         AMP PEAK 18(13Q34) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         23
                                          clus
vv                                         AMP PEAK 18(13Q34) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           93
[1] 2 2
[1] FALSE
D18V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 18(13Q34) MUTATED              3          12         20
  AMP PEAK 18(13Q34) WILD-TYPE           12          41         64
D18V38, multiclass
              clus
vv             AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  CURRENT USER                          3                           12
  FORMER USER                          12                           41
  NEVER USED                           20                           64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V39, continuous
D18V40, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   19  1
  AMP PEAK 18(13Q34) WILD-TYPE 73 16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     19    1
  AMP PEAK 18(13Q34) WILD-TYPE   73   16
         clus
vv        AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  ABSENT                          19                           73
  PRESENT                          1                           16
[1] 2 2
[1] FALSE
D18V41, continuous
[1] "Remove cluster labels:"     "AMP PEAK 18(13Q34) MUTATED"
clus
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                           1                           16 
                  TCGA-C5-A1BN                   TCGA-C5-A1MH 
"AMP PEAK 18(13Q34) WILD-TYPE" "AMP PEAK 18(13Q34) WILD-TYPE" 
                  TCGA-C5-A1ML                   TCGA-C5-A1MN 
"AMP PEAK 18(13Q34) WILD-TYPE" "AMP PEAK 18(13Q34) WILD-TYPE" 
                  TCGA-C5-A1MP                   TCGA-EK-A2RO 
"AMP PEAK 18(13Q34) WILD-TYPE" "AMP PEAK 18(13Q34) WILD-TYPE" 
                  TCGA-GH-A9DA                   TCGA-HM-A3JK 
"AMP PEAK 18(13Q34) WILD-TYPE" "AMP PEAK 18(13Q34) WILD-TYPE" 
                  TCGA-JW-A852                   TCGA-JX-A3Q8 
"AMP PEAK 18(13Q34) WILD-TYPE" "AMP PEAK 18(13Q34) WILD-TYPE" 
                  TCGA-MA-AA3W                   TCGA-MA-AA42 
"AMP PEAK 18(13Q34) WILD-TYPE" "AMP PEAK 18(13Q34) WILD-TYPE" 
                  TCGA-MU-A51Y                   TCGA-MU-A8JM 
"AMP PEAK 18(13Q34) WILD-TYPE" "AMP PEAK 18(13Q34) WILD-TYPE" 
                  TCGA-MY-A913                   TCGA-ZX-AA5X 
"AMP PEAK 18(13Q34) WILD-TYPE" "AMP PEAK 18(13Q34) WILD-TYPE" 
                              vv
clus                           T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 18(13Q34) MUTATED      0  11   11    9  1   3    4    2   6  2   0
  AMP PEAK 18(13Q34) WILD-TYPE    1  23   58   21  5   7    3    7  30  0   2
                              vv
clus                           T3B T4 TIS TX
  AMP PEAK 18(13Q34) MUTATED     3  1   0  5
  AMP PEAK 18(13Q34) WILD-TYPE  14  7   1 11
D18V42, multiclass
      clus
vv     AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  T1A1                          0                            1
  T1B                          11                           23
  T1B1                         11                           58
  T1B2                          9                           21
  T2                            1                            5
  T2A                           3                            7
  T2A1                          4                            3
  T2A2                          2                            7
  T2B                           6                           30
  T3                            2                            0
  T3A                           0                            2
  T3B                           3                           14
  T4                            1                            7
  TIS                           0                            1
  TX                            5                           11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 18(13Q34) MUTATED         3        1         0         0        9
  AMP PEAK 18(13Q34) WILD-TYPE       2        0         1         1       24
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 18(13Q34) MUTATED          16         8        1         2
  AMP PEAK 18(13Q34) WILD-TYPE        61        28        3         6
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 18(13Q34) MUTATED            2          1         9         1
  AMP PEAK 18(13Q34) WILD-TYPE          3          6        34         0
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 18(13Q34) MUTATED            1          9         1         2
  AMP PEAK 18(13Q34) WILD-TYPE          2         33         6        10
D18V44, multiclass
            clus
vv           AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                            1                            0
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            9                           24
  STAGE IB1                          16                           61
  STAGE IB2                           8                           28
  STAGE II                            1                            3
  STAGE IIA                           2                            6
  STAGE IIA1                          2                            3
  STAGE IIA2                          1                            6
  STAGE IIB                           9                           34
  STAGE III                           1                            0
  STAGE IIIA                          1                            2
  STAGE IIIB                          9                           33
  STAGE IVA                           1                            6
  STAGE IVB                           2                           10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(15Q26.1) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(15Q26.1) MUTATED    57  15
  AMP PEAK 19(15Q26.1) WILD-TYPE 156  50
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                            72                            206 
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                            15                             50 
$`AMP PEAK 19(15Q26.1) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1M6 TCGA-C5-A1M8 
       12.39        49.48        18.74       177.04        31.40        30.21 
TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ 
       57.73        35.61         2.43         3.58        73.18       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UI 
       33.24        52.01        18.02       101.82        20.35        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KL 
        9.34         2.73        20.91        11.87         1.12        44.94 
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A50E TCGA-EA-A556 
       87.75         2.66         8.28        37.35         7.46        14.89 
TCGA-EA-A5O9 TCGA-EK-A2PI TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EX-A3L1 
       13.91        19.27         4.04         0.03         2.24         6.94 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A9SC 
       19.79        15.55        23.84         1.97         9.01        10.82 
TCGA-HM-A3JK TCGA-IR-A3LA TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A5QV 
       20.78       137.16        27.42        21.44        15.58         7.99 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MA-AA3W TCGA-MA-AA43 TCGA-MY-A5BE TCGA-Q1-A73S 
       11.28         0.30        22.52        11.38        35.05        19.36 
TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q9 
       19.59        12.16        40.50        26.43        18.05        46.03 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A950 TCGA-VS-A959 TCGA-VS-A9UB TCGA-VS-A9UC 
       11.51        57.93        39.78        45.34        21.30        22.72 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-ZJ-A8QR 
       14.53        41.42        43.27        35.97        14.53        19.13 

$`AMP PEAK 19(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-A1ML TCGA-C5-A1MN 
       35.01        53.16        38.99         0.46        20.91        40.93 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A3HF 
       44.22        73.45        83.05        78.35        38.43        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
       20.42       210.67       154.32       134.33        15.48       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
       17.19       155.77       131.11        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35       146.86        99.91        23.51        27.52        20.81 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       58.88        50.76        40.04        58.88        36.76       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
      118.65        22.98        16.83        16.18        17.52        39.55 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50        26.40        24.56        14.50        26.01        12.66 
TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.82        26.79        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.48         0.36        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN 
       16.08         0.07         0.36         1.18        47.77         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       14.70         8.32         1.22         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 
        1.35         1.32         1.12        25.41        21.67        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
        9.44       147.39        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        29.85        36.36         3.29        24.56        20.48 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       195.85        30.31 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.89        12.49         0.82        13.35        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         9.17         8.52        13.87        34.62         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       54.81        20.84         5.49         2.96        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
        9.34        15.39         3.88        11.67        93.99        66.05 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA 
       10.03        37.78        19.96        59.51        32.15        36.13 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        36.26        16.64         4.73        24.39 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 
       50.86        15.68        50.63        48.07        50.14        44.94 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       43.40        42.41        25.74        19.69        46.92        40.96 
TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
        1.71        27.25        20.09         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         5.16        14.04        14.89         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       15.42        26.01        29.26        67.59         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                        177.04                         210.67 
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                         19.69                          19.91 
[1] "0.0 - 177.0 (19.7)" "0.0 - 210.7 (19.9)"
[1] "hr=" "1.1"
D19V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 19(15Q26.1) MUTATED    27  22   8   1
  AMP PEAK 19(15Q26.1) WILD-TYPE 107  46  13   7
D19V3, multiclass
    clus
vv   AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  T1                           27                            107
  T2                           22                             46
  T3                            8                             13
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   30 16
  AMP PEAK 19(15Q26.1) WILD-TYPE 97 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     30   16
  AMP PEAK 19(15Q26.1) WILD-TYPE   97   39
   clus
vv  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  0                           30                             97
  1                           16                             39
[1] 2 2
[1] FALSE
D19V5, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   28  0
  AMP PEAK 19(15Q26.1) WILD-TYPE 79 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     28    0
  AMP PEAK 19(15Q26.1) WILD-TYPE   79   10
   clus
vv  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  0                           28                             79
  1                            0                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(15Q26.1) MUTATED               3                               61
  AMP PEAK 19(15Q26.1) WILD-TYPE             2                              180
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 19(15Q26.1) MUTATED                                               3
  AMP PEAK 19(15Q26.1) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 19(15Q26.1) MUTATED                                     3
  AMP PEAK 19(15Q26.1) WILD-TYPE                                  19
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 19(15Q26.1) MUTATED                                           2
  AMP PEAK 19(15Q26.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 19(15Q26.1) MUTATED                                              4
  AMP PEAK 19(15Q26.1) WILD-TYPE                                           11
D19V6, multiclass
                                               clus
vv                                              AMP PEAK 19(15Q26.1) MUTATED
  ADENOSQUAMOUS                                                            3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        61
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              AMP PEAK 19(15Q26.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         180
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(15Q26.1) MUTATED     8  68
  AMP PEAK 19(15Q26.1) WILD-TYPE  22 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED      8   68
  AMP PEAK 19(15Q26.1) WILD-TYPE   22  194
     clus
vv    AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  NO                             8                             22
  YES                           68                            194
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(15Q26.1) MUTATED                                  4     5
  AMP PEAK 19(15Q26.1) WILD-TYPE                                4    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(15Q26.1) MUTATED                           4
  AMP PEAK 19(15Q26.1) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 19(15Q26.1) MUTATED                                           1
  AMP PEAK 19(15Q26.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 19(15Q26.1) MUTATED      50
  AMP PEAK 19(15Q26.1) WILD-TYPE   151
D19V10, multiclass
                                           clus
vv                                          AMP PEAK 19(15Q26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               50
                                           clus
vv                                          AMP PEAK 19(15Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                151
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                                cls
clus                               0   1
  AMP PEAK 19(15Q26.1) MUTATED     7  42
  AMP PEAK 19(15Q26.1) WILD-TYPE  16 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED      7   42
  AMP PEAK 19(15Q26.1) WILD-TYPE   16  119
                        clus
vv                       AMP PEAK 19(15Q26.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       AMP PEAK 19(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            119
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   36 12
  AMP PEAK 19(15Q26.1) WILD-TYPE 98 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     36   12
  AMP PEAK 19(15Q26.1) WILD-TYPE   98   29
            clus
vv           AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  TUMOR FREE                           36                             98
  WITH TUMOR                           12                             29
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 19(15Q26.1) MUTATED       15      2       0      3       1
  AMP PEAK 19(15Q26.1) WILD-TYPE     38      3       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 19(15Q26.1) MUTATED              52       3
  AMP PEAK 19(15Q26.1) WILD-TYPE           149      11
D19V14, multiclass
               clus
vv              AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  BRAZIL                                  15                             38
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   3                              8
  UKRAINE                                  1                              6
  UNITED STATES                           52                            149
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 19(15Q26.1) MUTATED     6  29  36   0   3
  AMP PEAK 19(15Q26.1) WILD-TYPE  12 100  77   1  21
D19V15, multiclass
    clus
vv   AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  G1                            6                             12
  G2                           29                            100
  G3                           36                             77
  G4                            0                              1
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V16, continuous
D19V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 19(15Q26.1) MUTATED                                            12
  AMP PEAK 19(15Q26.1) WILD-TYPE                                          25
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 19(15Q26.1) MUTATED                                        0
  AMP PEAK 19(15Q26.1) WILD-TYPE                                      9
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 19(15Q26.1) MUTATED                                                 0
  AMP PEAK 19(15Q26.1) WILD-TYPE                                               3
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 19(15Q26.1) MUTATED               19                  39
  AMP PEAK 19(15Q26.1) WILD-TYPE             43                 103
D19V18, multiclass
                                                 clus
vv                                                AMP PEAK 19(15Q26.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            19
  LIFELONG NON-SMOKER                                                       39
                                                 clus
vv                                                AMP PEAK 19(15Q26.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              3
  CURRENT SMOKER                                                              43
  LIFELONG NON-SMOKER                                                        103
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V19, continuous
D19V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 19(15Q26.1) MUTATED             5       29             3        8
  AMP PEAK 19(15Q26.1) WILD-TYPE          14       73             9       17
D19V21, multiclass
               clus
vv              AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  COMBINATION                              5                             14
  EXTERNAL                                29                             73
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 8                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V22, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED    6  1
  AMP PEAK 19(15Q26.1) WILD-TYPE 19  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED      6    1
  AMP PEAK 19(15Q26.1) WILD-TYPE   19    2
                         clus
vv                        AMP PEAK 19(15Q26.1) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 19(15Q26.1) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 19(15Q26.1) MUTATED                    1                0
  AMP PEAK 19(15Q26.1) WILD-TYPE                  1                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 19(15Q26.1) MUTATED                    14            12
  AMP PEAK 19(15Q26.1) WILD-TYPE                  22            21
D19V23, multiclass
                     clus
vv                    AMP PEAK 19(15Q26.1) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                           14
  REGIONAL SITE                                 12
                     clus
vv                    AMP PEAK 19(15Q26.1) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             22
  REGIONAL SITE                                   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"
D19V24, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   22  1
  AMP PEAK 19(15Q26.1) WILD-TYPE 34  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     22    1
  AMP PEAK 19(15Q26.1) WILD-TYPE   34    4
     clus
vv    AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  CGY                           22                             34
  GY                             1                              4
[1] 2 2
[1] FALSE
D19V25, continuous
D19V26, continuous
D19V27, continuous
D19V28, continuous
D19V29, continuous
D19V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 19(15Q26.1) MUTATED                                     0
  AMP PEAK 19(15Q26.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 19(15Q26.1) MUTATED                                     0
  AMP PEAK 19(15Q26.1) WILD-TYPE                                   7
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 19(15Q26.1) MUTATED                        11
  AMP PEAK 19(15Q26.1) WILD-TYPE                      24
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 19(15Q26.1) MUTATED                         1
  AMP PEAK 19(15Q26.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 19(15Q26.1) MUTATED                         1
  AMP PEAK 19(15Q26.1) WILD-TYPE                       7
D19V31, multiclass
                                     clus
vv                                    AMP PEAK 19(15Q26.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  OTHER LOCATION, SPECIFY                                       11
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 19(15Q26.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              7
  OTHER LOCATION, SPECIFY                                         24
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 19(15Q26.1) MUTATED                                               1
  AMP PEAK 19(15Q26.1) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 19(15Q26.1) MUTATED                                               10
  AMP PEAK 19(15Q26.1) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 19(15Q26.1) MUTATED                                                                                  20
  AMP PEAK 19(15Q26.1) WILD-TYPE                                                                                61
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 19(15Q26.1) MUTATED                                                                                             29
  AMP PEAK 19(15Q26.1) WILD-TYPE                                                                                           91
D19V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 19(15Q26.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           29
                                                                                              clus
vv                                                                                             AMP PEAK 19(15Q26.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V33, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   16 19
  AMP PEAK 19(15Q26.1) WILD-TYPE 54 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     16   19
  AMP PEAK 19(15Q26.1) WILD-TYPE   54   54
         clus
vv        AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  ABSENT                            16                             54
  PRESENT                           19                             54
[1] 2 2
[1] FALSE
D19V34, continuous
D19V35, continuous
D19V36, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   11 26
  AMP PEAK 19(15Q26.1) WILD-TYPE 37 90
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     11   26
  AMP PEAK 19(15Q26.1) WILD-TYPE   37   90
                                          clus
vv                                         AMP PEAK 19(15Q26.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           26
                                          clus
vv                                         AMP PEAK 19(15Q26.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             90
[1] 2 2
[1] FALSE
D19V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 19(15Q26.1) MUTATED              4           8         27
  AMP PEAK 19(15Q26.1) WILD-TYPE           11          45         57
D19V38, multiclass
              clus
vv             AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  CURRENT USER                            4                             11
  FORMER USER                             8                             45
  NEVER USED                             27                             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"
D19V39, continuous
D19V40, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   20  5
  AMP PEAK 19(15Q26.1) WILD-TYPE 72 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     20    5
  AMP PEAK 19(15Q26.1) WILD-TYPE   72   12
         clus
vv        AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  ABSENT                            20                             72
  PRESENT                            5                             12
[1] 2 2
[1] FALSE
D19V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 19(15Q26.1) MUTATED      0   6   14    7  1   7    3    1  10  0   1
  AMP PEAK 19(15Q26.1) WILD-TYPE    1  28   55   23  5   3    4    8  26  2   1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 19(15Q26.1) MUTATED     7  1   0  5
  AMP PEAK 19(15Q26.1) WILD-TYPE  10  7   1 11
D19V42, multiclass
      clus
vv     AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  T1A1                            0                              1
  T1B                             6                             28
  T1B1                           14                             55
  T1B2                            7                             23
  T2                              1                              5
  T2A                             7                              3
  T2A1                            3                              4
  T2A2                            1                              8
  T2B                            10                             26
  T3                              0                              2
  T3A                             1                              1
  T3B                             7                             10
  T4                              1                              7
  TIS                             0                              1
  TX                              5                             11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 19(15Q26.1) MUTATED         1        0         0         0        8
  AMP PEAK 19(15Q26.1) WILD-TYPE       4        1         1         1       25
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 19(15Q26.1) MUTATED          18         9        1         5
  AMP PEAK 19(15Q26.1) WILD-TYPE        59        27        3         3
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 19(15Q26.1) MUTATED            2          2        13         0
  AMP PEAK 19(15Q26.1) WILD-TYPE          3          5        30         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 19(15Q26.1) MUTATED            1         14         2         0
  AMP PEAK 19(15Q26.1) WILD-TYPE          2         28         5        12
D19V44, multiclass
            clus
vv           AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              8                             25
  STAGE IB1                            18                             59
  STAGE IB2                             9                             27
  STAGE II                              1                              3
  STAGE IIA                             5                              3
  STAGE IIA1                            2                              3
  STAGE IIA2                            2                              5
  STAGE IIB                            13                             30
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                           14                             28
  STAGE IVA                             2                              5
  STAGE IVB                             0                             12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(16P13.13) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(16P13.13) MUTATED    47  14
  AMP PEAK 20(16P13.13) WILD-TYPE 166  51
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                             61                             217 
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                             14                              51 
$`AMP PEAK 20(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-C5-A8YR TCGA-DG-A2KH 
       44.22        17.85       154.32         2.73        27.52         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3QD 
       58.88        44.94        22.98         8.28        37.35        13.05 
TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2PI 
       14.50        13.91        14.96         0.36        26.27        19.27 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-FU-A23L 
        4.04         0.03        47.77         0.10         0.03        23.84 
TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A40J TCGA-HM-A3JK 
        2.17         1.45         1.58         1.48         1.35        20.78 
TCGA-IR-A3LI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-MA-AA3X 
       81.96        21.44        15.58       195.85         7.99        20.28 
TCGA-PN-A8MA TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA 
        2.96        93.99        12.16        19.96        32.15        36.13 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC 
       50.86        15.68        44.94        43.40        21.30        22.72 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UU TCGA-XS-A8TJ 
       46.92        40.96        14.53        43.27        14.53        29.26 
TCGA-ZJ-AAXA 
        1.41 

$`AMP PEAK 20(16P13.13) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       19.86        67.46        30.21        35.01        57.73        53.16 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV 
        2.43        20.91        40.93         3.58        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       18.02        20.42       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34        13.61        50.99        45.83         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK 
       99.91        23.51        20.81        20.91        11.87        50.76 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT 
      118.65        16.83        16.18        17.52        39.55        12.36 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       30.90        31.53        31.36        25.02        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       24.56        26.01        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       26.79        15.02        14.99        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ 
        1.45         0.13        16.08         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-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        0.92        31.36        36.26         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41        10.82        21.67 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        78.71        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       24.56        20.48        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       30.31        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       13.35        22.52        17.82        19.56         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        13.87        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84         5.49        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB 
       19.36        19.59         3.88        11.67        66.05        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 
       40.50        37.78        26.43        18.05        59.51        46.03 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        57.93        39.78        31.27        36.26        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        24.39        39.78        50.63        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UJ TCGA-VS-A9UM 
       45.34        42.41        25.74        19.69         1.71        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.42        35.97        20.09         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         5.16        14.04        14.89         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
       15.42        26.01        67.59        19.13         0.69         0.16 
TCGA-ZX-AA5X 
        3.91 

  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                           0.03                            0.07 
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                         195.85                          210.67 
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                          20.78                           19.59 
[1] "0.0 - 195.8 (20.8)" "0.1 - 210.7 (19.6)"
[1] "hr=" "1.1"
D20V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 20(16P13.13) MUTATED    25  22   6   3
  AMP PEAK 20(16P13.13) WILD-TYPE 109  46  15   5
D20V3, multiclass
    clus
vv   AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  T1                            25                             109
  T2                            22                              46
  T3                             6                              15
  T4                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                                 cls
clus                                0   1
  AMP PEAK 20(16P13.13) MUTATED    26  16
  AMP PEAK 20(16P13.13) WILD-TYPE 101  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     26   16
  AMP PEAK 20(16P13.13) WILD-TYPE  101   39
   clus
vv  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  0                            26                             101
  1                            16                              39
[1] 2 2
[1] FALSE
D20V5, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   23  3
  AMP PEAK 20(16P13.13) WILD-TYPE 84  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     23    3
  AMP PEAK 20(16P13.13) WILD-TYPE   84    7
   clus
vv  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  0                            23                              84
  1                             3                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 20(16P13.13) MUTATED               1
  AMP PEAK 20(16P13.13) WILD-TYPE             4
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(16P13.13) MUTATED                                 54
  AMP PEAK 20(16P13.13) WILD-TYPE                              187
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 20(16P13.13) MUTATED                                               1
  AMP PEAK 20(16P13.13) WILD-TYPE                                             5
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 20(16P13.13) MUTATED                                     5
  AMP PEAK 20(16P13.13) WILD-TYPE                                  17
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 20(16P13.13) MUTATED                                           0
  AMP PEAK 20(16P13.13) WILD-TYPE                                         3
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 20(16P13.13) MUTATED                                              4
  AMP PEAK 20(16P13.13) WILD-TYPE                                           11
D20V6, multiclass
                                               clus
vv                                              AMP PEAK 20(16P13.13) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         54
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
                                               clus
vv                                              AMP PEAK 20(16P13.13) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          187
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(16P13.13) MUTATED     6  59
  AMP PEAK 20(16P13.13) WILD-TYPE  24 203
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED      6   59
  AMP PEAK 20(16P13.13) WILD-TYPE   24  203
     clus
vv    AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  NO                              6                              24
  YES                            59                             203
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(16P13.13) MUTATED                                  3     2
  AMP PEAK 20(16P13.13) WILD-TYPE                                5    16
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(16P13.13) MUTATED                           6
  AMP PEAK 20(16P13.13) WILD-TYPE                        22
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 20(16P13.13) MUTATED                                           1
  AMP PEAK 20(16P13.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 20(16P13.13) MUTATED      37
  AMP PEAK 20(16P13.13) WILD-TYPE   164
D20V10, multiclass
                                           clus
vv                                          AMP PEAK 20(16P13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 2
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                37
                                           clus
vv                                          AMP PEAK 20(16P13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        5
  ASIAN                                                                  16
  BLACK OR AFRICAN AMERICAN                                              22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 164
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, binary
                                 cls
clus                                0   1
  AMP PEAK 20(16P13.13) MUTATED     3  30
  AMP PEAK 20(16P13.13) WILD-TYPE  20 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED      3   30
  AMP PEAK 20(16P13.13) WILD-TYPE   20  131
                        clus
vv                       AMP PEAK 20(16P13.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            30
                        clus
vv                       AMP PEAK 20(16P13.13) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             131
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                                 cls
clus                                0   1
  AMP PEAK 20(16P13.13) MUTATED    24  12
  AMP PEAK 20(16P13.13) WILD-TYPE 110  29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     24   12
  AMP PEAK 20(16P13.13) WILD-TYPE  110   29
            clus
vv           AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  TUMOR FREE                            24                             110
  WITH TUMOR                            12                              29
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 20(16P13.13) MUTATED       15      3       1      1       2
  AMP PEAK 20(16P13.13) WILD-TYPE     38      2       0     10       5
                                 vv
clus                              UNITED STATES VIETNAM
  AMP PEAK 20(16P13.13) MUTATED              41       2
  AMP PEAK 20(16P13.13) WILD-TYPE           160      12
D20V14, multiclass
               clus
vv              AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  BRAZIL                                   15                              38
  CANADA                                    3                               2
  NIGERIA                                   1                               0
  RUSSIA                                    1                              10
  UKRAINE                                   2                               5
  UNITED STATES                            41                             160
  VIETNAM                                   2                              12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               G1  G2  G3  G4  GX
  AMP PEAK 20(16P13.13) MUTATED     5  27  25   0   6
  AMP PEAK 20(16P13.13) WILD-TYPE  13 102  88   1  18
D20V15, multiclass
    clus
vv   AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  G1                             5                              13
  G2                            27                             102
  G3                            25                              88
  G4                             0                               1
  GX                             6                              18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V16, continuous
D20V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 20(16P13.13) MUTATED                                             5
  AMP PEAK 20(16P13.13) WILD-TYPE                                          32
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 20(16P13.13) MUTATED                                        3
  AMP PEAK 20(16P13.13) WILD-TYPE                                      6
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 20(16P13.13) MUTATED                                                 1
  AMP PEAK 20(16P13.13) WILD-TYPE                                               2
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 20(16P13.13) MUTATED               15                  29
  AMP PEAK 20(16P13.13) WILD-TYPE             47                 113
D20V18, multiclass
                                                 clus
vv                                                AMP PEAK 20(16P13.13) 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                                                             15
  LIFELONG NON-SMOKER                                                        29
                                                 clus
vv                                                AMP PEAK 20(16P13.13) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               2
  CURRENT SMOKER                                                               47
  LIFELONG NON-SMOKER                                                         113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V19, continuous
D20V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 20(16P13.13) MUTATED             4       23             2        3
  AMP PEAK 20(16P13.13) WILD-TYPE          15       79            10       22
D20V21, multiclass
               clus
vv              AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  COMBINATION                               4                              15
  EXTERNAL                                 23                              79
  EXTERNAL BEAM                             2                              10
  INTERNAL                                  3                              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"
D20V22, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED    5  0
  AMP PEAK 20(16P13.13) WILD-TYPE 20  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED      5    0
  AMP PEAK 20(16P13.13) WILD-TYPE   20    3
                         clus
vv                        AMP PEAK 20(16P13.13) MUTATED
  COMPLETED AS PLANNED                                5
  TREATMENT NOT COMPLETED                             0
                         clus
vv                        AMP PEAK 20(16P13.13) WILD-TYPE
  COMPLETED AS PLANNED                                 20
  TREATMENT NOT COMPLETED                               3
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 20(16P13.13) MUTATED                    0                0
  AMP PEAK 20(16P13.13) WILD-TYPE                  2                2
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 20(16P13.13) MUTATED                     7             7
  AMP PEAK 20(16P13.13) WILD-TYPE                  29            26
D20V23, multiclass
                     clus
vv                    AMP PEAK 20(16P13.13) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                0
  PRIMARY TUMOR FIELD                             7
  REGIONAL SITE                                   7
                     clus
vv                    AMP PEAK 20(16P13.13) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  2
  PRIMARY TUMOR FIELD                              29
  REGIONAL SITE                                    26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V24, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   14  0
  AMP PEAK 20(16P13.13) WILD-TYPE 42  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     14    0
  AMP PEAK 20(16P13.13) WILD-TYPE   42    5
     clus
vv    AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  CGY                            14                              42
  GY                              0                               5
[1] 2 2
[1] FALSE
D20V25, continuous
D20V26, continuous
D20V27, continuous
D20V28, continuous
D20V29, continuous
D20V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 20(16P13.13) MUTATED                                     0
  AMP PEAK 20(16P13.13) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 20(16P13.13) MUTATED                                     1
  AMP PEAK 20(16P13.13) WILD-TYPE                                   6
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 20(16P13.13) MUTATED                         6
  AMP PEAK 20(16P13.13) WILD-TYPE                      29
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 20(16P13.13) MUTATED                         0
  AMP PEAK 20(16P13.13) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 20(16P13.13) MUTATED                         3
  AMP PEAK 20(16P13.13) WILD-TYPE                       5
D20V31, multiclass
                                     clus
vv                                    AMP PEAK 20(16P13.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         6
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         3
                                     clus
vv                                    AMP PEAK 20(16P13.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               6
  OTHER LOCATION, SPECIFY                                          29
  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 20(16P13.13) MUTATED                                               0
  AMP PEAK 20(16P13.13) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 20(16P13.13) MUTATED                                                7
  AMP PEAK 20(16P13.13) WILD-TYPE                                             18
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 20(16P13.13) MUTATED                                                                                  21
  AMP PEAK 20(16P13.13) WILD-TYPE                                                                                60
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 20(16P13.13) MUTATED                                                                                             21
  AMP PEAK 20(16P13.13) WILD-TYPE                                                                                           99
D20V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 20(16P13.13) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            21
                                                                                              clus
vv                                                                                             AMP PEAK 20(16P13.13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V33, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   19 16
  AMP PEAK 20(16P13.13) WILD-TYPE 51 57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     19   16
  AMP PEAK 20(16P13.13) WILD-TYPE   51   57
         clus
vv        AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  ABSENT                             19                              51
  PRESENT                            16                              57
[1] 2 2
[1] FALSE
D20V34, continuous
D20V35, continuous
D20V36, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   10 25
  AMP PEAK 20(16P13.13) WILD-TYPE 38 91
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     10   25
  AMP PEAK 20(16P13.13) WILD-TYPE   38   91
                                          clus
vv                                         AMP PEAK 20(16P13.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            25
                                          clus
vv                                         AMP PEAK 20(16P13.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              91
[1] 2 2
[1] FALSE
D20V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 20(16P13.13) MUTATED              1           8         21
  AMP PEAK 20(16P13.13) WILD-TYPE           14          45         63
D20V38, multiclass
              clus
vv             AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  CURRENT USER                             1                              14
  FORMER USER                              8                              45
  NEVER USED                              21                              63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V39, continuous
D20V40, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   17  5
  AMP PEAK 20(16P13.13) WILD-TYPE 75 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     17    5
  AMP PEAK 20(16P13.13) WILD-TYPE   75   12
         clus
vv        AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  ABSENT                             17                              75
  PRESENT                             5                              12
[1] 2 2
[1] FALSE
D20V41, continuous
[1] "Remove cluster labels:"        "AMP PEAK 20(16P13.13) MUTATED"
clus
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                              2                              15 
                     TCGA-C5-A1BN                      TCGA-C5-A1ML 
"AMP PEAK 20(16P13.13) WILD-TYPE" "AMP PEAK 20(16P13.13) WILD-TYPE" 
                     TCGA-C5-A1MN                      TCGA-C5-A1MP 
"AMP PEAK 20(16P13.13) WILD-TYPE" "AMP PEAK 20(16P13.13) WILD-TYPE" 
                     TCGA-EK-A2RO                      TCGA-GH-A9DA 
"AMP PEAK 20(16P13.13) WILD-TYPE" "AMP PEAK 20(16P13.13) WILD-TYPE" 
                     TCGA-JW-A852                      TCGA-JX-A3Q8 
"AMP PEAK 20(16P13.13) WILD-TYPE" "AMP PEAK 20(16P13.13) WILD-TYPE" 
                     TCGA-MA-AA3W                      TCGA-MA-AA3Z 
"AMP PEAK 20(16P13.13) WILD-TYPE" "AMP PEAK 20(16P13.13) WILD-TYPE" 
                     TCGA-MA-AA42                      TCGA-MU-A51Y 
"AMP PEAK 20(16P13.13) WILD-TYPE" "AMP PEAK 20(16P13.13) WILD-TYPE" 
                     TCGA-MU-A8JM                      TCGA-MY-A913 
"AMP PEAK 20(16P13.13) WILD-TYPE" "AMP PEAK 20(16P13.13) WILD-TYPE" 
                     TCGA-ZX-AA5X 
"AMP PEAK 20(16P13.13) WILD-TYPE" 
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 20(16P13.13) MUTATED      0   6   14    5  0   4    3    1  14  1
  AMP PEAK 20(16P13.13) WILD-TYPE    1  28   55   25  6   6    4    8  22  1
                                 vv
clus                              T3A T3B T4 TIS TX
  AMP PEAK 20(16P13.13) MUTATED     0   5  3   0  1
  AMP PEAK 20(16P13.13) WILD-TYPE   2  12  5   1 15
D20V42, multiclass
      clus
vv     AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  T1A1                             0                               1
  T1B                              6                              28
  T1B1                            14                              55
  T1B2                             5                              25
  T2                               0                               6
  T2A                              4                               6
  T2A1                             3                               4
  T2A2                             1                               8
  T2B                             14                              22
  T3                               1                               1
  T3A                              0                               2
  T3B                              5                              12
  T4                               3                               5
  TIS                              0                               1
  TX                               1                              15
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 20(16P13.13) MUTATED         0        0         0         0        5
  AMP PEAK 20(16P13.13) WILD-TYPE       5        1         1         1       28
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 20(16P13.13) MUTATED          15         7        1         2
  AMP PEAK 20(16P13.13) WILD-TYPE        62        29        3         6
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 20(16P13.13) MUTATED            2          2        13         1
  AMP PEAK 20(16P13.13) WILD-TYPE          3          5        30         0
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 20(16P13.13) MUTATED            0         12         2         2
  AMP PEAK 20(16P13.13) WILD-TYPE          3         30         5        10
D20V44, multiclass
            clus
vv           AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  STAGE I                                0                               5
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               5                              28
  STAGE IB1                             15                              62
  STAGE IB2                              7                              29
  STAGE II                               1                               3
  STAGE IIA                              2                               6
  STAGE IIA1                             2                               3
  STAGE IIA2                             2                               5
  STAGE IIB                             13                              30
  STAGE III                              1                               0
  STAGE IIIA                             0                               3
  STAGE IIIB                            12                              30
  STAGE IVA                              2                               5
  STAGE IVB                              2                              10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(17Q12) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(17Q12) MUTATED    40  13
  AMP PEAK 21(17Q12) WILD-TYPE 173  52
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                          53                          225 
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                          13                           52 
$`AMP PEAK 21(17Q12) MUTATED`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MP 
       12.39        23.67        31.40        35.01        35.61         3.58 
TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-C5-A8XJ 
      100.14       154.32       147.35       155.77         2.73       146.86 
TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WF 
       20.81         1.12        58.88       117.99        22.98        16.18 
TCGA-DS-A7WH TCGA-EA-A3HR TCGA-EA-A5ZF TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD 
       17.52        30.90        14.96         0.13        16.08         0.03 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A40J TCGA-JW-A69B 
        2.24         0.10         6.94         8.32         1.35        28.37 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U3 TCGA-MA-AA43 TCGA-MU-A51Y 
       30.31         7.99        11.28         0.82        11.38        13.87 
TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73R TCGA-UC-A7PF TCGA-UC-A7PI 
        5.49        16.41        15.95        15.39        93.99        66.05 
TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A959 TCGA-VS-A9U5 
       40.50        18.05        19.96        16.64        45.34        44.94 
TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-VS-A9V5 
       19.69        14.53        18.84         4.34        16.24 

$`AMP PEAK 21(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-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91        40.93        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.45        83.05        78.35        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       15.48        20.35        17.19       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
       13.61        50.99        45.83         8.35        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       27.52        20.91        11.87        50.76        44.94        40.04 
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        39.55        12.36        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       13.91        15.02        14.99        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC 
        0.43         0.59         0.59         1.45         0.07         4.04 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36         1.18        47.77         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF 
        0.03        20.35         7.92        14.70        19.79        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        1.45         1.58         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41        10.82        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AW TCGA-LP-A4AX 
        8.28        18.15        21.11       195.85         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30        13.35        22.52        20.28        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        9.17         8.52        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84         2.96        15.58         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88         9.34        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL 
       11.67        12.16        10.03        37.78        26.43        59.51 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        36.13        11.51        57.93        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       31.27        36.26         4.73        24.39        39.78        50.86 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 
       15.68        50.63        48.07        50.14        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       25.74        21.30        22.72        46.92        40.96         1.71 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU 
       27.25        41.42        43.27        35.97        20.09        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
        3.42        18.25        67.20         5.16        14.04        14.89 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                        0.03                         0.03 
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                      155.77                       210.67 
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                       16.64                        20.35 
[1] "0.0 - 155.8 (16.6)" "0.0 - 210.7 (20.4)"
[1] "hr=" "1.1"
D21V2, continuous
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 21(17Q12) MUTATED    21  12   7   1
  AMP PEAK 21(17Q12) WILD-TYPE 113  56  14   7
D21V3, multiclass
    clus
vv   AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  T1                         21                          113
  T2                         12                           56
  T3                          7                           14
  T4                          1                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                              cls
clus                             0   1
  AMP PEAK 21(17Q12) MUTATED    18  10
  AMP PEAK 21(17Q12) WILD-TYPE 109  45
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     18   10
  AMP PEAK 21(17Q12) WILD-TYPE  109   45
   clus
vv  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  0                         18                          109
  1                         10                           45
[1] 2 2
[1] FALSE
D21V5, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   19  2
  AMP PEAK 21(17Q12) WILD-TYPE 88  8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     19    2
  AMP PEAK 21(17Q12) WILD-TYPE   88    8
   clus
vv  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  0                         19                           88
  1                          2                            8
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(17Q12) MUTATED               2                               39
  AMP PEAK 21(17Q12) WILD-TYPE             3                              202
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 21(17Q12) MUTATED                                               0
  AMP PEAK 21(17Q12) WILD-TYPE                                             6
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 21(17Q12) MUTATED                                     8
  AMP PEAK 21(17Q12) WILD-TYPE                                  14
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 21(17Q12) MUTATED                                           1
  AMP PEAK 21(17Q12) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 21(17Q12) MUTATED                                              4
  AMP PEAK 21(17Q12) WILD-TYPE                                           11
D21V6, multiclass
                                               clus
vv                                              AMP PEAK 21(17Q12) MUTATED
  ADENOSQUAMOUS                                                          2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      39
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           4
                                               clus
vv                                              AMP PEAK 21(17Q12) WILD-TYPE
  ADENOSQUAMOUS                                                            3
  CERVICAL SQUAMOUS CELL CARCINOMA                                       202
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(17Q12) MUTATED     4  50
  AMP PEAK 21(17Q12) WILD-TYPE  26 212
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED      4   50
  AMP PEAK 21(17Q12) WILD-TYPE   26  212
     clus
vv    AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  NO                           4                           26
  YES                         50                          212
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(17Q12) MUTATED                                  1     4
  AMP PEAK 21(17Q12) WILD-TYPE                                7    14
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(17Q12) MUTATED                           3
  AMP PEAK 21(17Q12) WILD-TYPE                        25
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 21(17Q12) MUTATED                                           0    38
  AMP PEAK 21(17Q12) WILD-TYPE                                         2   163
D21V10, multiclass
                                           clus
vv                                          AMP PEAK 21(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              4
  BLACK OR AFRICAN AMERICAN                                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             38
                                           clus
vv                                          AMP PEAK 21(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     7
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                              163
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                              cls
clus                             0   1
  AMP PEAK 21(17Q12) MUTATED     6  28
  AMP PEAK 21(17Q12) WILD-TYPE  17 133
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED      6   28
  AMP PEAK 21(17Q12) WILD-TYPE   17  133
                        clus
vv                       AMP PEAK 21(17Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                         28
                        clus
vv                       AMP PEAK 21(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          133
[1] 2 2
[1] FALSE
D21V12, continuous
D21V13, binary
                              cls
clus                             0   1
  AMP PEAK 21(17Q12) MUTATED    26   9
  AMP PEAK 21(17Q12) WILD-TYPE 108  32
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     26    9
  AMP PEAK 21(17Q12) WILD-TYPE  108   32
            clus
vv           AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  TUMOR FREE                         26                          108
  WITH TUMOR                          9                           32
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 21(17Q12) MUTATED       11      2       0      2       0
  AMP PEAK 21(17Q12) WILD-TYPE     42      3       1      9       7
                              vv
clus                           UNITED STATES VIETNAM
  AMP PEAK 21(17Q12) MUTATED              36       3
  AMP PEAK 21(17Q12) WILD-TYPE           165      11
D21V14, multiclass
               clus
vv              AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  BRAZIL                                11                           42
  CANADA                                 2                            3
  NIGERIA                                0                            1
  RUSSIA                                 2                            9
  UKRAINE                                0                            7
  UNITED STATES                         36                          165
  VIETNAM                                3                           11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            G1  G2  G3  G4  GX
  AMP PEAK 21(17Q12) MUTATED     1  19  29   0   4
  AMP PEAK 21(17Q12) WILD-TYPE  17 110  84   1  20
D21V15, multiclass
    clus
vv   AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  G1                          1                           17
  G2                         19                          110
  G3                         29                           84
  G4                          0                            1
  GX                          4                           20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V16, continuous
D21V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 21(17Q12) MUTATED                                             6
  AMP PEAK 21(17Q12) WILD-TYPE                                          31
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 21(17Q12) MUTATED                                        2
  AMP PEAK 21(17Q12) WILD-TYPE                                      7
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 21(17Q12) MUTATED                                                 1
  AMP PEAK 21(17Q12) WILD-TYPE                                               2
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 21(17Q12) MUTATED                7                  31
  AMP PEAK 21(17Q12) WILD-TYPE             55                 111
D21V18, multiclass
                                                 clus
vv                                                AMP PEAK 21(17Q12) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          1
  CURRENT SMOKER                                                           7
  LIFELONG NON-SMOKER                                                     31
                                                 clus
vv                                                AMP PEAK 21(17Q12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            55
  LIFELONG NON-SMOKER                                                      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"
D21V19, continuous
D21V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 21(17Q12) MUTATED             2       21             2        6
  AMP PEAK 21(17Q12) WILD-TYPE          17       81            10       19
D21V21, multiclass
               clus
vv              AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  COMBINATION                            2                           17
  EXTERNAL                              21                           81
  EXTERNAL BEAM                          2                           10
  INTERNAL                               6                           19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V22, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED    4  0
  AMP PEAK 21(17Q12) WILD-TYPE 21  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED      4    0
  AMP PEAK 21(17Q12) WILD-TYPE   21    3
                         clus
vv                        AMP PEAK 21(17Q12) MUTATED
  COMPLETED AS PLANNED                             4
  TREATMENT NOT COMPLETED                          0
                         clus
vv                        AMP PEAK 21(17Q12) WILD-TYPE
  COMPLETED AS PLANNED                              21
  TREATMENT NOT COMPLETED                            3
[1] 2 2
[1] FALSE
                              vv
clus                           DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 21(17Q12) MUTATED                    1                0
  AMP PEAK 21(17Q12) WILD-TYPE                  1                2
                              vv
clus                           PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 21(17Q12) MUTATED                    10             6
  AMP PEAK 21(17Q12) WILD-TYPE                  26            27
D21V23, multiclass
                     clus
vv                    AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  DISTANT RECURRENCE                           1                            1
  LOCAL RECURRENCE                             0                            2
  PRIMARY TUMOR FIELD                         10                           26
  REGIONAL SITE                                6                           27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V24, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   13  1
  AMP PEAK 21(17Q12) WILD-TYPE 43  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     13    1
  AMP PEAK 21(17Q12) WILD-TYPE   43    4
     clus
vv    AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  CGY                         13                           43
  GY                           1                            4
[1] 2 2
[1] FALSE
D21V25, continuous
D21V26, continuous
D21V27, continuous
D21V28, continuous
D21V29, continuous
D21V30, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 21(17Q12) MUTATED                                     0
  AMP PEAK 21(17Q12) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 21(17Q12) MUTATED                                     1
  AMP PEAK 21(17Q12) WILD-TYPE                                   6
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 21(17Q12) MUTATED                         5                       0
  AMP PEAK 21(17Q12) WILD-TYPE                      30                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 21(17Q12) MUTATED                         0
  AMP PEAK 21(17Q12) WILD-TYPE                       8
D21V31, multiclass
                                     clus
vv                                    AMP PEAK 21(17Q12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          1
  OTHER LOCATION, SPECIFY                                      5
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      0
                                     clus
vv                                    AMP PEAK 21(17Q12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            6
  OTHER LOCATION, SPECIFY                                       30
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 21(17Q12) MUTATED                                               0
  AMP PEAK 21(17Q12) WILD-TYPE                                             2
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 21(17Q12) MUTATED                                                5
  AMP PEAK 21(17Q12) WILD-TYPE                                             20
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 21(17Q12) MUTATED                                                                                  15
  AMP PEAK 21(17Q12) WILD-TYPE                                                                                66
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 21(17Q12) MUTATED                                                                                             22
  AMP PEAK 21(17Q12) WILD-TYPE                                                                                           98
D21V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 21(17Q12) 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)                                    15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         22
                                                                                              clus
vv                                                                                             AMP PEAK 21(17Q12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      66
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V33, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   11 14
  AMP PEAK 21(17Q12) WILD-TYPE 59 59
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     11   14
  AMP PEAK 21(17Q12) WILD-TYPE   59   59
         clus
vv        AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  ABSENT                          11                           59
  PRESENT                         14                           59
[1] 2 2
[1] FALSE
D21V34, continuous
D21V35, continuous
D21V36, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED    4 18
  AMP PEAK 21(17Q12) WILD-TYPE 44 98
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED      4   18
  AMP PEAK 21(17Q12) WILD-TYPE   44   98
                                          clus
vv                                         AMP PEAK 21(17Q12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         18
                                          clus
vv                                         AMP PEAK 21(17Q12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           98
[1] 2 2
[1] FALSE
D21V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 21(17Q12) MUTATED              2          11         16
  AMP PEAK 21(17Q12) WILD-TYPE           13          42         68
D21V38, multiclass
              clus
vv             AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  CURRENT USER                          2                           13
  FORMER USER                          11                           42
  NEVER USED                           16                           68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V39, continuous
D21V40, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   17  3
  AMP PEAK 21(17Q12) WILD-TYPE 75 14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     17    3
  AMP PEAK 21(17Q12) WILD-TYPE   75   14
         clus
vv        AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  ABSENT                          17                           75
  PRESENT                          3                           14
[1] 2 2
[1] FALSE
D21V41, continuous
                              vv
clus                           T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 21(17Q12) MUTATED      0   2   14    5  1   2    3    1   5  0   1
  AMP PEAK 21(17Q12) WILD-TYPE    1  32   55   25  5   8    4    8  31  2   1
                              vv
clus                           T3B T4 TIS TX
  AMP PEAK 21(17Q12) MUTATED     6  1   1  3
  AMP PEAK 21(17Q12) WILD-TYPE  11  7   0 13
D21V42, multiclass
      clus
vv     AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  T1A1                          0                            1
  T1B                           2                           32
  T1B1                         14                           55
  T1B2                          5                           25
  T2                            1                            5
  T2A                           2                            8
  T2A1                          3                            4
  T2A2                          1                            8
  T2B                           5                           31
  T3                            0                            2
  T3A                           1                            1
  T3B                           6                           11
  T4                            1                            7
  TIS                           1                            0
  TX                            3                           13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 21(17Q12) MUTATED         1        0         0         0        4
  AMP PEAK 21(17Q12) WILD-TYPE       4        1         1         1       29
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 21(17Q12) MUTATED          17         6        1         2
  AMP PEAK 21(17Q12) WILD-TYPE        60        30        3         6
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 21(17Q12) MUTATED            2          1         8         0
  AMP PEAK 21(17Q12) WILD-TYPE          3          6        35         1
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 21(17Q12) MUTATED            1          8         1         0
  AMP PEAK 21(17Q12) WILD-TYPE          2         34         6        12
D21V44, multiclass
            clus
vv           AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                            0                            1
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            4                           29
  STAGE IB1                          17                           60
  STAGE IB2                           6                           30
  STAGE II                            1                            3
  STAGE IIA                           2                            6
  STAGE IIA1                          2                            3
  STAGE IIA2                          1                            6
  STAGE IIB                           8                           35
  STAGE III                           0                            1
  STAGE IIIA                          1                            2
  STAGE IIIB                          8                           34
  STAGE IVA                           1                            6
  STAGE IVB                           0                           12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(17Q25.1) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(17Q25.1) MUTATED    55  15
  AMP PEAK 22(17Q25.1) WILD-TYPE 158  50
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            70                            208 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            15                             50 
$`AMP PEAK 22(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       154.32       134.33        20.35       147.35       155.77 
TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VK 
       13.61        45.83        23.51         1.12        58.88        36.76 
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A556 
       22.98        37.35        30.90        13.05        14.50        14.89 
TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R9 
       13.91        14.96         6.64        19.27         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-EX-A69M 
       16.08         0.03         2.24         0.10         6.94         8.32 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A4S6 
       31.36         1.45         1.58         1.35        10.82        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV 
      147.39       117.40        24.56        28.37        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y 
       11.28         0.89         0.30         9.17        11.38        13.87 
TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73Q TCGA-UC-A7PF TCGA-UC-A7PI 
        5.49        16.41        15.95         9.34        93.99        66.05 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A9U5 
       10.03        40.50        18.05        19.96        16.64        44.94 
TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9V0 
       21.30        19.69        14.53        18.84 

$`AMP PEAK 22(17Q25.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        57.04        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-A1ME TCGA-C5-A1MH 
       19.86        67.46        46.32        30.21        57.73        38.99 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91        40.93        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.45        83.05        78.35        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CL 
       18.02        17.85        20.42       210.67       101.82        15.48 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
       17.19       131.11        94.95         9.34         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35       146.86        99.91        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       11.87        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99       118.65        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
        8.28        39.55        12.36        31.53        31.36        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50        26.40        24.56        26.01        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        7.46        26.79        15.02        14.99        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PL 
        0.36        12.59        45.96        26.27         1.51         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         1.45         0.07         4.04         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 
       47.77         0.10         0.07         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        7.92        14.70        19.79        15.55         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        36.26         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.32         1.97         1.12         9.01        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH 
       20.78         9.44       137.16        66.81        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ 
       81.96        29.85        36.36        27.42         3.29        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       20.48        15.58         8.28        18.15        21.11       195.85 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
       12.49         0.82        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       19.56         8.52        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84         2.96        15.58         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 
       11.67        12.16        37.78        26.43        59.51        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       46.03        36.13        11.51        57.93        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       36.26         4.73        24.39        39.78        50.86        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 
       50.63        48.07        50.14        45.34        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM 
       25.74        22.72        46.92        40.96         1.71        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV 
       41.42        43.27        35.97        20.09        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       18.25        67.20         5.16        14.04        14.89         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                        155.77                         210.67 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                        16.525                         20.450 
[1] "0.0 - 155.8 (16.5)" "0.0 - 210.7 (20.5)"
[1] "hr=" "1"  
D22V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 22(17Q25.1) MUTATED    30  18   8   0
  AMP PEAK 22(17Q25.1) WILD-TYPE 104  50  13   8
D22V3, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  T1                           30                            104
  T2                           18                             50
  T3                            8                             13
  T4                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED    27  17
  AMP PEAK 22(17Q25.1) WILD-TYPE 100  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     27   17
  AMP PEAK 22(17Q25.1) WILD-TYPE  100   38
   clus
vv  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  0                           27                            100
  1                           17                             38
[1] 2 2
[1] FALSE
D22V5, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   25  4
  AMP PEAK 22(17Q25.1) WILD-TYPE 82  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     25    4
  AMP PEAK 22(17Q25.1) WILD-TYPE   82    6
   clus
vv  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  0                           25                             82
  1                            4                              6
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(17Q25.1) MUTATED               2                               59
  AMP PEAK 22(17Q25.1) WILD-TYPE             3                              182
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 22(17Q25.1) MUTATED                                               3
  AMP PEAK 22(17Q25.1) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 22(17Q25.1) MUTATED                                     6
  AMP PEAK 22(17Q25.1) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 22(17Q25.1) MUTATED                                           2
  AMP PEAK 22(17Q25.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 22(17Q25.1) MUTATED                                              1
  AMP PEAK 22(17Q25.1) WILD-TYPE                                           14
D22V6, multiclass
                                               clus
vv                                              AMP PEAK 22(17Q25.1) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        59
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 22(17Q25.1) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         182
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED     5  68
  AMP PEAK 22(17Q25.1) WILD-TYPE  25 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      5   68
  AMP PEAK 22(17Q25.1) WILD-TYPE   25  194
     clus
vv    AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  NO                             5                             25
  YES                           68                            194
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(17Q25.1) MUTATED                                  2     6
  AMP PEAK 22(17Q25.1) WILD-TYPE                                6    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(17Q25.1) MUTATED                           4
  AMP PEAK 22(17Q25.1) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 22(17Q25.1) MUTATED                                           0
  AMP PEAK 22(17Q25.1) WILD-TYPE                                         2
                                vv
clus                             WHITE
  AMP PEAK 22(17Q25.1) MUTATED      54
  AMP PEAK 22(17Q25.1) WILD-TYPE   147
D22V10, multiclass
                                           clus
vv                                          AMP PEAK 22(17Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               54
                                           clus
vv                                          AMP PEAK 22(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED     8  41
  AMP PEAK 22(17Q25.1) WILD-TYPE  15 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      8   41
  AMP PEAK 22(17Q25.1) WILD-TYPE   15  120
                        clus
vv                       AMP PEAK 22(17Q25.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       AMP PEAK 22(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            120
[1] 2 2
[1] FALSE
D22V12, continuous
D22V13, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED    33  10
  AMP PEAK 22(17Q25.1) WILD-TYPE 101  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     33   10
  AMP PEAK 22(17Q25.1) WILD-TYPE  101   31
            clus
vv           AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  TUMOR FREE                           33                            101
  WITH TUMOR                           10                             31
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 22(17Q25.1) MUTATED       10      2       0      3       1
  AMP PEAK 22(17Q25.1) WILD-TYPE     43      3       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 22(17Q25.1) MUTATED              52       5
  AMP PEAK 22(17Q25.1) WILD-TYPE           149       9
D22V14, multiclass
               clus
vv              AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  BRAZIL                                  10                             43
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   3                              8
  UKRAINE                                  1                              6
  UNITED STATES                           52                            149
  VIETNAM                                  5                              9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 22(17Q25.1) MUTATED     2  26  38   0   5
  AMP PEAK 22(17Q25.1) WILD-TYPE  16 103  75   1  19
D22V15, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  G1                            2                             16
  G2                           26                            103
  G3                           38                             75
  G4                            0                              1
  GX                            5                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V16, continuous
D22V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 22(17Q25.1) MUTATED                                            11
  AMP PEAK 22(17Q25.1) WILD-TYPE                                          26
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 22(17Q25.1) MUTATED                                        3
  AMP PEAK 22(17Q25.1) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 22(17Q25.1) MUTATED                                                 2
  AMP PEAK 22(17Q25.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 22(17Q25.1) MUTATED               13                  33
  AMP PEAK 22(17Q25.1) WILD-TYPE             49                 109
D22V18, multiclass
                                                 clus
vv                                                AMP PEAK 22(17Q25.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            13
  LIFELONG NON-SMOKER                                                       33
                                                 clus
vv                                                AMP PEAK 22(17Q25.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              49
  LIFELONG NON-SMOKER                                                        109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V19, continuous
D22V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 22(17Q25.1) MUTATED             3       28             3        5
  AMP PEAK 22(17Q25.1) WILD-TYPE          16       74             9       20
D22V21, multiclass
               clus
vv              AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  COMBINATION                              3                             16
  EXTERNAL                                28                             74
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V22, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED    5  0
  AMP PEAK 22(17Q25.1) WILD-TYPE 20  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      5    0
  AMP PEAK 22(17Q25.1) WILD-TYPE   20    3
                         clus
vv                        AMP PEAK 22(17Q25.1) MUTATED
  COMPLETED AS PLANNED                               5
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        AMP PEAK 22(17Q25.1) WILD-TYPE
  COMPLETED AS PLANNED                                20
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 22(17Q25.1) MUTATED                    0                0
  AMP PEAK 22(17Q25.1) WILD-TYPE                  2                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 22(17Q25.1) MUTATED                    15             5
  AMP PEAK 22(17Q25.1) WILD-TYPE                  21            28
D22V23, multiclass
                     clus
vv                    AMP PEAK 22(17Q25.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                           15
  REGIONAL SITE                                  5
                     clus
vv                    AMP PEAK 22(17Q25.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             21
  REGIONAL SITE                                   28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V24, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   15  1
  AMP PEAK 22(17Q25.1) WILD-TYPE 41  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     15    1
  AMP PEAK 22(17Q25.1) WILD-TYPE   41    4
     clus
vv    AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  CGY                           15                             41
  GY                             1                              4
[1] 2 2
[1] FALSE
D22V25, continuous
D22V26, continuous
D22V27, continuous
D22V28, continuous
D22V29, continuous
D22V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 22(17Q25.1) MUTATED                                     0
  AMP PEAK 22(17Q25.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 22(17Q25.1) MUTATED                                     1
  AMP PEAK 22(17Q25.1) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 22(17Q25.1) MUTATED                         6
  AMP PEAK 22(17Q25.1) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 22(17Q25.1) MUTATED                         0
  AMP PEAK 22(17Q25.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 22(17Q25.1) MUTATED                         1
  AMP PEAK 22(17Q25.1) WILD-TYPE                       7
D22V31, multiclass
                                     clus
vv                                    AMP PEAK 22(17Q25.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        6
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 22(17Q25.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 22(17Q25.1) MUTATED                                               0
  AMP PEAK 22(17Q25.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 22(17Q25.1) MUTATED                                                6
  AMP PEAK 22(17Q25.1) WILD-TYPE                                             19
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 22(17Q25.1) MUTATED                                                                                  18
  AMP PEAK 22(17Q25.1) WILD-TYPE                                                                                63
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 22(17Q25.1) MUTATED                                                                                             32
  AMP PEAK 22(17Q25.1) WILD-TYPE                                                                                           88
D22V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 22(17Q25.1) 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)                                      18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           32
                                                                                              clus
vv                                                                                             AMP PEAK 22(17Q25.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        63
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V33, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   12 22
  AMP PEAK 22(17Q25.1) WILD-TYPE 58 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     12   22
  AMP PEAK 22(17Q25.1) WILD-TYPE   58   51
         clus
vv        AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  ABSENT                            12                             58
  PRESENT                           22                             51
[1] 2 2
[1] FALSE
D22V34, continuous
D22V35, continuous
D22V36, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   14 22
  AMP PEAK 22(17Q25.1) WILD-TYPE 34 94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     14   22
  AMP PEAK 22(17Q25.1) WILD-TYPE   34   94
                                          clus
vv                                         AMP PEAK 22(17Q25.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           22
                                          clus
vv                                         AMP PEAK 22(17Q25.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             94
[1] 2 2
[1] FALSE
D22V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 22(17Q25.1) MUTATED              3          17         18
  AMP PEAK 22(17Q25.1) WILD-TYPE           12          36         66
D22V38, multiclass
              clus
vv             AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                            17                             36
  NEVER USED                             18                             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V39, continuous
D22V40, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   23  5
  AMP PEAK 22(17Q25.1) WILD-TYPE 69 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     23    5
  AMP PEAK 22(17Q25.1) WILD-TYPE   69   12
         clus
vv        AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  ABSENT                            23                             69
  PRESENT                            5                             12
[1] 2 2
[1] FALSE
D22V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 22(17Q25.1) MUTATED      0   3   19    8  2   3    4    1   8  0   1
  AMP PEAK 22(17Q25.1) WILD-TYPE    1  31   50   22  4   7    3    8  28  2   1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 22(17Q25.1) MUTATED     7  0   1  3
  AMP PEAK 22(17Q25.1) WILD-TYPE  10  8   0 13
D22V42, multiclass
      clus
vv     AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  T1A1                            0                              1
  T1B                             3                             31
  T1B1                           19                             50
  T1B2                            8                             22
  T2                              2                              4
  T2A                             3                              7
  T2A1                            4                              3
  T2A2                            1                              8
  T2B                             8                             28
  T3                              0                              2
  T3A                             1                              1
  T3B                             7                             10
  T4                              0                              8
  TIS                             1                              0
  TX                              3                             13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 22(17Q25.1) MUTATED         1        1         0         0        3
  AMP PEAK 22(17Q25.1) WILD-TYPE       4        0         1         1       30
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 22(17Q25.1) MUTATED          20         9        2         2
  AMP PEAK 22(17Q25.1) WILD-TYPE        57        27        2         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 22(17Q25.1) MUTATED            3          1        12         0
  AMP PEAK 22(17Q25.1) WILD-TYPE          2          6        31         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 22(17Q25.1) MUTATED            1         14         1         1
  AMP PEAK 22(17Q25.1) WILD-TYPE          2         28         6        11
D22V44, multiclass
            clus
vv           AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              3                             30
  STAGE IB1                            20                             57
  STAGE IB2                             9                             27
  STAGE II                              2                              2
  STAGE IIA                             2                              6
  STAGE IIA1                            3                              2
  STAGE IIA2                            1                              6
  STAGE IIB                            12                             31
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                           14                             28
  STAGE IVA                             1                              6
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(19P13.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(19P13.3) MUTATED    31   5
  AMP PEAK 23(19P13.3) WILD-TYPE 182  60
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                            36                            242 
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                             5                             60 
$`AMP PEAK 23(19P13.3) MUTATED`
TCGA-C5-A1BE TCGA-C5-A1BK TCGA-C5-A1MH TCGA-C5-A7CG TCGA-C5-A7CH TCGA-DG-A2KJ 
       68.84       177.04        38.99       210.67       154.32        58.88 
TCGA-DG-A2KL TCGA-DS-A0VL TCGA-EK-A2IP TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-FU-A3NI 
       44.94         2.66         6.64         0.59         0.13         1.45 
TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A852 
        1.35        20.78       117.40        36.36        24.56         8.28 
TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BE TCGA-Q1-A5R2 
      195.85        11.28         0.30        13.35        35.05        16.41 
TCGA-Q1-A73R TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A9U5 
       15.39        93.99        18.05        15.68        50.63        44.94 
TCGA-VS-A9UD TCGA-VS-A9UU TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-WL-A834 TCGA-ZJ-AAXA 
       19.69        14.53        18.84        14.04        26.01         1.41 

$`AMP PEAK 23(19P13.3) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF 
       12.39        49.48        57.04        23.67        11.44        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       20.42       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19       155.77       131.11        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        11.87         1.12 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       50.76        40.04        87.75        58.88        36.76       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        12.36        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI 
        0.36        12.59        45.96        26.27         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.43         0.59         1.45        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.03         0.36         1.18        47.77         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         8.32        15.55         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        31.36        36.26         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
        9.01        25.41        10.82        21.67        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      147.39       137.16        66.81        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       29.85        27.42         3.29        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW 
       28.37        18.15        21.11        30.31         7.99         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
       12.49         0.82        22.52        20.28        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        9.17         8.52        11.38        13.87        34.62         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       54.81        20.84         5.49         2.96        15.58        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI 
       19.36        19.59         3.88        11.67        12.16        66.05 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        40.50        37.78        26.43        19.96        59.51 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        36.13        11.51        57.93        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        36.26        16.64         4.73        24.39        39.78 
TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 
       50.86        48.07        50.14        45.34        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       25.74        21.30        22.72        46.92        40.96         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        41.42        43.27        35.97        20.09 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V4 
        3.42        18.25        67.20         5.16        14.89         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       16.24        15.42        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                        210.67                         173.29 
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                        19.265                         19.910 
[1] "0.1 - 210.7 (19.3)" "0.0 - 173.3 (19.9)"
[1] "hr=" "2.2"
D23V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 23(19P13.3) MUTATED    16  11   5   1
  AMP PEAK 23(19P13.3) WILD-TYPE 118  57  16   7
D23V3, multiclass
    clus
vv   AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  T1                           16                            118
  T2                           11                             57
  T3                            5                             16
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.3) MUTATED    15  10
  AMP PEAK 23(19P13.3) WILD-TYPE 112  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED     15   10
  AMP PEAK 23(19P13.3) WILD-TYPE  112   45
   clus
vv  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  0                           15                            112
  1                           10                             45
[1] 2 2
[1] FALSE
D23V5, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED   12  0
  AMP PEAK 23(19P13.3) WILD-TYPE 95 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED     12    0
  AMP PEAK 23(19P13.3) WILD-TYPE   95   10
   clus
vv  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  0                           12                             95
  1                            0                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(19P13.3) MUTATED               0                               33
  AMP PEAK 23(19P13.3) WILD-TYPE             5                              208
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 23(19P13.3) MUTATED                                               1
  AMP PEAK 23(19P13.3) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 23(19P13.3) MUTATED                                     3
  AMP PEAK 23(19P13.3) WILD-TYPE                                  19
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 23(19P13.3) MUTATED                                           0
  AMP PEAK 23(19P13.3) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 23(19P13.3) MUTATED                                              1
  AMP PEAK 23(19P13.3) WILD-TYPE                                           14
D23V6, multiclass
                                               clus
vv                                              AMP PEAK 23(19P13.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        33
  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                                              AMP PEAK 23(19P13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         208
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.3) MUTATED     3  35
  AMP PEAK 23(19P13.3) WILD-TYPE  27 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      3   35
  AMP PEAK 23(19P13.3) WILD-TYPE   27  227
     clus
vv    AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  NO                             3                             27
  YES                           35                            227
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(19P13.3) MUTATED                                  1     3
  AMP PEAK 23(19P13.3) WILD-TYPE                                7    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(19P13.3) MUTATED                           3
  AMP PEAK 23(19P13.3) WILD-TYPE                        25
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 23(19P13.3) MUTATED                                           0
  AMP PEAK 23(19P13.3) WILD-TYPE                                         2
                                vv
clus                             WHITE
  AMP PEAK 23(19P13.3) MUTATED      22
  AMP PEAK 23(19P13.3) WILD-TYPE   179
D23V10, multiclass
                                           clus
vv                                          AMP PEAK 23(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               22
                                           clus
vv                                          AMP PEAK 23(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.3) MUTATED     2  16
  AMP PEAK 23(19P13.3) WILD-TYPE  21 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      2   16
  AMP PEAK 23(19P13.3) WILD-TYPE   21  145
                        clus
vv                       AMP PEAK 23(19P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       AMP PEAK 23(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            145
[1] 2 2
[1] FALSE
D23V12, continuous
D23V13, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.3) MUTATED    21   5
  AMP PEAK 23(19P13.3) WILD-TYPE 113  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED     21    5
  AMP PEAK 23(19P13.3) WILD-TYPE  113   36
            clus
vv           AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  TUMOR FREE                           21                            113
  WITH TUMOR                            5                             36
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 23(19P13.3) MUTATED        8      2       0      0       0
  AMP PEAK 23(19P13.3) WILD-TYPE     45      3       1     11       7
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 23(19P13.3) MUTATED              25       3
  AMP PEAK 23(19P13.3) WILD-TYPE           176      11
D23V14, multiclass
               clus
vv              AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  BRAZIL                                   8                             45
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   0                             11
  UKRAINE                                  0                              7
  UNITED STATES                           25                            176
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 23(19P13.3) MUTATED     2  15  18   0   3
  AMP PEAK 23(19P13.3) WILD-TYPE  16 114  95   1  21
D23V15, multiclass
    clus
vv   AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  G1                            2                             16
  G2                           15                            114
  G3                           18                             95
  G4                            0                              1
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V16, continuous
D23V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 23(19P13.3) MUTATED                                             4
  AMP PEAK 23(19P13.3) WILD-TYPE                                          33
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 23(19P13.3) MUTATED                                        3
  AMP PEAK 23(19P13.3) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 23(19P13.3) MUTATED                                                 0
  AMP PEAK 23(19P13.3) WILD-TYPE                                               3
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 23(19P13.3) MUTATED                5                  20
  AMP PEAK 23(19P13.3) WILD-TYPE             57                 122
D23V18, multiclass
                                                 clus
vv                                                AMP PEAK 23(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                                                             5
  LIFELONG NON-SMOKER                                                       20
                                                 clus
vv                                                AMP PEAK 23(19P13.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              3
  CURRENT SMOKER                                                              57
  LIFELONG NON-SMOKER                                                        122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V19, continuous
D23V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 23(19P13.3) MUTATED             2       16             1        1
  AMP PEAK 23(19P13.3) WILD-TYPE          17       86            11       24
D23V21, multiclass
               clus
vv              AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  COMBINATION                              2                             17
  EXTERNAL                                16                             86
  EXTERNAL BEAM                            1                             11
  INTERNAL                                 1                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V22, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED    2  0
  AMP PEAK 23(19P13.3) WILD-TYPE 23  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      2    0
  AMP PEAK 23(19P13.3) WILD-TYPE   23    3
                         clus
vv                        AMP PEAK 23(19P13.3) MUTATED
  COMPLETED AS PLANNED                               2
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        AMP PEAK 23(19P13.3) WILD-TYPE
  COMPLETED AS PLANNED                                23
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 23(19P13.3) MUTATED                    0                0
  AMP PEAK 23(19P13.3) WILD-TYPE                  2                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 23(19P13.3) MUTATED                     7             2
  AMP PEAK 23(19P13.3) WILD-TYPE                  29            31
D23V23, multiclass
                     clus
vv                    AMP PEAK 23(19P13.3) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            7
  REGIONAL SITE                                  2
                     clus
vv                    AMP PEAK 23(19P13.3) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             29
  REGIONAL SITE                                   31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V24, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED    8  0
  AMP PEAK 23(19P13.3) WILD-TYPE 48  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      8    0
  AMP PEAK 23(19P13.3) WILD-TYPE   48    5
     clus
vv    AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  CGY                            8                             48
  GY                             0                              5
[1] 2 2
[1] FALSE
D23V25, continuous
D23V26, continuous
D23V27, continuous
D23V28, continuous
D23V29, continuous
D23V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 23(19P13.3) MUTATED                                     0
  AMP PEAK 23(19P13.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 23(19P13.3) MUTATED                                     1
  AMP PEAK 23(19P13.3) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 23(19P13.3) MUTATED                         5
  AMP PEAK 23(19P13.3) WILD-TYPE                      30
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 23(19P13.3) MUTATED                         0
  AMP PEAK 23(19P13.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 23(19P13.3) MUTATED                         1
  AMP PEAK 23(19P13.3) WILD-TYPE                       7
D23V31, multiclass
                                     clus
vv                                    AMP PEAK 23(19P13.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        5
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 23(19P13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         30
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 23(19P13.3) MUTATED                                               0
  AMP PEAK 23(19P13.3) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 23(19P13.3) MUTATED                                                2
  AMP PEAK 23(19P13.3) WILD-TYPE                                             23
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 23(19P13.3) MUTATED                                                                                  13
  AMP PEAK 23(19P13.3) WILD-TYPE                                                                                68
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 23(19P13.3) MUTATED                                                                                             15
  AMP PEAK 23(19P13.3) WILD-TYPE                                                                                          105
D23V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 23(19P13.3) 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)                                      13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           15
                                                                                              clus
vv                                                                                             AMP PEAK 23(19P13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V33, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED    4 11
  AMP PEAK 23(19P13.3) WILD-TYPE 66 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      4   11
  AMP PEAK 23(19P13.3) WILD-TYPE   66   62
         clus
vv        AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  ABSENT                             4                             66
  PRESENT                           11                             62
[1] 2 2
[1] FALSE
D23V34, continuous
D23V35, continuous
D23V36, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.3) MUTATED    10  10
  AMP PEAK 23(19P13.3) WILD-TYPE  38 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED     10   10
  AMP PEAK 23(19P13.3) WILD-TYPE   38  106
                                          clus
vv                                         AMP PEAK 23(19P13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           10
                                          clus
vv                                         AMP PEAK 23(19P13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            106
[1] 2 2
[1] FALSE
D23V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 23(19P13.3) MUTATED              2           3         13
  AMP PEAK 23(19P13.3) WILD-TYPE           13          50         71
D23V38, multiclass
              clus
vv             AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                             3                             50
  NEVER USED                             13                             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V39, continuous
D23V40, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED   10  2
  AMP PEAK 23(19P13.3) WILD-TYPE 82 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED     10    2
  AMP PEAK 23(19P13.3) WILD-TYPE   82   15
         clus
vv        AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  ABSENT                            10                             82
  PRESENT                            2                             15
[1] 2 2
[1] FALSE
D23V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 23(19P13.3) MUTATED      0   7    9    0  2   2    1    0   6  1   1
  AMP PEAK 23(19P13.3) WILD-TYPE    1  27   60   30  4   8    6    9  30  1   1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 23(19P13.3) MUTATED     3  1   0  2
  AMP PEAK 23(19P13.3) WILD-TYPE  14  7   1 14
D23V42, multiclass
      clus
vv     AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  T1A1                            0                              1
  T1B                             7                             27
  T1B1                            9                             60
  T1B2                            0                             30
  T2                              2                              4
  T2A                             2                              8
  T2A1                            1                              6
  T2A2                            0                              9
  T2B                             6                             30
  T3                              1                              1
  T3A                             1                              1
  T3B                             3                             14
  T4                              1                              7
  TIS                             0                              1
  TX                              2                             14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 23(19P13.3) MUTATED         1        0         0         0        4
  AMP PEAK 23(19P13.3) WILD-TYPE       4        1         1         1       29
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 23(19P13.3) MUTATED           9         1        1         1
  AMP PEAK 23(19P13.3) WILD-TYPE        68        35        3         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 23(19P13.3) MUTATED            0          1         8         1
  AMP PEAK 23(19P13.3) WILD-TYPE          5          6        35         0
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 23(19P13.3) MUTATED            1          7         1         0
  AMP PEAK 23(19P13.3) WILD-TYPE          2         35         6        12
D23V44, multiclass
            clus
vv           AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              4                             29
  STAGE IB1                             9                             68
  STAGE IB2                             1                             35
  STAGE II                              1                              3
  STAGE IIA                             1                              7
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             8                             35
  STAGE III                             1                              0
  STAGE IIIA                            1                              2
  STAGE IIIB                            7                             35
  STAGE IVA                             1                              6
  STAGE IVB                             0                             12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(19P13.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(19P13.2) MUTATED    35   5
  AMP PEAK 24(19P13.2) WILD-TYPE 178  60
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                            40                            238 
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                             5                             60 
$`AMP PEAK 24(19P13.2) MUTATED`
TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A2LY TCGA-C5-A7CG 
       18.74       177.04        53.16        38.99        78.35       210.67 
TCGA-C5-A7CH TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VL 
      154.32        13.61        50.99        58.88        44.94         2.66 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A5O9 TCGA-EA-A97N TCGA-EK-A2PM TCGA-EK-A2RN 
       22.98        16.83        13.91         0.36         0.59         0.10 
TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LA TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JX-A3Q0 
        1.35        20.78       137.16        36.36        24.56       195.85 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BE TCGA-MY-A913 
       11.28        12.49         0.30        13.35        35.05         5.49 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       18.05        32.15        46.03        50.86        15.68        50.63 
TCGA-VS-A9U5 TCGA-VS-A9UU TCGA-WL-A834 TCGA-ZJ-AAXA 
       44.94        14.53        26.01         1.41 

$`AMP PEAK 24(19P13.2) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
       33.24        52.01        18.02        17.85        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI 
      131.11        94.95         9.34         2.73        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
      146.86        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       11.87         1.12        50.76        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       36.76       117.99       118.65        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        12.36        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       15.02        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
       45.96        26.27         6.64         1.51        19.27         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO 
        0.03         0.36         1.18        47.77         2.24         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
        9.01        25.41        10.82        21.67        14.93         9.44 
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-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       29.85        27.42         3.29        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV 
       28.37         8.28        18.15        21.11        30.31         7.99 
TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.89         0.82        22.52        20.28        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        9.17         8.52        11.38        13.87        34.62         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       54.81        20.84         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        66.05        10.03        40.50        37.78        26.43 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       19.96        59.51        36.13        11.51        57.93        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        36.26        16.64         4.73        24.39        39.78 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       48.07        50.14        45.34        43.40        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       21.30        22.72        19.69        46.92        40.96         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        41.42        43.27        35.97        20.09 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        14.04 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       14.89         4.34        16.24        15.42        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         0.16         3.91 

  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                        210.67                         173.29 
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                         23.77                          19.64 
[1] "0.1 - 210.7 (23.8)" "0.0 - 173.3 (19.6)"
[1] "hr=" "2.6"
D24V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 24(19P13.2) MUTATED    18  11   5   1
  AMP PEAK 24(19P13.2) WILD-TYPE 116  57  16   7
D24V3, multiclass
    clus
vv   AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  T1                           18                            116
  T2                           11                             57
  T3                            5                             16
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                                cls
clus                               0   1
  AMP PEAK 24(19P13.2) MUTATED    23   8
  AMP PEAK 24(19P13.2) WILD-TYPE 104  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     23    8
  AMP PEAK 24(19P13.2) WILD-TYPE  104   47
   clus
vv  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  0                           23                            104
  1                            8                             47
[1] 2 2
[1] FALSE
D24V5, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED   17  1
  AMP PEAK 24(19P13.2) WILD-TYPE 90  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     17    1
  AMP PEAK 24(19P13.2) WILD-TYPE   90    9
   clus
vv  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  0                           17                             90
  1                            1                              9
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(19P13.2) MUTATED               0                               37
  AMP PEAK 24(19P13.2) WILD-TYPE             5                              204
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 24(19P13.2) MUTATED                                               1
  AMP PEAK 24(19P13.2) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 24(19P13.2) MUTATED                                     2
  AMP PEAK 24(19P13.2) WILD-TYPE                                  20
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 24(19P13.2) MUTATED                                           1
  AMP PEAK 24(19P13.2) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 24(19P13.2) MUTATED                                              1
  AMP PEAK 24(19P13.2) WILD-TYPE                                           14
D24V6, multiclass
                                               clus
vv                                              AMP PEAK 24(19P13.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 24(19P13.2) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         204
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(19P13.2) MUTATED     6  36
  AMP PEAK 24(19P13.2) WILD-TYPE  24 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      6   36
  AMP PEAK 24(19P13.2) WILD-TYPE   24  226
     clus
vv    AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  NO                             6                             24
  YES                           36                            226
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(19P13.2) MUTATED                                  1     4
  AMP PEAK 24(19P13.2) WILD-TYPE                                7    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(19P13.2) MUTATED                           5
  AMP PEAK 24(19P13.2) WILD-TYPE                        23
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 24(19P13.2) MUTATED                                           0
  AMP PEAK 24(19P13.2) WILD-TYPE                                         2
                                vv
clus                             WHITE
  AMP PEAK 24(19P13.2) MUTATED      24
  AMP PEAK 24(19P13.2) WILD-TYPE   177
D24V10, multiclass
                                           clus
vv                                          AMP PEAK 24(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               24
                                           clus
vv                                          AMP PEAK 24(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                                cls
clus                               0   1
  AMP PEAK 24(19P13.2) MUTATED     2  21
  AMP PEAK 24(19P13.2) WILD-TYPE  21 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      2   21
  AMP PEAK 24(19P13.2) WILD-TYPE   21  140
                        clus
vv                       AMP PEAK 24(19P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       AMP PEAK 24(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            140
[1] 2 2
[1] FALSE
D24V12, continuous
D24V13, binary
                                cls
clus                               0   1
  AMP PEAK 24(19P13.2) MUTATED    23   3
  AMP PEAK 24(19P13.2) WILD-TYPE 111  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     23    3
  AMP PEAK 24(19P13.2) WILD-TYPE  111   38
            clus
vv           AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  TUMOR FREE                           23                            111
  WITH TUMOR                            3                             38
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 24(19P13.2) MUTATED        8      2       0      0       2
  AMP PEAK 24(19P13.2) WILD-TYPE     45      3       1     11       5
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 24(19P13.2) MUTATED              26       4
  AMP PEAK 24(19P13.2) WILD-TYPE           175      10
D24V14, multiclass
               clus
vv              AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  BRAZIL                                   8                             45
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   0                             11
  UKRAINE                                  2                              5
  UNITED STATES                           26                            175
  VIETNAM                                  4                             10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 24(19P13.2) MUTATED     3  19  18   0   2
  AMP PEAK 24(19P13.2) WILD-TYPE  15 110  95   1  22
D24V15, multiclass
    clus
vv   AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  G1                            3                             15
  G2                           19                            110
  G3                           18                             95
  G4                            0                              1
  GX                            2                             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V16, continuous
D24V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 24(19P13.2) MUTATED                                             4
  AMP PEAK 24(19P13.2) WILD-TYPE                                          33
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 24(19P13.2) MUTATED                                        3
  AMP PEAK 24(19P13.2) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 24(19P13.2) MUTATED                                                 1
  AMP PEAK 24(19P13.2) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 24(19P13.2) MUTATED                6                  22
  AMP PEAK 24(19P13.2) WILD-TYPE             56                 120
D24V18, multiclass
                                                 clus
vv                                                AMP PEAK 24(19P13.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             6
  LIFELONG NON-SMOKER                                                       22
                                                 clus
vv                                                AMP PEAK 24(19P13.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              56
  LIFELONG NON-SMOKER                                                        120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V19, continuous
D24V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 24(19P13.2) MUTATED             4       18             2        2
  AMP PEAK 24(19P13.2) WILD-TYPE          15       84            10       23
D24V21, multiclass
               clus
vv              AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                18                             84
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 2                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V22, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED    5  0
  AMP PEAK 24(19P13.2) WILD-TYPE 20  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      5    0
  AMP PEAK 24(19P13.2) WILD-TYPE   20    3
                         clus
vv                        AMP PEAK 24(19P13.2) MUTATED
  COMPLETED AS PLANNED                               5
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        AMP PEAK 24(19P13.2) WILD-TYPE
  COMPLETED AS PLANNED                                20
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 24(19P13.2) MUTATED                    1                0
  AMP PEAK 24(19P13.2) WILD-TYPE                  1                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 24(19P13.2) MUTATED                     8             3
  AMP PEAK 24(19P13.2) WILD-TYPE                  28            30
D24V23, multiclass
                     clus
vv                    AMP PEAK 24(19P13.2) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            8
  REGIONAL SITE                                  3
                     clus
vv                    AMP PEAK 24(19P13.2) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             28
  REGIONAL SITE                                   30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V24, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED    8  1
  AMP PEAK 24(19P13.2) WILD-TYPE 48  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      8    1
  AMP PEAK 24(19P13.2) WILD-TYPE   48    4
     clus
vv    AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  CGY                            8                             48
  GY                             1                              4
[1] 2 2
[1] FALSE
D24V25, continuous
D24V26, continuous
D24V27, continuous
D24V28, continuous
D24V29, continuous
D24V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 24(19P13.2) MUTATED                                     0
  AMP PEAK 24(19P13.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 24(19P13.2) MUTATED                                     1
  AMP PEAK 24(19P13.2) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 24(19P13.2) MUTATED                         7
  AMP PEAK 24(19P13.2) WILD-TYPE                      28
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 24(19P13.2) MUTATED                         0
  AMP PEAK 24(19P13.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 24(19P13.2) MUTATED                         1
  AMP PEAK 24(19P13.2) WILD-TYPE                       7
D24V31, multiclass
                                     clus
vv                                    AMP PEAK 24(19P13.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        7
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 24(19P13.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         28
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 24(19P13.2) MUTATED                                               0
  AMP PEAK 24(19P13.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 24(19P13.2) MUTATED                                                2
  AMP PEAK 24(19P13.2) WILD-TYPE                                             23
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 24(19P13.2) MUTATED                                                                                  15
  AMP PEAK 24(19P13.2) WILD-TYPE                                                                                66
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 24(19P13.2) MUTATED                                                                                             16
  AMP PEAK 24(19P13.2) WILD-TYPE                                                                                          104
D24V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 24(19P13.2) 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)                                      15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           16
                                                                                              clus
vv                                                                                             AMP PEAK 24(19P13.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        66
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V33, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED    9 11
  AMP PEAK 24(19P13.2) WILD-TYPE 61 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      9   11
  AMP PEAK 24(19P13.2) WILD-TYPE   61   62
         clus
vv        AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  ABSENT                             9                             61
  PRESENT                           11                             62
[1] 2 2
[1] FALSE
D24V34, continuous
D24V35, continuous
D24V36, binary
                                cls
clus                               0   1
  AMP PEAK 24(19P13.2) MUTATED    13  10
  AMP PEAK 24(19P13.2) WILD-TYPE  35 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     13   10
  AMP PEAK 24(19P13.2) WILD-TYPE   35  106
                                          clus
vv                                         AMP PEAK 24(19P13.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           10
                                          clus
vv                                         AMP PEAK 24(19P13.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            106
[1] 2 2
[1] FALSE
D24V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 24(19P13.2) MUTATED              1           6         14
  AMP PEAK 24(19P13.2) WILD-TYPE           14          47         70
D24V38, multiclass
              clus
vv             AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  CURRENT USER                            1                             14
  FORMER USER                             6                             47
  NEVER USED                             14                             70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V39, continuous
D24V40, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED   14  0
  AMP PEAK 24(19P13.2) WILD-TYPE 78 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     14    0
  AMP PEAK 24(19P13.2) WILD-TYPE   78   17
         clus
vv        AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  ABSENT                            14                             78
  PRESENT                            0                             17
[1] 2 2
[1] FALSE
D24V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 24(19P13.2) MUTATED      0   7    8    3  2   2    1    0   6  1   0
  AMP PEAK 24(19P13.2) WILD-TYPE    1  27   61   27  4   8    6    9  30  1   2
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 24(19P13.2) MUTATED     4  1   1  2
  AMP PEAK 24(19P13.2) WILD-TYPE  13  7   0 14
D24V42, multiclass
      clus
vv     AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  T1A1                            0                              1
  T1B                             7                             27
  T1B1                            8                             61
  T1B2                            3                             27
  T2                              2                              4
  T2A                             2                              8
  T2A1                            1                              6
  T2A2                            0                              9
  T2B                             6                             30
  T3                              1                              1
  T3A                             0                              2
  T3B                             4                             13
  T4                              1                              7
  TIS                             1                              0
  TX                              2                             14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 24(19P13.2) MUTATED         0        0         0         0        5
  AMP PEAK 24(19P13.2) WILD-TYPE       5        1         1         1       28
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 24(19P13.2) MUTATED          11         3        1         2
  AMP PEAK 24(19P13.2) WILD-TYPE        66        33        3         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 24(19P13.2) MUTATED            0          1         7         1
  AMP PEAK 24(19P13.2) WILD-TYPE          5          6        36         0
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 24(19P13.2) MUTATED            0          8         1         1
  AMP PEAK 24(19P13.2) WILD-TYPE          3         34         6        11
D24V44, multiclass
            clus
vv           AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              5                             28
  STAGE IB1                            11                             66
  STAGE IB2                             3                             33
  STAGE II                              1                              3
  STAGE IIA                             2                              6
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             7                             36
  STAGE III                             1                              0
  STAGE IIIA                            0                              3
  STAGE IIIB                            8                             34
  STAGE IVA                             1                              6
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(19Q13.13) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(19Q13.13) MUTATED    62  21
  AMP PEAK 25(19Q13.13) WILD-TYPE 151  44
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                             83                             195 
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                             21                              44 
$`AMP PEAK 25(19Q13.13) 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       210.67       154.32       134.33        20.35       147.35 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KJ 
        9.34        13.61        45.83        27.52        11.87        58.88 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HR 
       44.94        40.04         2.66        22.98         8.28        30.90 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 
       14.50        24.56        14.50        26.01         7.46        13.91 
TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA 
       14.96         0.36         0.43         0.59         0.59        16.08 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A40J 
        1.18         2.24         0.10        23.84         1.45         1.35 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI 
       10.82        21.67        20.78        29.85        36.36        24.56 
TCGA-JW-A5VK TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-MY-A5BE 
       20.48       195.85         0.30        13.35        54.81        35.05 
TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73S TCGA-UC-A7PG TCGA-VS-A8EB 
        2.96        15.95         9.04        19.36        12.16        10.03 
TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A953 TCGA-VS-A954 
       18.05        57.93        36.26        16.64        15.68        50.63 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UI 
       50.14        45.34        44.94        25.74        19.69        40.96 
TCGA-VS-A9UP TCGA-VS-A9UU TCGA-VS-A9V4 TCGA-WL-A834 TCGA-ZJ-AAXA 
       43.27        14.53         4.34        26.01         1.41 

$`AMP PEAK 25(19Q13.13) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       12.39        49.48        57.04        68.84        18.74        36.56 
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-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       30.21        35.01         0.46        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD 
       44.22        73.45        83.05       100.14        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7UC 
       18.02        17.85        20.42       101.82        15.48        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI 
      155.77       131.11        94.95         2.73        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH 
      146.86        99.91        23.51        20.81        20.91         1.12 
TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       50.76        87.75        58.88        36.76       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18        17.52        39.55        12.36        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S 
       31.53        31.36        13.05        25.02        26.40        12.66 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       12.82        14.89        26.79        15.02        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       19.27         1.45         0.13         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        47.77         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55         1.22         0.92         2.17        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.12         9.01        25.41        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       27.42         3.29        21.44        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       18.15        21.11        30.31         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
       12.49         0.82        22.52        20.28        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        9.17         8.52        11.38        13.87        34.62         5.42 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84         5.49        15.58        16.41        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88         9.34        15.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       11.67        93.99        66.05        40.50        37.78        26.43 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       19.96        59.51        32.15        46.03        36.13        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       39.78        31.27         4.73        24.39        39.78        50.86 
TCGA-VS-A957 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH 
       48.07        43.40        42.41        21.30        22.72        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
        1.71        14.53        27.25        41.42        35.97        20.09 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        14.04 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       14.89        16.24        15.42        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         0.16         3.91 

  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                           0.10                            0.03 
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                         210.67                          177.04 
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                          20.78                           19.56 
[1] "0.1 - 210.7 (20.8)" "0.0 - 177.0 (19.6)"
[1] "hr=" "1.1"
D25V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 25(19Q13.13) MUTATED    32  25  11   3
  AMP PEAK 25(19Q13.13) WILD-TYPE 102  43  10   5
D25V3, multiclass
    clus
vv   AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  T1                            32                             102
  T2                            25                              43
  T3                            11                              10
  T4                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   33 21
  AMP PEAK 25(19Q13.13) WILD-TYPE 94 34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     33   21
  AMP PEAK 25(19Q13.13) WILD-TYPE   94   34
   clus
vv  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  0                            33                              94
  1                            21                              34
[1] 2 2
[1] FALSE
D25V5, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   33  1
  AMP PEAK 25(19Q13.13) WILD-TYPE 74  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     33    1
  AMP PEAK 25(19Q13.13) WILD-TYPE   74    9
   clus
vv  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  0                            33                              74
  1                             1                               9
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 25(19Q13.13) MUTATED               2
  AMP PEAK 25(19Q13.13) WILD-TYPE             3
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(19Q13.13) MUTATED                                 79
  AMP PEAK 25(19Q13.13) WILD-TYPE                              162
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 25(19Q13.13) MUTATED                                               3
  AMP PEAK 25(19Q13.13) WILD-TYPE                                             3
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 25(19Q13.13) MUTATED                                     5
  AMP PEAK 25(19Q13.13) WILD-TYPE                                  17
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 25(19Q13.13) MUTATED                                           0
  AMP PEAK 25(19Q13.13) WILD-TYPE                                         3
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 25(19Q13.13) MUTATED                                              2
  AMP PEAK 25(19Q13.13) WILD-TYPE                                           13
D25V6, multiclass
                                               clus
vv                                              AMP PEAK 25(19Q13.13) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         79
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              2
                                               clus
vv                                              AMP PEAK 25(19Q13.13) WILD-TYPE
  ADENOSQUAMOUS                                                               3
  CERVICAL SQUAMOUS CELL CARCINOMA                                          162
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19Q13.13) MUTATED    13  78
  AMP PEAK 25(19Q13.13) WILD-TYPE  17 184
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     13   78
  AMP PEAK 25(19Q13.13) WILD-TYPE   17  184
     clus
vv    AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  NO                             13                              17
  YES                            78                             184
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(19Q13.13) MUTATED                                  1     5
  AMP PEAK 25(19Q13.13) WILD-TYPE                                7    13
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(19Q13.13) MUTATED                           8
  AMP PEAK 25(19Q13.13) WILD-TYPE                        20
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 25(19Q13.13) MUTATED                                           0
  AMP PEAK 25(19Q13.13) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  AMP PEAK 25(19Q13.13) MUTATED      64
  AMP PEAK 25(19Q13.13) WILD-TYPE   137
D25V10, multiclass
                                           clus
vv                                          AMP PEAK 25(19Q13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                64
                                           clus
vv                                          AMP PEAK 25(19Q13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  WHITE                                                                 137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19Q13.13) MUTATED     5  52
  AMP PEAK 25(19Q13.13) WILD-TYPE  18 109
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED      5   52
  AMP PEAK 25(19Q13.13) WILD-TYPE   18  109
                        clus
vv                       AMP PEAK 25(19Q13.13) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            52
                        clus
vv                       AMP PEAK 25(19Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                  18
  NOT HISPANIC OR LATINO                             109
[1] 2 2
[1] FALSE
D25V12, continuous
D25V13, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   43 16
  AMP PEAK 25(19Q13.13) WILD-TYPE 91 25
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     43   16
  AMP PEAK 25(19Q13.13) WILD-TYPE   91   25
            clus
vv           AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  TUMOR FREE                            43                              91
  WITH TUMOR                            16                              25
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 25(19Q13.13) MUTATED       16      3       1      2       4
  AMP PEAK 25(19Q13.13) WILD-TYPE     37      2       0      9       3
                                 vv
clus                              UNITED STATES VIETNAM
  AMP PEAK 25(19Q13.13) MUTATED              60       5
  AMP PEAK 25(19Q13.13) WILD-TYPE           141       9
D25V14, multiclass
               clus
vv              AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  BRAZIL                                   16                              37
  CANADA                                    3                               2
  NIGERIA                                   1                               0
  RUSSIA                                    2                               9
  UKRAINE                                   4                               3
  UNITED STATES                            60                             141
  VIETNAM                                   5                               9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  AMP PEAK 25(19Q13.13) MUTATED    5 40 38  0  5
  AMP PEAK 25(19Q13.13) WILD-TYPE 13 89 75  1 19
D25V15, multiclass
    clus
vv   AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  G1                             5                              13
  G2                            40                              89
  G3                            38                              75
  G4                             0                               1
  GX                             5                              19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V16, continuous
D25V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 25(19Q13.13) MUTATED                                            15
  AMP PEAK 25(19Q13.13) WILD-TYPE                                          22
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 25(19Q13.13) MUTATED                                        5
  AMP PEAK 25(19Q13.13) WILD-TYPE                                      4
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 25(19Q13.13) MUTATED                                                 1
  AMP PEAK 25(19Q13.13) WILD-TYPE                                               2
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 25(19Q13.13) MUTATED               10                  45
  AMP PEAK 25(19Q13.13) WILD-TYPE             52                  97
D25V18, multiclass
                                                 clus
vv                                                AMP PEAK 25(19Q13.13) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             10
  LIFELONG NON-SMOKER                                                        45
                                                 clus
vv                                                AMP PEAK 25(19Q13.13) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               2
  CURRENT SMOKER                                                               52
  LIFELONG NON-SMOKER                                                          97
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V19, continuous
D25V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 25(19Q13.13) MUTATED             8       34             5        5
  AMP PEAK 25(19Q13.13) WILD-TYPE          11       68             7       20
D25V21, multiclass
               clus
vv              AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  COMBINATION                               8                              11
  EXTERNAL                                 34                              68
  EXTERNAL BEAM                             5                               7
  INTERNAL                                  5                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V22, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   10  2
  AMP PEAK 25(19Q13.13) WILD-TYPE 15  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     10    2
  AMP PEAK 25(19Q13.13) WILD-TYPE   15    1
                         clus
vv                        AMP PEAK 25(19Q13.13) MUTATED
  COMPLETED AS PLANNED                               10
  TREATMENT NOT COMPLETED                             2
                         clus
vv                        AMP PEAK 25(19Q13.13) WILD-TYPE
  COMPLETED AS PLANNED                                 15
  TREATMENT NOT COMPLETED                               1
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 25(19Q13.13) MUTATED                    0                2
  AMP PEAK 25(19Q13.13) WILD-TYPE                  2                0
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 25(19Q13.13) MUTATED                    15             9
  AMP PEAK 25(19Q13.13) WILD-TYPE                  21            24
D25V23, multiclass
                     clus
vv                    AMP PEAK 25(19Q13.13) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                2
  PRIMARY TUMOR FIELD                            15
  REGIONAL SITE                                   9
                     clus
vv                    AMP PEAK 25(19Q13.13) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  0
  PRIMARY TUMOR FIELD                              21
  REGIONAL SITE                                    24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V24, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   21  1
  AMP PEAK 25(19Q13.13) WILD-TYPE 35  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     21    1
  AMP PEAK 25(19Q13.13) WILD-TYPE   35    4
     clus
vv    AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  CGY                            21                              35
  GY                              1                               4
[1] 2 2
[1] FALSE
D25V25, continuous
D25V26, continuous
D25V27, continuous
D25V28, continuous
D25V29, continuous
D25V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 25(19Q13.13) MUTATED                                     0
  AMP PEAK 25(19Q13.13) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 25(19Q13.13) MUTATED                                     4
  AMP PEAK 25(19Q13.13) WILD-TYPE                                   3
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 25(19Q13.13) MUTATED                         9
  AMP PEAK 25(19Q13.13) WILD-TYPE                      26
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 25(19Q13.13) MUTATED                         1
  AMP PEAK 25(19Q13.13) WILD-TYPE                       0
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 25(19Q13.13) MUTATED                         1
  AMP PEAK 25(19Q13.13) WILD-TYPE                       7
D25V31, multiclass
                                     clus
vv                                    AMP PEAK 25(19Q13.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                         9
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         1
                                     clus
vv                                    AMP PEAK 25(19Q13.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               3
  OTHER LOCATION, SPECIFY                                          26
  POSITIVE BLADDER MARGIN                                           0
  POSITIVE VAGINAL MARGIN                                           7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 25(19Q13.13) MUTATED                                               0
  AMP PEAK 25(19Q13.13) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 25(19Q13.13) MUTATED                                                4
  AMP PEAK 25(19Q13.13) WILD-TYPE                                             21
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 25(19Q13.13) MUTATED                                                                                  27
  AMP PEAK 25(19Q13.13) WILD-TYPE                                                                                54
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 25(19Q13.13) MUTATED                                                                                             35
  AMP PEAK 25(19Q13.13) WILD-TYPE                                                                                           85
D25V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 25(19Q13.13) 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)                                       27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            35
                                                                                              clus
vv                                                                                             AMP PEAK 25(19Q13.13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V33, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   17 25
  AMP PEAK 25(19Q13.13) WILD-TYPE 53 48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     17   25
  AMP PEAK 25(19Q13.13) WILD-TYPE   53   48
         clus
vv        AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  ABSENT                             17                              53
  PRESENT                            25                              48
[1] 2 2
[1] FALSE
D25V34, continuous
D25V35, continuous
D25V36, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   19 33
  AMP PEAK 25(19Q13.13) WILD-TYPE 29 83
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     19   33
  AMP PEAK 25(19Q13.13) WILD-TYPE   29   83
                                          clus
vv                                         AMP PEAK 25(19Q13.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            33
                                          clus
vv                                         AMP PEAK 25(19Q13.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              83
[1] 2 2
[1] FALSE
D25V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 25(19Q13.13) MUTATED              3          17         28
  AMP PEAK 25(19Q13.13) WILD-TYPE           12          36         56
D25V38, multiclass
              clus
vv             AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  CURRENT USER                             3                              12
  FORMER USER                             17                              36
  NEVER USED                              28                              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V39, continuous
D25V40, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   23  7
  AMP PEAK 25(19Q13.13) WILD-TYPE 69 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     23    7
  AMP PEAK 25(19Q13.13) WILD-TYPE   69   10
         clus
vv        AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  ABSENT                             23                              69
  PRESENT                             7                              10
[1] 2 2
[1] FALSE
D25V41, continuous
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 25(19Q13.13) MUTATED      0   7   18    7  1   4    3    2  15  2
  AMP PEAK 25(19Q13.13) WILD-TYPE    1  27   51   23  5   6    4    7  21  0
                                 vv
clus                              T3A T3B T4 TIS TX
  AMP PEAK 25(19Q13.13) MUTATED     1   8  3   0  3
  AMP PEAK 25(19Q13.13) WILD-TYPE   1   9  5   1 13
D25V42, multiclass
      clus
vv     AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  T1A1                             0                               1
  T1B                              7                              27
  T1B1                            18                              51
  T1B2                             7                              23
  T2                               1                               5
  T2A                              4                               6
  T2A1                             3                               4
  T2A2                             2                               7
  T2B                             15                              21
  T3                               2                               0
  T3A                              1                               1
  T3B                              8                               9
  T4                               3                               5
  TIS                              0                               1
  TX                               3                              13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 25(19Q13.13) MUTATED         1        0         0         0        7
  AMP PEAK 25(19Q13.13) WILD-TYPE       4        1         1         1       26
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 25(19Q13.13) MUTATED          18        12        2         3
  AMP PEAK 25(19Q13.13) WILD-TYPE        59        24        2         5
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 25(19Q13.13) MUTATED            2          3        19         1
  AMP PEAK 25(19Q13.13) WILD-TYPE          3          4        24         0
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 25(19Q13.13) MUTATED            2         14         4         1
  AMP PEAK 25(19Q13.13) WILD-TYPE          1         28         3        11
D25V44, multiclass
            clus
vv           AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               7                              26
  STAGE IB1                             18                              59
  STAGE IB2                             12                              24
  STAGE II                               2                               2
  STAGE IIA                              3                               5
  STAGE IIA1                             2                               3
  STAGE IIA2                             3                               4
  STAGE IIB                             19                              24
  STAGE III                              1                               0
  STAGE IIIA                             2                               1
  STAGE IIIB                            14                              28
  STAGE IVA                              4                               3
  STAGE IVB                              1                              11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = AMP PEAK 26(20Q11.21) MUTATION ANALYSIS
D26V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 26(20Q11.21) MUTATED    99  29
  AMP PEAK 26(20Q11.21) WILD-TYPE 114  36
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                            128                             150 
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                             29                              36 
$`AMP PEAK 26(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       210.67 
TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 
      154.32        20.35       147.35        17.19       131.11        13.61 
TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        2.73       146.86        27.52         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VK TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS 
       44.94        40.04        36.76        22.98        17.52        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A439 
       12.36        37.35        30.90        31.53        13.05        14.50 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ 
       14.89        26.79        14.96        13.58         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96        26.27         1.51        19.27         0.59         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN 
        0.13        16.08         1.18         2.24         0.10         0.03 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A40J 
        1.22        23.84         2.17        31.36         1.45         1.35 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LF 
        9.01        25.41        21.67        20.78       147.39        96.95 
TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       78.71        20.48        28.37        21.11       195.85         7.99 
TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MY-A913 
       12.49        13.35        20.28        11.38        34.62         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
        2.96        15.58        16.41        15.95         9.04        17.56 
TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       15.88        19.36         3.88        93.99        12.16        66.05 
TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       40.50        18.05        19.96        36.13        11.51        57.93 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A952 
       39.78        31.27        36.26        16.64        39.78        50.86 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UH 
       15.68        50.63        45.34        44.94        19.69        46.92 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UU TCGA-VS-A9UY 
       40.96        14.53        27.25        43.27        14.53        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-WL-A834 TCGA-ZJ-AAX4 
       67.20         5.16        14.89         4.34        26.01         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        1.41         0.16 

$`AMP PEAK 26(20Q11.21) WILD-TYPE`
TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM 
       12.39        11.44        18.74        36.56       177.04        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF 
        5.46        19.86        67.46        46.32        30.21        53.16 
TCGA-C5-A1MH TCGA-C5-A1ML TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
       38.99        20.91        73.45        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
       33.24        52.01        18.02        17.85        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC 
      134.33        15.48       155.77        94.95         9.34        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ 
       45.83         8.35        99.91        23.51        20.81        20.91 
TCGA-C5-A907 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       11.87        87.75        58.88         2.66       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 
       16.83        16.18         8.28        31.36        25.02        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        26.01        12.66        12.82         7.46 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2PL 
       13.91        15.02        14.99        13.48         6.64         0.43 
TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        1.45         0.07         4.04         0.03         0.36        47.77 
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-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3HZ 
       14.70        19.79         8.32        15.55         0.92        36.26 
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-A9SC TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.12        10.82        14.93         9.44       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 
       24.56        21.44        15.58         8.28        18.15        30.31 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3Y 
       11.28         0.89         0.30         0.82        22.52        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD 
       19.56         9.17         8.52        13.87         5.42        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R 
       35.05        20.84        16.14        14.07         9.34        15.39 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL 
       19.59        11.67        10.03        37.78        26.43        59.51 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A957 TCGA-VS-A958 
       32.15        46.03         4.73        24.39        48.07        50.14 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ 
       43.40        42.41        25.74        21.30        22.72         1.71 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9V0 TCGA-VS-A9V2 
       41.42        35.97        20.09         3.42        18.84        14.04 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       16.24        15.42        29.26        67.59        19.13         3.91 

  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                           0.03                            0.03 
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                         210.67                          177.04 
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                         20.630                          18.985 
[1] "0.0 - 210.7 (20.6)" "0.0 - 177.0 (19.0)"
[1] "hr=" "1.2"
D26V2, continuous
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 26(20Q11.21) MUTATED   58 25 16  4
  AMP PEAK 26(20Q11.21) WILD-TYPE 76 43  5  4
D26V3, multiclass
    clus
vv   AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  T1                            58                              76
  T2                            25                              43
  T3                            16                               5
  T4                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   52 26
  AMP PEAK 26(20Q11.21) WILD-TYPE 75 29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     52   26
  AMP PEAK 26(20Q11.21) WILD-TYPE   75   29
   clus
vv  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  0                            52                              75
  1                            26                              29
[1] 2 2
[1] FALSE
D26V5, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   51  3
  AMP PEAK 26(20Q11.21) WILD-TYPE 56  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     51    3
  AMP PEAK 26(20Q11.21) WILD-TYPE   56    7
   clus
vv  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  0                            51                              56
  1                             3                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 26(20Q11.21) MUTATED               2
  AMP PEAK 26(20Q11.21) WILD-TYPE             3
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(20Q11.21) MUTATED                                107
  AMP PEAK 26(20Q11.21) WILD-TYPE                              134
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 26(20Q11.21) MUTATED                                               4
  AMP PEAK 26(20Q11.21) WILD-TYPE                                             2
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 26(20Q11.21) MUTATED                                    11
  AMP PEAK 26(20Q11.21) WILD-TYPE                                  11
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 26(20Q11.21) MUTATED                                           2
  AMP PEAK 26(20Q11.21) WILD-TYPE                                         1
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 26(20Q11.21) MUTATED                                              8
  AMP PEAK 26(20Q11.21) WILD-TYPE                                            7
D26V6, multiclass
                                               clus
vv                                              AMP PEAK 26(20Q11.21) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        107
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              8
                                               clus
vv                                              AMP PEAK 26(20Q11.21) WILD-TYPE
  ADENOSQUAMOUS                                                               3
  CERVICAL SQUAMOUS CELL CARCINOMA                                          134
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                7
[1] 6 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
  AMP PEAK 26(20Q11.21) MUTATED    13 121
  AMP PEAK 26(20Q11.21) WILD-TYPE  17 141
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     13  121
  AMP PEAK 26(20Q11.21) WILD-TYPE   17  141
     clus
vv    AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  NO                             13                              17
  YES                           121                             141
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(20Q11.21) MUTATED                                  0     6
  AMP PEAK 26(20Q11.21) WILD-TYPE                                8    12
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(20Q11.21) MUTATED                          15
  AMP PEAK 26(20Q11.21) WILD-TYPE                        13
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 26(20Q11.21) MUTATED                                           0
  AMP PEAK 26(20Q11.21) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  AMP PEAK 26(20Q11.21) MUTATED      93
  AMP PEAK 26(20Q11.21) WILD-TYPE   108
D26V10, multiclass
                                           clus
vv                                          AMP PEAK 26(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                93
                                           clus
vv                                          AMP PEAK 26(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  12
  BLACK OR AFRICAN AMERICAN                                              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  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"
D26V11, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED    6 73
  AMP PEAK 26(20Q11.21) WILD-TYPE 17 88
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED      6   73
  AMP PEAK 26(20Q11.21) WILD-TYPE   17   88
                        clus
vv                       AMP PEAK 26(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            73
                        clus
vv                       AMP PEAK 26(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  17
  NOT HISPANIC OR LATINO                              88
[1] 2 2
[1] FALSE
D26V12, continuous
D26V13, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   64 17
  AMP PEAK 26(20Q11.21) WILD-TYPE 70 24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     64   17
  AMP PEAK 26(20Q11.21) WILD-TYPE   70   24
            clus
vv           AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  TUMOR FREE                            64                              70
  WITH TUMOR                            17                              24
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 26(20Q11.21) MUTATED       28      5       1      6       2
  AMP PEAK 26(20Q11.21) WILD-TYPE     25      0       0      5       5
                                 vv
clus                              UNITED STATES VIETNAM
  AMP PEAK 26(20Q11.21) MUTATED              86       6
  AMP PEAK 26(20Q11.21) WILD-TYPE           115       8
D26V14, multiclass
               clus
vv              AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  BRAZIL                                   28                              25
  CANADA                                    5                               0
  NIGERIA                                   1                               0
  RUSSIA                                    6                               5
  UKRAINE                                   2                               5
  UNITED STATES                            86                             115
  VIETNAM                                   6                               8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  AMP PEAK 26(20Q11.21) MUTATED    8 55 57  1 11
  AMP PEAK 26(20Q11.21) WILD-TYPE 10 74 56  0 13
D26V15, multiclass
    clus
vv   AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  G1                             8                              10
  G2                            55                              74
  G3                            57                              56
  G4                             1                               0
  GX                            11                              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V16, continuous
D26V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 26(20Q11.21) MUTATED                                            21
  AMP PEAK 26(20Q11.21) WILD-TYPE                                          16
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 26(20Q11.21) MUTATED                                        6
  AMP PEAK 26(20Q11.21) WILD-TYPE                                      3
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 26(20Q11.21) MUTATED                                                 1
  AMP PEAK 26(20Q11.21) WILD-TYPE                                               2
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 26(20Q11.21) MUTATED               23                  61
  AMP PEAK 26(20Q11.21) WILD-TYPE             39                  81
D26V18, multiclass
                                                 clus
vv                                                AMP PEAK 26(20Q11.21) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             23
  LIFELONG NON-SMOKER                                                        61
                                                 clus
vv                                                AMP PEAK 26(20Q11.21) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               2
  CURRENT SMOKER                                                               39
  LIFELONG NON-SMOKER                                                          81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V19, continuous
D26V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 26(20Q11.21) MUTATED             7       48             7       12
  AMP PEAK 26(20Q11.21) WILD-TYPE          12       54             5       13
D26V21, multiclass
               clus
vv              AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  COMBINATION                               7                              12
  EXTERNAL                                 48                              54
  EXTERNAL BEAM                             7                               5
  INTERNAL                                 12                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V22, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   10  2
  AMP PEAK 26(20Q11.21) WILD-TYPE 15  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     10    2
  AMP PEAK 26(20Q11.21) WILD-TYPE   15    1
                         clus
vv                        AMP PEAK 26(20Q11.21) MUTATED
  COMPLETED AS PLANNED                               10
  TREATMENT NOT COMPLETED                             2
                         clus
vv                        AMP PEAK 26(20Q11.21) WILD-TYPE
  COMPLETED AS PLANNED                                 15
  TREATMENT NOT COMPLETED                               1
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 26(20Q11.21) MUTATED                    0                1
  AMP PEAK 26(20Q11.21) WILD-TYPE                  2                1
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 26(20Q11.21) MUTATED                    19            17
  AMP PEAK 26(20Q11.21) WILD-TYPE                  17            16
D26V23, multiclass
                     clus
vv                    AMP PEAK 26(20Q11.21) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                1
  PRIMARY TUMOR FIELD                            19
  REGIONAL SITE                                  17
                     clus
vv                    AMP PEAK 26(20Q11.21) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  1
  PRIMARY TUMOR FIELD                              17
  REGIONAL SITE                                    16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V24, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   30  2
  AMP PEAK 26(20Q11.21) WILD-TYPE 26  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     30    2
  AMP PEAK 26(20Q11.21) WILD-TYPE   26    3
     clus
vv    AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  CGY                            30                              26
  GY                              2                               3
[1] 2 2
[1] FALSE
D26V25, continuous
D26V26, continuous
D26V27, continuous
D26V28, continuous
D26V29, continuous
D26V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 26(20Q11.21) MUTATED                                     0
  AMP PEAK 26(20Q11.21) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 26(20Q11.21) MUTATED                                     2
  AMP PEAK 26(20Q11.21) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 26(20Q11.21) MUTATED                        11
  AMP PEAK 26(20Q11.21) WILD-TYPE                      24
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 26(20Q11.21) MUTATED                         0
  AMP PEAK 26(20Q11.21) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 26(20Q11.21) MUTATED                         6
  AMP PEAK 26(20Q11.21) WILD-TYPE                       2
D26V31, multiclass
                                     clus
vv                                    AMP PEAK 26(20Q11.21) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        11
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         6
                                     clus
vv                                    AMP PEAK 26(20Q11.21) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                          24
  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 26(20Q11.21) MUTATED                                               0
  AMP PEAK 26(20Q11.21) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 26(20Q11.21) MUTATED                                               12
  AMP PEAK 26(20Q11.21) WILD-TYPE                                             13
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 26(20Q11.21) MUTATED                                                                                  40
  AMP PEAK 26(20Q11.21) WILD-TYPE                                                                                41
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 26(20Q11.21) MUTATED                                                                                             48
  AMP PEAK 26(20Q11.21) WILD-TYPE                                                                                           72
D26V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 26(20Q11.21) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            48
                                                                                              clus
vv                                                                                             AMP PEAK 26(20Q11.21) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V33, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   30 35
  AMP PEAK 26(20Q11.21) WILD-TYPE 40 38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     30   35
  AMP PEAK 26(20Q11.21) WILD-TYPE   40   38
         clus
vv        AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  ABSENT                             30                              40
  PRESENT                            35                              38
[1] 2 2
[1] FALSE
D26V34, continuous
D26V35, continuous
D26V36, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   17 50
  AMP PEAK 26(20Q11.21) WILD-TYPE 31 66
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     17   50
  AMP PEAK 26(20Q11.21) WILD-TYPE   31   66
                                          clus
vv                                         AMP PEAK 26(20Q11.21) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            50
                                          clus
vv                                         AMP PEAK 26(20Q11.21) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              66
[1] 2 2
[1] FALSE
D26V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 26(20Q11.21) MUTATED              5          24         36
  AMP PEAK 26(20Q11.21) WILD-TYPE           10          29         48
D26V38, multiclass
              clus
vv             AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  CURRENT USER                             5                              10
  FORMER USER                             24                              29
  NEVER USED                              36                              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"
D26V39, continuous
D26V40, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   39  9
  AMP PEAK 26(20Q11.21) WILD-TYPE 53  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     39    9
  AMP PEAK 26(20Q11.21) WILD-TYPE   53    8
         clus
vv        AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  ABSENT                             39                              53
  PRESENT                             9                               8
[1] 2 2
[1] FALSE
D26V41, continuous
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 26(20Q11.21) MUTATED      1  15   32   10  2   5    4    1  13  1
  AMP PEAK 26(20Q11.21) WILD-TYPE    0  19   37   20  4   5    3    8  23  1
                                 vv
clus                              T3A T3B T4 TIS TX
  AMP PEAK 26(20Q11.21) MUTATED     2  13  4   1  9
  AMP PEAK 26(20Q11.21) WILD-TYPE   0   4  4   0  7
D26V42, multiclass
      clus
vv     AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  T1A1                             1                               0
  T1B                             15                              19
  T1B1                            32                              37
  T1B2                            10                              20
  T2                               2                               4
  T2A                              5                               5
  T2A1                             4                               3
  T2A2                             1                               8
  T2B                             13                              23
  T3                               1                               1
  T3A                              2                               0
  T3B                             13                               4
  T4                               4                               4
  TIS                              1                               0
  TX                               9                               7
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 26(20Q11.21) MUTATED         2        0         1         0       14
  AMP PEAK 26(20Q11.21) WILD-TYPE       3        1         0         1       19
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 26(20Q11.21) MUTATED          32        13        4         4
  AMP PEAK 26(20Q11.21) WILD-TYPE        45        23        0         4
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 26(20Q11.21) MUTATED            3          2        19         1
  AMP PEAK 26(20Q11.21) WILD-TYPE          2          5        24         0
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 26(20Q11.21) MUTATED            2         23         4         6
  AMP PEAK 26(20Q11.21) WILD-TYPE          1         19         3         6
D26V44, multiclass
            clus
vv           AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                               0                               1
  STAGE IA1                              1                               0
  STAGE IA2                              0                               1
  STAGE IB                              14                              19
  STAGE IB1                             32                              45
  STAGE IB2                             13                              23
  STAGE II                               4                               0
  STAGE IIA                              4                               4
  STAGE IIA1                             3                               2
  STAGE IIA2                             2                               5
  STAGE IIB                             19                              24
  STAGE III                              1                               0
  STAGE IIIA                             2                               1
  STAGE IIIB                            23                              19
  STAGE IVA                              4                               3
  STAGE IVB                              6                               6
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(21Q22.13) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 27(21Q22.13) MUTATED    34  11
  AMP PEAK 27(21Q22.13) WILD-TYPE 179  54
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                             45                             233 
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                             11                              54 
$`AMP PEAK 27(21Q22.13) MUTATED`
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK 
        5.46        19.86        31.40        38.99        35.61         2.43 
TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-DG-A2KH TCGA-DG-A2KL 
        3.58       100.14         2.73        45.83         1.12        44.94 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A5O9 TCGA-EK-A2PI TCGA-EK-A2PM 
       39.55        12.36        37.35        13.91        19.27         0.59 
TCGA-EK-A2RA TCGA-EK-A2RM TCGA-FU-A3TX TCGA-HG-A9SC TCGA-HM-A3JK TCGA-IR-A3LL 
       16.08         2.24         1.48        10.82        20.78        36.36 
TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE 
       21.44        21.11        30.31        11.28         0.30        35.05 
TCGA-MY-A913 TCGA-Q1-A73R TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
        5.49        15.39        40.50        26.43        18.05        19.96 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A9U7 TCGA-VS-A9UI TCGA-VS-A9UU 
       36.13        57.93         4.73        42.41        40.96        14.53 
TCGA-VS-A9V3 TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       14.89         0.69         1.41 

$`AMP PEAK 27(21Q22.13) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        0.46        20.91        40.93        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95         9.34        13.61        50.99         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52        20.81        20.91        11.87 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       58.88        50.76        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       17.52         8.28        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       12.66        12.82         7.46        14.89        26.79        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.99        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 
       45.96        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45         0.13         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        47.77         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        8.32        15.55         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26         1.45         1.58         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        1.35         1.32         1.97         1.12         9.01        25.41 
TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       21.67        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        29.85        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       18.15       195.85         7.99         0.89        12.49         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       13.35        22.52        20.28        17.82        19.56         9.17 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        13.87        34.62         5.42        54.81 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S 
       16.14        17.56        14.07        15.88         9.34        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59         3.88        11.67        93.99        12.16        66.05 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC 
       10.03        37.78        59.51        32.15        46.03        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 
       39.78        31.27        36.26        16.64        24.39        39.78 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       50.86        15.68        50.63        48.07        50.14        45.34 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       44.94        43.40        25.74        21.30        22.72        19.69 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       46.92         1.71        14.53        27.25        41.42        43.27 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       35.97        20.09         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        14.04         4.34        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        67.59        19.13         0.16         3.91 

  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                           0.30                            0.03 
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                         100.14                          210.67 
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                          19.27                           20.09 
[1] "0.3 - 100.1 (19.3)" "0.0 - 210.7 (20.1)"
[1] "hr=" "1.4"
D27V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 27(21Q22.13) MUTATED    16  15   4   1
  AMP PEAK 27(21Q22.13) WILD-TYPE 118  53  17   7
D27V3, multiclass
    clus
vv   AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  T1                            16                             118
  T2                            15                              53
  T3                             4                              17
  T4                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                                 cls
clus                                0   1
  AMP PEAK 27(21Q22.13) MUTATED    20   8
  AMP PEAK 27(21Q22.13) WILD-TYPE 107  47
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     20    8
  AMP PEAK 27(21Q22.13) WILD-TYPE  107   47
   clus
vv  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  0                            20                             107
  1                             8                              47
[1] 2 2
[1] FALSE
D27V5, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED   19  2
  AMP PEAK 27(21Q22.13) WILD-TYPE 88  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     19    2
  AMP PEAK 27(21Q22.13) WILD-TYPE   88    8
   clus
vv  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  0                            19                              88
  1                             2                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 27(21Q22.13) MUTATED               2
  AMP PEAK 27(21Q22.13) WILD-TYPE             3
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(21Q22.13) MUTATED                                 42
  AMP PEAK 27(21Q22.13) WILD-TYPE                              199
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 27(21Q22.13) MUTATED                                               1
  AMP PEAK 27(21Q22.13) WILD-TYPE                                             5
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 27(21Q22.13) MUTATED                                     2
  AMP PEAK 27(21Q22.13) WILD-TYPE                                  20
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 27(21Q22.13) MUTATED                                           0
  AMP PEAK 27(21Q22.13) WILD-TYPE                                         3
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 27(21Q22.13) MUTATED                                              1
  AMP PEAK 27(21Q22.13) WILD-TYPE                                           14
D27V6, multiclass
                                               clus
vv                                              AMP PEAK 27(21Q22.13) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         42
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              1
                                               clus
vv                                              AMP PEAK 27(21Q22.13) WILD-TYPE
  ADENOSQUAMOUS                                                               3
  CERVICAL SQUAMOUS CELL CARCINOMA                                          199
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(21Q22.13) MUTATED     6  42
  AMP PEAK 27(21Q22.13) WILD-TYPE  24 220
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      6   42
  AMP PEAK 27(21Q22.13) WILD-TYPE   24  220
     clus
vv    AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  NO                              6                              24
  YES                            42                             220
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(21Q22.13) MUTATED                                  1     3
  AMP PEAK 27(21Q22.13) WILD-TYPE                                7    15
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(21Q22.13) MUTATED                           3
  AMP PEAK 27(21Q22.13) WILD-TYPE                        25
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 27(21Q22.13) MUTATED                                           0
  AMP PEAK 27(21Q22.13) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  AMP PEAK 27(21Q22.13) MUTATED      32
  AMP PEAK 27(21Q22.13) WILD-TYPE   169
D27V10, multiclass
                                           clus
vv                                          AMP PEAK 27(21Q22.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 3
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                32
                                           clus
vv                                          AMP PEAK 27(21Q22.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  15
  BLACK OR AFRICAN AMERICAN                                              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  WHITE                                                                 169
[1] 5 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
  AMP PEAK 27(21Q22.13) MUTATED     3  23
  AMP PEAK 27(21Q22.13) WILD-TYPE  20 138
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      3   23
  AMP PEAK 27(21Q22.13) WILD-TYPE   20  138
                        clus
vv                       AMP PEAK 27(21Q22.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            23
                        clus
vv                       AMP PEAK 27(21Q22.13) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             138
[1] 2 2
[1] FALSE
D27V12, continuous
D27V13, binary
                                 cls
clus                                0   1
  AMP PEAK 27(21Q22.13) MUTATED    22   9
  AMP PEAK 27(21Q22.13) WILD-TYPE 112  32
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     22    9
  AMP PEAK 27(21Q22.13) WILD-TYPE  112   32
            clus
vv           AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  TUMOR FREE                            22                             112
  WITH TUMOR                             9                              32
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 27(21Q22.13) MUTATED       11      2       0      3       1
  AMP PEAK 27(21Q22.13) WILD-TYPE     42      3       1      8       6
                                 vv
clus                              UNITED STATES VIETNAM
  AMP PEAK 27(21Q22.13) MUTATED              29       2
  AMP PEAK 27(21Q22.13) WILD-TYPE           172      12
D27V14, multiclass
               clus
vv              AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  BRAZIL                                   11                              42
  CANADA                                    2                               3
  NIGERIA                                   0                               1
  RUSSIA                                    3                               8
  UKRAINE                                   1                               6
  UNITED STATES                            29                             172
  VIETNAM                                   2                              12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               G1  G2  G3  G4  GX
  AMP PEAK 27(21Q22.13) MUTATED     2  15  23   0   6
  AMP PEAK 27(21Q22.13) WILD-TYPE  16 114  90   1  18
D27V15, multiclass
    clus
vv   AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  G1                             2                              16
  G2                            15                             114
  G3                            23                              90
  G4                             0                               1
  GX                             6                              18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V16, continuous
D27V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 27(21Q22.13) MUTATED                                             8
  AMP PEAK 27(21Q22.13) WILD-TYPE                                          29
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 27(21Q22.13) MUTATED                                        2
  AMP PEAK 27(21Q22.13) WILD-TYPE                                      7
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 27(21Q22.13) MUTATED                                                 1
  AMP PEAK 27(21Q22.13) WILD-TYPE                                               2
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 27(21Q22.13) MUTATED                8                  22
  AMP PEAK 27(21Q22.13) WILD-TYPE             54                 120
D27V18, multiclass
                                                 clus
vv                                                AMP PEAK 27(21Q22.13) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                              8
  LIFELONG NON-SMOKER                                                        22
                                                 clus
vv                                                AMP PEAK 27(21Q22.13) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               2
  CURRENT SMOKER                                                               54
  LIFELONG NON-SMOKER                                                         120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V19, continuous
D27V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 27(21Q22.13) MUTATED             5       15             1        4
  AMP PEAK 27(21Q22.13) WILD-TYPE          14       87            11       21
D27V21, multiclass
               clus
vv              AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  COMBINATION                               5                              14
  EXTERNAL                                 15                              87
  EXTERNAL BEAM                             1                              11
  INTERNAL                                  4                              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"
D27V22, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED    4  1
  AMP PEAK 27(21Q22.13) WILD-TYPE 21  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      4    1
  AMP PEAK 27(21Q22.13) WILD-TYPE   21    2
                         clus
vv                        AMP PEAK 27(21Q22.13) MUTATED
  COMPLETED AS PLANNED                                4
  TREATMENT NOT COMPLETED                             1
                         clus
vv                        AMP PEAK 27(21Q22.13) WILD-TYPE
  COMPLETED AS PLANNED                                 21
  TREATMENT NOT COMPLETED                               2
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 27(21Q22.13) MUTATED                    0                0
  AMP PEAK 27(21Q22.13) WILD-TYPE                  2                2
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 27(21Q22.13) MUTATED                     5             7
  AMP PEAK 27(21Q22.13) WILD-TYPE                  31            26
D27V23, multiclass
                     clus
vv                    AMP PEAK 27(21Q22.13) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                0
  PRIMARY TUMOR FIELD                             5
  REGIONAL SITE                                   7
                     clus
vv                    AMP PEAK 27(21Q22.13) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  2
  PRIMARY TUMOR FIELD                              31
  REGIONAL SITE                                    26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V24, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED    9  1
  AMP PEAK 27(21Q22.13) WILD-TYPE 47  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      9    1
  AMP PEAK 27(21Q22.13) WILD-TYPE   47    4
     clus
vv    AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  CGY                             9                              47
  GY                              1                               4
[1] 2 2
[1] FALSE
D27V25, continuous
D27V26, continuous
D27V27, continuous
D27V28, continuous
D27V29, continuous
D27V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 27(21Q22.13) MUTATED                                     0
  AMP PEAK 27(21Q22.13) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 27(21Q22.13) MUTATED                                     0
  AMP PEAK 27(21Q22.13) WILD-TYPE                                   7
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 27(21Q22.13) MUTATED                         3
  AMP PEAK 27(21Q22.13) WILD-TYPE                      32
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 27(21Q22.13) MUTATED                         0
  AMP PEAK 27(21Q22.13) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 27(21Q22.13) MUTATED                         3
  AMP PEAK 27(21Q22.13) WILD-TYPE                       5
D27V31, multiclass
                                     clus
vv                                    AMP PEAK 27(21Q22.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  OTHER LOCATION, SPECIFY                                         3
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         3
                                     clus
vv                                    AMP PEAK 27(21Q22.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               7
  OTHER LOCATION, SPECIFY                                          32
  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 27(21Q22.13) MUTATED                                               0
  AMP PEAK 27(21Q22.13) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 27(21Q22.13) MUTATED                                                4
  AMP PEAK 27(21Q22.13) WILD-TYPE                                             21
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 27(21Q22.13) MUTATED                                                                                  18
  AMP PEAK 27(21Q22.13) WILD-TYPE                                                                                63
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 27(21Q22.13) MUTATED                                                                                             16
  AMP PEAK 27(21Q22.13) WILD-TYPE                                                                                          104
D27V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 27(21Q22.13) 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)                                       18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            16
                                                                                              clus
vv                                                                                             AMP PEAK 27(21Q22.13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         63
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V33, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED   11 11
  AMP PEAK 27(21Q22.13) WILD-TYPE 59 62
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     11   11
  AMP PEAK 27(21Q22.13) WILD-TYPE   59   62
         clus
vv        AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  ABSENT                             11                              59
  PRESENT                            11                              62
[1] 2 2
[1] FALSE
D27V34, continuous
D27V35, continuous
D27V36, binary
                                 cls
clus                                0   1
  AMP PEAK 27(21Q22.13) MUTATED    10  10
  AMP PEAK 27(21Q22.13) WILD-TYPE  38 106
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     10   10
  AMP PEAK 27(21Q22.13) WILD-TYPE   38  106
                                          clus
vv                                         AMP PEAK 27(21Q22.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            10
                                          clus
vv                                         AMP PEAK 27(21Q22.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             106
[1] 2 2
[1] FALSE
D27V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 27(21Q22.13) MUTATED              3           5         13
  AMP PEAK 27(21Q22.13) WILD-TYPE           12          48         71
D27V38, multiclass
              clus
vv             AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  CURRENT USER                             3                              12
  FORMER USER                              5                              48
  NEVER USED                              13                              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V39, continuous
D27V40, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED   11  1
  AMP PEAK 27(21Q22.13) WILD-TYPE 81 16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     11    1
  AMP PEAK 27(21Q22.13) WILD-TYPE   81   16
         clus
vv        AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  ABSENT                             11                              81
  PRESENT                             1                              16
[1] 2 2
[1] FALSE
D27V41, continuous
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 27(21Q22.13) MUTATED      0   4    9    3  2   4    0    1   8  0
  AMP PEAK 27(21Q22.13) WILD-TYPE    1  30   60   27  4   6    7    8  28  2
                                 vv
clus                              T3A T3B T4 TIS TX
  AMP PEAK 27(21Q22.13) MUTATED     0   4  1   1  2
  AMP PEAK 27(21Q22.13) WILD-TYPE   2  13  7   0 14
D27V42, multiclass
      clus
vv     AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  T1A1                             0                               1
  T1B                              4                              30
  T1B1                             9                              60
  T1B2                             3                              27
  T2                               2                               4
  T2A                              4                               6
  T2A1                             0                               7
  T2A2                             1                               8
  T2B                              8                              28
  T3                               0                               2
  T3A                              0                               2
  T3B                              4                              13
  T4                               1                               7
  TIS                              1                               0
  TX                               2                              14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 27(21Q22.13) MUTATED         1        0         0         1        3
  AMP PEAK 27(21Q22.13) WILD-TYPE       4        1         1         0       30
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 27(21Q22.13) MUTATED          11         4        2         2
  AMP PEAK 27(21Q22.13) WILD-TYPE        66        32        2         6
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 27(21Q22.13) MUTATED            0          2        11         0
  AMP PEAK 27(21Q22.13) WILD-TYPE          5          5        32         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 27(21Q22.13) MUTATED            0         10         0         1
  AMP PEAK 27(21Q22.13) WILD-TYPE          3         32         7        11
D27V44, multiclass
            clus
vv           AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                               3                              30
  STAGE IB1                             11                              66
  STAGE IB2                              4                              32
  STAGE II                               2                               2
  STAGE IIA                              2                               6
  STAGE IIA1                             0                               5
  STAGE IIA2                             2                               5
  STAGE IIB                             11                              32
  STAGE III                              0                               1
  STAGE IIIA                             0                               3
  STAGE IIIB                            10                              32
  STAGE IVA                              0                               7
  STAGE IVB                              1                              11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = AMP PEAK 28(XQ28) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 28(XQ28) MUTATED    61  11
  AMP PEAK 28(XQ28) WILD-TYPE 152  54
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         72                         206 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         11                          54 
$`AMP PEAK 28(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-C5-A8XI 
       73.45        83.05       154.32       101.82       131.11         8.35 
TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-EA-A3HQ TCGA-EA-A3QD 
       23.51         1.12        22.98        16.18        37.35        13.05 
TCGA-EA-A3QE TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2H0 
       25.02        14.50        14.89        13.91        14.96        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RB TCGA-EK-A2RD 
        6.64         1.51         0.43         0.59         0.07         0.03 
TCGA-EK-A2RE TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A8YF 
        0.36         0.07         0.10         0.10         0.03        15.55 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LL 
       23.84         1.45       137.16        66.81        78.71        36.36 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A5U2 TCGA-MA-AA3Z TCGA-MY-A5BD TCGA-MY-A5BF 
      195.85        30.31         0.30        19.56        54.81        20.84 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-R2-A69V TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       15.95        16.14        19.59        66.05        10.03        37.78 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A950 
       26.43        18.05        11.51        57.93        16.64        39.78 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UM 
       15.68        50.63        42.41        21.30        22.72        27.25 
TCGA-VS-A9UP TCGA-VS-A9UZ TCGA-VS-A9V5 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       43.27        67.20        16.24        67.59        19.13         1.41 

$`AMP PEAK 28(XQ28) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
       36.56       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        30.21        35.01        57.73        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91        40.93        44.22        73.18 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       17.85        20.42       210.67       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19       155.77        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR 
        2.73        50.99        45.83       146.86        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.81        20.91        11.87        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
      118.65        16.83        17.52         8.28        39.55        12.36 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       30.90        31.53        31.36        14.50        26.40        24.56 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD 
       26.01        12.66        12.82         7.46        26.79        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 
       14.99        13.58        13.48         0.36        12.59        26.27 
TCGA-EK-A2PI TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
       19.27         0.59         1.45         0.13        16.08         4.04 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A1H6 
        1.18        47.77         2.24         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        19.79         8.32         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17        31.36        36.26         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        10.82        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      147.39       117.40        96.95        81.96        29.85        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        8.28        18.15        21.11         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
       12.49         0.82        13.35        22.52        20.28        17.82 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        9.17         8.52        11.38        13.87        34.62         5.42 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       35.05         5.49         2.96        15.58        16.41         9.04 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EJ 
        3.88        11.67        93.99        12.16        40.50        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM 
       59.51        32.15        46.03        36.13        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 
       36.26         4.73        24.39        50.86        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH 
       45.34        44.94        43.40        25.74        19.69        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
       40.96         1.71        14.53        41.42        35.97        20.09 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
       14.53         3.42        18.25        18.84         5.16        14.04 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAX4 
       14.89         4.34        15.42        26.01        29.26         0.69 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                     195.85                      210.67 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                      21.07                       19.74 
[1] "0.0 - 195.8 (21.1)" "0.1 - 210.7 (19.7)"
[1] "hr=" "2"  
D28V2, continuous
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 28(XQ28) MUTATED    32  17  10   1
  AMP PEAK 28(XQ28) WILD-TYPE 102  51  11   7
D28V3, multiclass
    clus
vv   AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  T1                        32                         102
  T2                        17                          51
  T3                        10                          11
  T4                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   36 11
  AMP PEAK 28(XQ28) WILD-TYPE 91 44
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     36   11
  AMP PEAK 28(XQ28) WILD-TYPE   91   44
   clus
vv  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  0                        36                          91
  1                        11                          44
[1] 2 2
[1] FALSE
D28V5, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   27  1
  AMP PEAK 28(XQ28) WILD-TYPE 80  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     27    1
  AMP PEAK 28(XQ28) WILD-TYPE   80    9
   clus
vv  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  0                        27                          80
  1                         1                           9
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(XQ28) MUTATED               2                               62
  AMP PEAK 28(XQ28) WILD-TYPE             3                              179
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 28(XQ28) MUTATED                                               1
  AMP PEAK 28(XQ28) WILD-TYPE                                             5
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 28(XQ28) MUTATED                                     3
  AMP PEAK 28(XQ28) WILD-TYPE                                  19
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 28(XQ28) MUTATED                                           3
  AMP PEAK 28(XQ28) WILD-TYPE                                         0
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 28(XQ28) MUTATED                                              4
  AMP PEAK 28(XQ28) WILD-TYPE                                           11
D28V6, multiclass
                                               clus
vv                                              AMP PEAK 28(XQ28) MUTATED
  ADENOSQUAMOUS                                                         2
  CERVICAL SQUAMOUS CELL CARCINOMA                                     62
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          4
                                               clus
vv                                              AMP PEAK 28(XQ28) WILD-TYPE
  ADENOSQUAMOUS                                                           3
  CERVICAL SQUAMOUS CELL CARCINOMA                                      179
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED     5  70
  AMP PEAK 28(XQ28) WILD-TYPE  25 192
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED      5   70
  AMP PEAK 28(XQ28) WILD-TYPE   25  192
     clus
vv    AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  NO                          5                          25
  YES                        70                         192
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(XQ28) MUTATED                                  2     5
  AMP PEAK 28(XQ28) WILD-TYPE                                6    13
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK 28(XQ28) MUTATED                           9
  AMP PEAK 28(XQ28) WILD-TYPE                        19
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 28(XQ28) MUTATED                                           2    44
  AMP PEAK 28(XQ28) WILD-TYPE                                         0   157
D28V10, multiclass
                                           clus
vv                                          AMP PEAK 28(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                         9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            44
                                           clus
vv                                          AMP PEAK 28(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                          19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             157
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED     4  37
  AMP PEAK 28(XQ28) WILD-TYPE  19 124
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED      4   37
  AMP PEAK 28(XQ28) WILD-TYPE   19  124
                        clus
vv                       AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             4                          19
  NOT HISPANIC OR LATINO                        37                         124
[1] 2 2
[1] FALSE
D28V12, continuous
D28V13, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   37  6
  AMP PEAK 28(XQ28) WILD-TYPE 97 35
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     37    6
  AMP PEAK 28(XQ28) WILD-TYPE   97   35
            clus
vv           AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  TUMOR FREE                        37                          97
  WITH TUMOR                         6                          35
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 28(XQ28) MUTATED       17      1       0      3       1
  AMP PEAK 28(XQ28) WILD-TYPE     36      4       1      8       6
                             vv
clus                          UNITED STATES VIETNAM
  AMP PEAK 28(XQ28) MUTATED              50       3
  AMP PEAK 28(XQ28) WILD-TYPE           151      11
D28V14, multiclass
               clus
vv              AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  BRAZIL                               17                          36
  CANADA                                1                           4
  NIGERIA                               0                           1
  RUSSIA                                3                           8
  UKRAINE                               1                           6
  UNITED STATES                        50                         151
  VIETNAM                               3                          11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  AMP PEAK 28(XQ28) MUTATED    4 30 29  1  8
  AMP PEAK 28(XQ28) WILD-TYPE 14 99 84  0 16
D28V15, multiclass
    clus
vv   AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  G1                         4                          14
  G2                        30                          99
  G3                        29                          84
  G4                         1                           0
  GX                         8                          16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V16, continuous
D28V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 28(XQ28) MUTATED                                             7
  AMP PEAK 28(XQ28) WILD-TYPE                                          30
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 28(XQ28) MUTATED                                        3
  AMP PEAK 28(XQ28) WILD-TYPE                                      6
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 28(XQ28) MUTATED                                                 0
  AMP PEAK 28(XQ28) WILD-TYPE                                               3
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 28(XQ28) MUTATED               17                  35
  AMP PEAK 28(XQ28) WILD-TYPE             45                 107
D28V18, multiclass
                                                 clus
vv                                                AMP PEAK 28(XQ28) 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                                                         17
  LIFELONG NON-SMOKER                                                    35
                                                 clus
vv                                                AMP PEAK 28(XQ28) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           3
  CURRENT SMOKER                                                           45
  LIFELONG NON-SMOKER                                                     107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V19, continuous
D28V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 28(XQ28) MUTATED             3       27             2        7
  AMP PEAK 28(XQ28) WILD-TYPE          16       75            10       18
D28V21, multiclass
               clus
vv              AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  COMBINATION                           3                          16
  EXTERNAL                             27                          75
  EXTERNAL BEAM                         2                          10
  INTERNAL                              7                          18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V22, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED    4  1
  AMP PEAK 28(XQ28) WILD-TYPE 21  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED      4    1
  AMP PEAK 28(XQ28) WILD-TYPE   21    2
                         clus
vv                        AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  COMPLETED AS PLANNED                            4                          21
  TREATMENT NOT COMPLETED                         1                           2
[1] 2 2
[1] FALSE
                             vv
clus                          DISTANT RECURRENCE LOCAL RECURRENCE
  AMP PEAK 28(XQ28) MUTATED                    1                0
  AMP PEAK 28(XQ28) WILD-TYPE                  1                2
                             vv
clus                          PRIMARY TUMOR FIELD REGIONAL SITE
  AMP PEAK 28(XQ28) MUTATED                     7            11
  AMP PEAK 28(XQ28) WILD-TYPE                  29            22
D28V23, multiclass
                     clus
vv                    AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  DISTANT RECURRENCE                          1                           1
  LOCAL RECURRENCE                            0                           2
  PRIMARY TUMOR FIELD                         7                          29
  REGIONAL SITE                              11                          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"
D28V24, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   17  1
  AMP PEAK 28(XQ28) WILD-TYPE 39  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     17    1
  AMP PEAK 28(XQ28) WILD-TYPE   39    4
     clus
vv    AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  CGY                        17                          39
  GY                          1                           4
[1] 2 2
[1] FALSE
D28V25, continuous
D28V26, continuous
D28V27, continuous
D28V28, continuous
D28V29, continuous
D28V30, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 28(XQ28) MUTATED                                     1
  AMP PEAK 28(XQ28) WILD-TYPE                                   1
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 28(XQ28) MUTATED                                     0
  AMP PEAK 28(XQ28) WILD-TYPE                                   7
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 28(XQ28) MUTATED                         8                       0
  AMP PEAK 28(XQ28) WILD-TYPE                      27                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK 28(XQ28) MUTATED                         2
  AMP PEAK 28(XQ28) WILD-TYPE                       6
D28V31, multiclass
                                     clus
vv                                    AMP PEAK 28(XQ28) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  OTHER LOCATION, SPECIFY                                     8
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     2
                                     clus
vv                                    AMP PEAK 28(XQ28) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           7
  OTHER LOCATION, SPECIFY                                      27
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 28(XQ28) MUTATED                                               0
  AMP PEAK 28(XQ28) WILD-TYPE                                             2
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 28(XQ28) MUTATED                                                9
  AMP PEAK 28(XQ28) WILD-TYPE                                             16
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 28(XQ28) MUTATED                                                                                  21
  AMP PEAK 28(XQ28) WILD-TYPE                                                                                60
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 28(XQ28) MUTATED                                                                                             31
  AMP PEAK 28(XQ28) WILD-TYPE                                                                                           89
D28V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 28(XQ28) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        31
                                                                                              clus
vv                                                                                             AMP PEAK 28(XQ28) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V33, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   17 18
  AMP PEAK 28(XQ28) WILD-TYPE 53 55
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     17   18
  AMP PEAK 28(XQ28) WILD-TYPE   53   55
         clus
vv        AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  ABSENT                         17                          53
  PRESENT                        18                          55
[1] 2 2
[1] FALSE
D28V34, continuous
D28V35, continuous
D28V36, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   13 25
  AMP PEAK 28(XQ28) WILD-TYPE 35 91
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     13   25
  AMP PEAK 28(XQ28) WILD-TYPE   35   91
                                          clus
vv                                         AMP PEAK 28(XQ28) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        25
                                          clus
vv                                         AMP PEAK 28(XQ28) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          91
[1] 2 2
[1] FALSE
D28V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK 28(XQ28) MUTATED              4          11         25
  AMP PEAK 28(XQ28) WILD-TYPE           11          42         59
D28V38, multiclass
              clus
vv             AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  CURRENT USER                         4                          11
  FORMER USER                         11                          42
  NEVER USED                          25                          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"
D28V39, continuous
D28V40, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   24  3
  AMP PEAK 28(XQ28) WILD-TYPE 68 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     24    3
  AMP PEAK 28(XQ28) WILD-TYPE   68   14
         clus
vv        AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  ABSENT                         24                          68
  PRESENT                         3                          14
[1] 2 2
[1] FALSE
D28V41, continuous
                             vv
clus                          T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  AMP PEAK 28(XQ28) MUTATED      0   8   17    7  1   4    4    2   6  1   1
  AMP PEAK 28(XQ28) WILD-TYPE    1  26   52   23  5   6    3    7  30  1   1
                             vv
clus                          T3B T4 TIS TX
  AMP PEAK 28(XQ28) MUTATED     8  1   0  5
  AMP PEAK 28(XQ28) WILD-TYPE   9  7   1 11
D28V42, multiclass
      clus
vv     AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  T1A1                         0                           1
  T1B                          8                          26
  T1B1                        17                          52
  T1B2                         7                          23
  T2                           1                           5
  T2A                          4                           6
  T2A1                         4                           3
  T2A2                         2                           7
  T2B                          6                          30
  T3                           1                           1
  T3A                          1                           1
  T3B                          8                           9
  T4                           1                           7
  TIS                          0                           1
  TX                           5                          11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 28(XQ28) MUTATED         1        0         0         0        6
  AMP PEAK 28(XQ28) WILD-TYPE       4        1         1         1       27
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK 28(XQ28) MUTATED          21         6        1         3          3
  AMP PEAK 28(XQ28) WILD-TYPE        56        30        3         5          2
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  AMP PEAK 28(XQ28) MUTATED            1        14         1          1
  AMP PEAK 28(XQ28) WILD-TYPE          6        29         0          2
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 28(XQ28) MUTATED           11         2         2
  AMP PEAK 28(XQ28) WILD-TYPE         31         5        10
D28V44, multiclass
            clus
vv           AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                           0                           1
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           6                          27
  STAGE IB1                         21                          56
  STAGE IB2                          6                          30
  STAGE II                           1                           3
  STAGE IIA                          3                           5
  STAGE IIA1                         3                           2
  STAGE IIA2                         1                           6
  STAGE IIB                         14                          29
  STAGE III                          1                           0
  STAGE IIIA                         1                           2
  STAGE IIIB                        11                          31
  STAGE IVA                          2                           5
  STAGE IVB                          2                          10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.23) MUTATED    27  10
  DEL PEAK  1(1P36.23) WILD-TYPE 186  55
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            37                            241 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            10                             55 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LT 
       11.44        57.73        53.16        35.61         0.46        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CM TCGA-C5-A7UH TCGA-C5-A7X3 
       73.45        83.05        52.01        20.35       131.11         9.34 
TCGA-C5-A8YQ TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A556 TCGA-EK-A2PG TCGA-EK-A2PI 
       23.51        30.90        14.50        14.89         1.51        19.27 
TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A3EO 
        0.59         1.18         2.24        14.70        19.79         2.17 
TCGA-IR-A3LF TCGA-JX-A3Q8 TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EJ TCGA-VS-A8Q9 
       96.95        30.31         5.49         9.04        19.96        46.03 
TCGA-VS-A8QH TCGA-VS-A950 TCGA-VS-A9UD TCGA-VS-A9UO TCGA-VS-A9V3 TCGA-VS-A9V4 
       39.78        39.78        19.69        41.42        14.89         4.34 
TCGA-VS-A9V5 
       16.24 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        57.04        23.67        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35       100.14        38.43        33.24        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 
      147.35        17.19       155.77        94.95        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR 
       50.99        45.83         8.35       146.86        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.81        20.91        11.87         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        39.55        12.36        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05        25.02        14.50        26.40        24.56        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.66        12.82         7.46        26.79        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.99        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       45.96        26.27         6.64         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       47.77         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       20.35         7.92         6.94         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84         0.92        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41        10.82        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       18.15        21.11       195.85         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       12.49         0.30         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         9.17         8.52        11.38        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62         5.42        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        66.05        10.03        40.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA 
       37.78        26.43        18.05        59.51        32.15        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        57.93        31.27        36.26        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       24.39        50.86        15.68        50.63        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       45.34        44.94        43.40        42.41        25.74        21.30 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       22.72        46.92        40.96         1.71        14.53        27.25 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       43.27        35.97        20.09        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-AA62 TCGA-WL-A834 
       67.20        18.84         5.16        14.04        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                          0.46                           0.03 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        131.11                         210.67 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         19.79                          19.86 
[1] "0.5 - 131.1 (19.8)" "0.0 - 210.7 (19.9)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.23) MUTATED    15   7   2   2
  DEL PEAK  1(1P36.23) WILD-TYPE 119  61  19   6
D29V3, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1                           15                            119
  T2                            7                             61
  T3                            2                             19
  T4                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED    15   5
  DEL PEAK  1(1P36.23) WILD-TYPE 112  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     15    5
  DEL PEAK  1(1P36.23) WILD-TYPE  112   50
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           15                            112
  1                            5                             50
[1] 2 2
[1] FALSE
D29V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   10  3
  DEL PEAK  1(1P36.23) WILD-TYPE 97  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     10    3
  DEL PEAK  1(1P36.23) WILD-TYPE   97    7
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           10                             97
  1                            3                              7
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.23) MUTATED               0                               26
  DEL PEAK  1(1P36.23) WILD-TYPE             5                              215
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  1(1P36.23) MUTATED                                               3
  DEL PEAK  1(1P36.23) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  1(1P36.23) MUTATED                                     6
  DEL PEAK  1(1P36.23) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  1(1P36.23) MUTATED                                           1
  DEL PEAK  1(1P36.23) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  1(1P36.23) MUTATED                                              4
  DEL PEAK  1(1P36.23) WILD-TYPE                                           11
D29V6, multiclass
                                               clus
vv                                              DEL PEAK  1(1P36.23) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        26
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              DEL PEAK  1(1P36.23) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         215
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED     6  34
  DEL PEAK  1(1P36.23) WILD-TYPE  24 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      6   34
  DEL PEAK  1(1P36.23) WILD-TYPE   24  228
     clus
vv    DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  NO                             6                             24
  YES                           34                            228
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.23) MUTATED                                  0     3
  DEL PEAK  1(1P36.23) WILD-TYPE                                8    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.23) MUTATED                           4
  DEL PEAK  1(1P36.23) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  1(1P36.23) MUTATED                                           0
  DEL PEAK  1(1P36.23) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK  1(1P36.23) MUTATED      32
  DEL PEAK  1(1P36.23) WILD-TYPE   169
D29V10, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               32
                                           clus
vv                                          DEL PEAK  1(1P36.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                169
[1] 5 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  1(1P36.23) MUTATED     3  23
  DEL PEAK  1(1P36.23) WILD-TYPE  20 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      3   23
  DEL PEAK  1(1P36.23) WILD-TYPE   20  138
                        clus
vv                       DEL PEAK  1(1P36.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       DEL PEAK  1(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            138
[1] 2 2
[1] FALSE
D29V12, continuous
D29V13, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED    17   5
  DEL PEAK  1(1P36.23) WILD-TYPE 117  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     17    5
  DEL PEAK  1(1P36.23) WILD-TYPE  117   36
            clus
vv           DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  TUMOR FREE                           17                            117
  WITH TUMOR                            5                             36
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  1(1P36.23) MUTATED        9      0       0      2       0
  DEL PEAK  1(1P36.23) WILD-TYPE     44      5       1      9       7
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK  1(1P36.23) MUTATED              28       1
  DEL PEAK  1(1P36.23) WILD-TYPE           173      13
D29V14, multiclass
               clus
vv              DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  BRAZIL                                   9                             44
  CANADA                                   0                              5
  NIGERIA                                  0                              1
  RUSSIA                                   2                              9
  UKRAINE                                  0                              7
  UNITED STATES                           28                            173
  VIETNAM                                  1                             13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK  1(1P36.23) MUTATED     2  19  17   0   1
  DEL PEAK  1(1P36.23) WILD-TYPE  16 110  96   1  23
D29V15, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  G1                            2                             16
  G2                           19                            110
  G3                           17                             96
  G4                            0                              1
  GX                            1                             23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V16, continuous
D29V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  1(1P36.23) MUTATED                                             5
  DEL PEAK  1(1P36.23) WILD-TYPE                                          32
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  1(1P36.23) MUTATED                                        0
  DEL PEAK  1(1P36.23) WILD-TYPE                                      9
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  1(1P36.23) MUTATED                                                 1
  DEL PEAK  1(1P36.23) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  1(1P36.23) MUTATED                8                  20
  DEL PEAK  1(1P36.23) WILD-TYPE             54                 122
D29V18, multiclass
                                                 clus
vv                                                DEL PEAK  1(1P36.23) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             8
  LIFELONG NON-SMOKER                                                       20
                                                 clus
vv                                                DEL PEAK  1(1P36.23) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              54
  LIFELONG NON-SMOKER                                                        122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V19, continuous
D29V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  1(1P36.23) MUTATED             4       11             2        5
  DEL PEAK  1(1P36.23) WILD-TYPE          15       91            10       20
D29V21, multiclass
               clus
vv              DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                11                             91
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V22, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    5  1
  DEL PEAK  1(1P36.23) WILD-TYPE 20  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      5    1
  DEL PEAK  1(1P36.23) WILD-TYPE   20    2
                         clus
vv                        DEL PEAK  1(1P36.23) MUTATED
  COMPLETED AS PLANNED                               5
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK  1(1P36.23) WILD-TYPE
  COMPLETED AS PLANNED                                20
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  1(1P36.23) MUTATED                    0                1
  DEL PEAK  1(1P36.23) WILD-TYPE                  2                1
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  1(1P36.23) MUTATED                     8             4
  DEL PEAK  1(1P36.23) WILD-TYPE                  28            29
D29V23, multiclass
                     clus
vv                    DEL PEAK  1(1P36.23) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            8
  REGIONAL SITE                                  4
                     clus
vv                    DEL PEAK  1(1P36.23) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             28
  REGIONAL SITE                                   29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V24, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   10  1
  DEL PEAK  1(1P36.23) WILD-TYPE 46  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     10    1
  DEL PEAK  1(1P36.23) WILD-TYPE   46    4
     clus
vv    DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  CGY                           10                             46
  GY                             1                              4
[1] 2 2
[1] FALSE
D29V25, continuous
D29V26, continuous
D29V27, continuous
D29V28, continuous
D29V29, continuous
D29V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  1(1P36.23) MUTATED                                     1
  DEL PEAK  1(1P36.23) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  1(1P36.23) MUTATED                                     1
  DEL PEAK  1(1P36.23) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK  1(1P36.23) MUTATED                         5
  DEL PEAK  1(1P36.23) WILD-TYPE                      30
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK  1(1P36.23) MUTATED                         0
  DEL PEAK  1(1P36.23) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK  1(1P36.23) MUTATED                         2
  DEL PEAK  1(1P36.23) WILD-TYPE                       6
D29V31, multiclass
                                     clus
vv                                    DEL PEAK  1(1P36.23) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        5
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK  1(1P36.23) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         30
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  1(1P36.23) MUTATED                                               0
  DEL PEAK  1(1P36.23) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  1(1P36.23) MUTATED                                                2
  DEL PEAK  1(1P36.23) WILD-TYPE                                             23
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  1(1P36.23) MUTATED                                                                                  15
  DEL PEAK  1(1P36.23) WILD-TYPE                                                                                66
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  1(1P36.23) MUTATED                                                                                             13
  DEL PEAK  1(1P36.23) WILD-TYPE                                                                                          107
D29V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  1(1P36.23) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           13
                                                                                              clus
vv                                                                                             DEL PEAK  1(1P36.23) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        66
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V33, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    9  8
  DEL PEAK  1(1P36.23) WILD-TYPE 61 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      9    8
  DEL PEAK  1(1P36.23) WILD-TYPE   61   65
         clus
vv        DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  ABSENT                             9                             61
  PRESENT                            8                             65
[1] 2 2
[1] FALSE
D29V34, continuous
D29V35, continuous
D29V36, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED     6   8
  DEL PEAK  1(1P36.23) WILD-TYPE  42 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      6    8
  DEL PEAK  1(1P36.23) WILD-TYPE   42  108
                                          clus
vv                                         DEL PEAK  1(1P36.23) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            8
                                          clus
vv                                         DEL PEAK  1(1P36.23) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            108
[1] 2 2
[1] FALSE
D29V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK  1(1P36.23) MUTATED              1           8         10
  DEL PEAK  1(1P36.23) WILD-TYPE           14          45         74
D29V38, multiclass
              clus
vv             DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  CURRENT USER                            1                             14
  FORMER USER                             8                             45
  NEVER USED                             10                             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V39, continuous
D29V40, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   15  1
  DEL PEAK  1(1P36.23) WILD-TYPE 77 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     15    1
  DEL PEAK  1(1P36.23) WILD-TYPE   77   16
         clus
vv        DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  ABSENT                            15                             77
  PRESENT                            1                             16
[1] 2 2
[1] FALSE
D29V41, continuous
[1] "Remove cluster labels:"       "DEL PEAK  1(1P36.23) MUTATED"
clus
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-C5-A1ML                     TCGA-C5-A1MN 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-GH-A9DA                     TCGA-HM-A3JK 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-MA-AA3W 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"DEL PEAK  1(1P36.23) WILD-TYPE" 
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  1(1P36.23) MUTATED      0   3    8    4  1   1    1    0   4  0   2
  DEL PEAK  1(1P36.23) WILD-TYPE    1  31   61   26  5   9    6    9  32  2   0
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK  1(1P36.23) MUTATED     0  2   1  3
  DEL PEAK  1(1P36.23) WILD-TYPE  17  6   0 13
D29V42, multiclass
      clus
vv     DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1A1                            0                              1
  T1B                             3                             31
  T1B1                            8                             61
  T1B2                            4                             26
  T2                              1                              5
  T2A                             1                              9
  T2A1                            1                              6
  T2A2                            0                              9
  T2B                             4                             32
  T3                              0                              2
  T3A                             2                              0
  T3B                             0                             17
  T4                              2                              6
  TIS                             1                              0
  TX                              3                             13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  1(1P36.23) MUTATED         1        0         0         0        3
  DEL PEAK  1(1P36.23) WILD-TYPE       4        1         1         1       30
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  1(1P36.23) MUTATED          11         6        1         2
  DEL PEAK  1(1P36.23) WILD-TYPE        66        30        3         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  1(1P36.23) MUTATED            1          0         6         0
  DEL PEAK  1(1P36.23) WILD-TYPE          4          7        37         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.23) MUTATED            2          3         1         2
  DEL PEAK  1(1P36.23) WILD-TYPE          1         39         6        10
D29V44, multiclass
            clus
vv           DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              3                             30
  STAGE IB1                            11                             66
  STAGE IB2                             6                             30
  STAGE II                              1                              3
  STAGE IIA                             2                              6
  STAGE IIA1                            1                              4
  STAGE IIA2                            0                              7
  STAGE IIB                             6                             37
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                            3                             39
  STAGE IVA                             1                              6
  STAGE IVB                             2                             10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    19  12
  DEL PEAK  2(1P13.2) WILD-TYPE 194  53
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           31                           247 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           12                            53 
$`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       154.32       131.11 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-DS-A0VN TCGA-EA-A3HR 
       94.95        13.61        45.83        23.51       118.65        30.90 
TCGA-EA-A3QE TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EX-A69L TCGA-FU-A3NI TCGA-HG-A2PA 
       25.02        19.27         0.43        19.79         1.45        25.41 
TCGA-HM-A6W2 TCGA-LP-A4AW TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EB TCGA-VS-A8EC 
        9.44         0.89         5.49         9.04        10.03        40.50 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A950 
       59.51        46.03        11.51        39.78         4.73        39.78 
TCGA-VS-A9UI 
       40.96 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       57.73        53.16        38.99         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ 
       40.93         3.58        44.22        73.45        83.05       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      210.67       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI 
       17.19       155.77         9.34         2.73        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        27.52        20.81        20.91        11.87 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        12.36        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.53        31.36        13.05        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50        26.01        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.48         0.36        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        1.51         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
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-A69M TCGA-EX-A8YF 
       20.35         7.92         6.94        14.70         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.97         1.12         9.01        10.82        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       195.85        30.31         7.99        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       12.49         0.30         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         9.17         8.52        11.38        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62         5.42        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH 
       11.67        93.99        12.16        66.05        37.78        26.43 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM 
       18.05        19.96        32.15        36.13        57.93        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       36.26        16.64        24.39        50.86        15.68        50.63 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       48.07        50.14        45.34        44.94        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ 
       25.74        21.30        22.72        19.69        46.92         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        41.42        43.27        35.97        20.09 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
       14.04        14.89         4.34        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.43                          0.03 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       154.32                        210.67 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        25.41                         19.56 
[1] "0.4 - 154.3 (25.4)" "0.0 - 210.7 (19.6)"
[1] "hr=" "1.4"
D30V2, continuous
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  2(1P13.2) MUTATED    12   5   3   0
  DEL PEAK  2(1P13.2) WILD-TYPE 122  63  18   8
D30V3, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                          12                           122
  T2                           5                            63
  T3                           3                            18
  T4                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    13   3
  DEL PEAK  2(1P13.2) WILD-TYPE 114  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     13    3
  DEL PEAK  2(1P13.2) WILD-TYPE  114   52
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          13                           114
  1                           3                            52
[1] 2 2
[1] FALSE
D30V5, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   12  3
  DEL PEAK  2(1P13.2) WILD-TYPE 95  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     12    3
  DEL PEAK  2(1P13.2) WILD-TYPE   95    7
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          12                            95
  1                           3                             7
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.2) MUTATED               1                               30
  DEL PEAK  2(1P13.2) WILD-TYPE             4                              211
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  2(1P13.2) MUTATED                                               0
  DEL PEAK  2(1P13.2) WILD-TYPE                                             6
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  2(1P13.2) MUTATED                                     1
  DEL PEAK  2(1P13.2) WILD-TYPE                                  21
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  2(1P13.2) MUTATED                                           0
  DEL PEAK  2(1P13.2) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  2(1P13.2) MUTATED                                              1
  DEL PEAK  2(1P13.2) WILD-TYPE                                           14
D30V6, multiclass
                                               clus
vv                                              DEL PEAK  2(1P13.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       30
  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  2(1P13.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        211
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     5  28
  DEL PEAK  2(1P13.2) WILD-TYPE  25 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      5   28
  DEL PEAK  2(1P13.2) WILD-TYPE   25  234
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                            5                            25
  YES                          28                           234
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P13.2) MUTATED                                  0     2
  DEL PEAK  2(1P13.2) WILD-TYPE                                8    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P13.2) MUTATED                           5
  DEL PEAK  2(1P13.2) WILD-TYPE                        23
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           0    25
  DEL PEAK  2(1P13.2) WILD-TYPE                                         2   176
D30V10, multiclass
                                           clus
vv                                          DEL PEAK  2(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              25
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     2  19
  DEL PEAK  2(1P13.2) WILD-TYPE  21 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      2   19
  DEL PEAK  2(1P13.2) WILD-TYPE   21  142
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           142
[1] 2 2
[1] FALSE
D30V12, continuous
D30V13, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    12   5
  DEL PEAK  2(1P13.2) WILD-TYPE 122  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     12    5
  DEL PEAK  2(1P13.2) WILD-TYPE  122   36
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  TUMOR FREE                          12                           122
  WITH TUMOR                           5                            36
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  2(1P13.2) MUTATED        9      0       0      2       0
  DEL PEAK  2(1P13.2) WILD-TYPE     44      5       1      9       7
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  2(1P13.2) MUTATED              21       1
  DEL PEAK  2(1P13.2) WILD-TYPE           180      13
D30V14, multiclass
               clus
vv              DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  BRAZIL                                  9                            44
  CANADA                                  0                             5
  NIGERIA                                 0                             1
  RUSSIA                                  2                             9
  UKRAINE                                 0                             7
  UNITED STATES                          21                           180
  VIETNAM                                 1                            13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK  2(1P13.2) MUTATED     2  15   9   0   4
  DEL PEAK  2(1P13.2) WILD-TYPE  16 114 104   1  20
D30V15, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  G1                           2                            16
  G2                          15                           114
  G3                           9                           104
  G4                           0                             1
  GX                           4                            20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V16, 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 
                            1                            41 
                   TCGA-BI-A0VR                    TCGA-C5-A1BJ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1BL                    TCGA-C5-A1BQ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1ME                    TCGA-C5-A1MF 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1MH                    TCGA-C5-A2M2 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A3HD                    TCGA-C5-A7CM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A7CO                    TCGA-C5-A907 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-DG-A2KK                    TCGA-DS-A3LQ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EK-A2RA                    TCGA-EX-A69M 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FU-A2QG                    TCGA-FU-A3TX 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FU-A3WB                    TCGA-HM-A3JK 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-HM-A4S6                    TCGA-IR-A3L7 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-IR-A3LB                    TCGA-IR-A3LH 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-JX-A3Q0                    TCGA-MA-AA43 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MU-A5YI                    TCGA-MU-A8JM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-Q1-A6DW                    TCGA-Q1-A73S 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-RA-A741                    TCGA-VS-A8QF 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-VS-A94Z                    TCGA-VS-A9V0 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-VS-A9V4                    TCGA-WL-A834 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-ZJ-A8QR                    TCGA-ZJ-AAX4 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-ZJ-AAXA                    TCGA-ZJ-AAXT 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-ZJ-AB0I 
"DEL PEAK  2(1P13.2) WILD-TYPE" 
D30V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  2(1P13.2) MUTATED                                             1
  DEL PEAK  2(1P13.2) WILD-TYPE                                          36
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  2(1P13.2) MUTATED                                        0
  DEL PEAK  2(1P13.2) WILD-TYPE                                      9
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  2(1P13.2) MUTATED                                                 1
  DEL PEAK  2(1P13.2) WILD-TYPE                                               2
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  2(1P13.2) MUTATED               12                  15
  DEL PEAK  2(1P13.2) WILD-TYPE             50                 127
D30V18, multiclass
                                                 clus
vv                                                DEL PEAK  2(1P13.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           12
  LIFELONG NON-SMOKER                                                      15
                                                 clus
vv                                                DEL PEAK  2(1P13.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             50
  LIFELONG NON-SMOKER                                                       127
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V19, continuous
D30V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  2(1P13.2) MUTATED             3       11             2        3
  DEL PEAK  2(1P13.2) WILD-TYPE          16       91            10       22
D30V21, multiclass
               clus
vv              DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  COMBINATION                             3                            16
  EXTERNAL                               11                            91
  EXTERNAL BEAM                           2                            10
  INTERNAL                                3                            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"
D30V22, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    4  0
  DEL PEAK  2(1P13.2) WILD-TYPE 21  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      4    0
  DEL PEAK  2(1P13.2) WILD-TYPE   21    3
                         clus
vv                        DEL PEAK  2(1P13.2) MUTATED
  COMPLETED AS PLANNED                              4
  TREATMENT NOT COMPLETED                           0
                         clus
vv                        DEL PEAK  2(1P13.2) WILD-TYPE
  COMPLETED AS PLANNED                               21
  TREATMENT NOT COMPLETED                             3
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  2(1P13.2) MUTATED                    1                0
  DEL PEAK  2(1P13.2) WILD-TYPE                  1                2
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  2(1P13.2) MUTATED                     6             5
  DEL PEAK  2(1P13.2) WILD-TYPE                  30            28
D30V23, multiclass
                     clus
vv                    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  DISTANT RECURRENCE                            1                             1
  LOCAL RECURRENCE                              0                             2
  PRIMARY TUMOR FIELD                           6                            30
  REGIONAL SITE                                 5                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V24, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    8  1
  DEL PEAK  2(1P13.2) WILD-TYPE 48  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      8    1
  DEL PEAK  2(1P13.2) WILD-TYPE   48    4
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CGY                           8                            48
  GY                            1                             4
[1] 2 2
[1] FALSE
D30V25, continuous
D30V26, continuous
D30V27, continuous
D30V28, continuous
D30V29, continuous
D30V30, 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                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  2(1P13.2) MUTATED                         4                       0
  DEL PEAK  2(1P13.2) WILD-TYPE                      31                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  2(1P13.2) MUTATED                         0
  DEL PEAK  2(1P13.2) WILD-TYPE                       8
D30V31, multiclass
                                     clus
vv                                    DEL PEAK  2(1P13.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       4
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    DEL PEAK  2(1P13.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        31
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                                4
  DEL PEAK  2(1P13.2) WILD-TYPE                                             21
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  2(1P13.2) MUTATED                                                                                   7
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                74
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  2(1P13.2) MUTATED                                                                                             13
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                          107
D30V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  2(1P13.2) 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)                                      7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          13
                                                                                              clus
vv                                                                                             DEL PEAK  2(1P13.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       74
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V33, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6  4
  DEL PEAK  2(1P13.2) WILD-TYPE 64 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6    4
  DEL PEAK  2(1P13.2) WILD-TYPE   64   69
         clus
vv        DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ABSENT                            6                            64
  PRESENT                           4                            69
[1] 2 2
[1] FALSE
D30V34, continuous
D30V35, continuous
D30V36, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     8   9
  DEL PEAK  2(1P13.2) WILD-TYPE  40 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      8    9
  DEL PEAK  2(1P13.2) WILD-TYPE   40  107
                                          clus
vv                                         DEL PEAK  2(1P13.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           9
                                          clus
vv                                         DEL PEAK  2(1P13.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           107
[1] 2 2
[1] FALSE
D30V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  2(1P13.2) MUTATED              2           6          6
  DEL PEAK  2(1P13.2) WILD-TYPE           13          47         78
D30V38, multiclass
              clus
vv             DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CURRENT USER                           2                            13
  FORMER USER                            6                            47
  NEVER USED                             6                            78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V39, continuous
D30V40, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    7  1
  DEL PEAK  2(1P13.2) WILD-TYPE 85 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7    1
  DEL PEAK  2(1P13.2) WILD-TYPE   85   16
         clus
vv        DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ABSENT                            7                            85
  PRESENT                           1                            16
[1] 2 2
[1] FALSE
D30V41, 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 
                            1                            16 
                   TCGA-C5-A1BN                    TCGA-C5-A1MH 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1ML                    TCGA-C5-A1MN 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1MP                    TCGA-EK-A2RO 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-GH-A9DA                    TCGA-HM-A3JK 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-JW-A852                    TCGA-JX-A3Q8 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MA-AA3W                    TCGA-MA-AA3Z 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MA-AA42                    TCGA-MU-A51Y 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MU-A8JM                    TCGA-ZX-AA5X 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  2(1P13.2) MUTATED      0   3    6    3  0   2    0    0   3  0   1
  DEL PEAK  2(1P13.2) WILD-TYPE    1  31   63   27  6   8    7    9  33  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  2(1P13.2) MUTATED     2  0   1  5
  DEL PEAK  2(1P13.2) WILD-TYPE  15  8   0 11
D30V42, multiclass
      clus
vv     DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1A1                           0                             1
  T1B                            3                            31
  T1B1                           6                            63
  T1B2                           3                            27
  T2                             0                             6
  T2A                            2                             8
  T2A1                           0                             7
  T2A2                           0                             9
  T2B                            3                            33
  T3                             0                             2
  T3A                            1                             1
  T3B                            2                            15
  T4                             0                             8
  TIS                            1                             0
  TX                             5                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  2(1P13.2) MUTATED         1        1         0         0        4
  DEL PEAK  2(1P13.2) WILD-TYPE       4        0         1         1       29
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED           9         2        1         2
  DEL PEAK  2(1P13.2) WILD-TYPE        68        34        3         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  2(1P13.2) MUTATED            0          0         4         0
  DEL PEAK  2(1P13.2) WILD-TYPE          5          7        39         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  2(1P13.2) MUTATED            1          5         1         2
  DEL PEAK  2(1P13.2) WILD-TYPE          2         37         6        10
D30V44, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             4                            29
  STAGE IB1                            9                            68
  STAGE IB2                            2                            34
  STAGE II                             1                             3
  STAGE IIA                            2                             6
  STAGE IIA1                           0                             5
  STAGE IIA2                           0                             7
  STAGE IIB                            4                            39
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                           5                            37
  STAGE IVA                            1                             6
  STAGE IVB                            2                            10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    50  12
  DEL PEAK  3(2Q22.1) WILD-TYPE 163  53
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           62                           216 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           12                            53 
$`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-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH 
       18.02       210.67       131.11        23.51        27.52         1.12 
TCGA-DG-A2KL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A3HR TCGA-EA-A411 
       44.94       118.65        22.98        17.52        30.90        24.56 
TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG 
       12.66        14.99        14.96         0.36         6.64         1.51 
TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EX-A69L TCGA-EX-A8YF TCGA-HM-A3JJ 
        1.45         1.18         0.10        19.79        15.55        21.67 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        9.44       147.39        78.71       195.85        30.31         7.99 
TCGA-LP-A7HU TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MY-A5BF 
       13.35        17.82        19.56         9.17        11.38        20.84 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EH 
        5.49        15.58        16.41        19.59        12.16        26.43 
TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A953 TCGA-VS-A9U7 
       59.51        11.51         4.73        24.39        15.68        42.41 
TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UY TCGA-VS-A9V3 TCGA-VS-A9V5 
       19.69        40.96        27.25        18.25        14.89        16.24 
TCGA-XS-A8TJ TCGA-ZJ-AAX4 
       29.26         0.69 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       18.74       144.16       177.04       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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        17.85        20.42       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
      146.86        99.91        20.81        20.91        11.87        58.88 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       50.76        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
      117.99        16.83        16.18         8.28        39.55        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       37.35        31.53        31.36        13.05        25.02        14.50 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       26.40        14.50        26.01        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       26.79        13.91        15.02        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96        26.27        19.27         0.43         0.59         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       47.77         2.24         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K 
       20.35         7.92         6.94        14.70         8.32         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        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
        1.97         1.12         9.01        25.41        10.82        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-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        28.37         8.28        18.15        21.11 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W 
       11.28         0.89        12.49         0.30         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
       20.28         8.52        13.87        34.62         5.42        54.81 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       35.05         2.96        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       14.07        15.88         9.34        15.39        19.36         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        93.99        66.05        10.03        40.50        37.78 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF 
       18.05        19.96        32.15        46.03        36.13        57.93 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A952 
       39.78        31.27        36.26        16.64        39.78        50.86 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       50.63        48.07        50.14        45.34        44.94        43.40 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL 
       25.74        21.30        22.72        46.92         1.71        14.53 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV 
       41.42        43.27        35.97        20.09        14.53         3.42 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-AA62 
       67.20        18.84         5.16        14.04         4.34        15.42 
TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       26.01        67.59        19.13         1.41         0.16         3.91 

  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 
                       210.67                        177.04 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       18.905                        20.315 
[1] "0.1 - 210.7 (18.9)" "0.0 - 177.0 (20.3)"
[1] "hr=" "1.2"
D31V2, continuous
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(2Q22.1) MUTATED    29  17   8   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 105  51  13   6
D31V3, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                          29                           105
  T2                          17                            51
  T3                           8                            13
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   31 12
  DEL PEAK  3(2Q22.1) WILD-TYPE 96 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     31   12
  DEL PEAK  3(2Q22.1) WILD-TYPE   96   43
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          31                            96
  1                          12                            43
[1] 2 2
[1] FALSE
D31V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   31  3
  DEL PEAK  3(2Q22.1) WILD-TYPE 76  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     31    3
  DEL PEAK  3(2Q22.1) WILD-TYPE   76    7
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          31                            76
  1                           3                             7
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED               2                               58
  DEL PEAK  3(2Q22.1) WILD-TYPE             3                              183
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  3(2Q22.1) MUTATED                                               0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             6
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                     3
  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                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  3(2Q22.1) MUTATED                                              2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                           13
D31V6, multiclass
                                               clus
vv                                              DEL PEAK  3(2Q22.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       58
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              DEL PEAK  3(2Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        183
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     8  57
  DEL PEAK  3(2Q22.1) WILD-TYPE  22 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      8   57
  DEL PEAK  3(2Q22.1) WILD-TYPE   22  205
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                            8                            22
  YES                          57                           205
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q22.1) MUTATED                                  0     5
  DEL PEAK  3(2Q22.1) WILD-TYPE                                8    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(2Q22.1) MUTATED                          10
  DEL PEAK  3(2Q22.1) WILD-TYPE                        18
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(2Q22.1) MUTATED                                           0    42
  DEL PEAK  3(2Q22.1) WILD-TYPE                                         2   159
D31V10, multiclass
                                           clus
vv                                          DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              42
                                           clus
vv                                          DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               159
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     6  34
  DEL PEAK  3(2Q22.1) WILD-TYPE  17 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      6   34
  DEL PEAK  3(2Q22.1) WILD-TYPE   17  127
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          34
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           127
[1] 2 2
[1] FALSE
D31V12, continuous
D31V13, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    31   7
  DEL PEAK  3(2Q22.1) WILD-TYPE 103  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     31    7
  DEL PEAK  3(2Q22.1) WILD-TYPE  103   34
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  TUMOR FREE                          31                           103
  WITH TUMOR                           7                            34
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  3(2Q22.1) MUTATED       14      2       0      2       2
  DEL PEAK  3(2Q22.1) WILD-TYPE     39      3       1      9       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  3(2Q22.1) MUTATED              42       3
  DEL PEAK  3(2Q22.1) WILD-TYPE           159      11
D31V14, multiclass
               clus
vv              DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  BRAZIL                                 14                            39
  CANADA                                  2                             3
  NIGERIA                                 0                             1
  RUSSIA                                  2                             9
  UKRAINE                                 2                             5
  UNITED STATES                          42                           159
  VIETNAM                                 3                            11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK  3(2Q22.1) MUTATED     3  24  30   1   5
  DEL PEAK  3(2Q22.1) WILD-TYPE  15 105  83   0  19
D31V15, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  G1                           3                            15
  G2                          24                           105
  G3                          30                            83
  G4                           1                             0
  GX                           5                            19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V16, continuous
D31V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  3(2Q22.1) MUTATED                                             7
  DEL PEAK  3(2Q22.1) WILD-TYPE                                          30
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  3(2Q22.1) MUTATED                                        2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  3(2Q22.1) MUTATED                                                 2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  3(2Q22.1) MUTATED               13                  33
  DEL PEAK  3(2Q22.1) WILD-TYPE             49                 109
D31V18, multiclass
                                                 clus
vv                                                DEL PEAK  3(2Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           13
  LIFELONG NON-SMOKER                                                      33
                                                 clus
vv                                                DEL PEAK  3(2Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             49
  LIFELONG NON-SMOKER                                                       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"
D31V19, continuous
D31V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  3(2Q22.1) MUTATED             3       25             5        6
  DEL PEAK  3(2Q22.1) WILD-TYPE          16       77             7       19
D31V21, multiclass
               clus
vv              DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  COMBINATION                             3                            16
  EXTERNAL                               25                            77
  EXTERNAL BEAM                           5                             7
  INTERNAL                                6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V22, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED    7  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 18  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      7    0
  DEL PEAK  3(2Q22.1) WILD-TYPE   18    3
                         clus
vv                        DEL PEAK  3(2Q22.1) MUTATED
  COMPLETED AS PLANNED                              7
  TREATMENT NOT COMPLETED                           0
                         clus
vv                        DEL PEAK  3(2Q22.1) WILD-TYPE
  COMPLETED AS PLANNED                               18
  TREATMENT NOT COMPLETED                             3
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  3(2Q22.1) MUTATED                    0                1
  DEL PEAK  3(2Q22.1) WILD-TYPE                  2                1
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  3(2Q22.1) MUTATED                    11             8
  DEL PEAK  3(2Q22.1) WILD-TYPE                  25            25
D31V23, multiclass
                     clus
vv                    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              1                             1
  PRIMARY TUMOR FIELD                          11                            25
  REGIONAL SITE                                 8                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V24, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   17  2
  DEL PEAK  3(2Q22.1) WILD-TYPE 39  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     17    2
  DEL PEAK  3(2Q22.1) WILD-TYPE   39    3
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  CGY                          17                            39
  GY                            2                             3
[1] 2 2
[1] FALSE
D31V25, continuous
D31V26, continuous
D31V27, continuous
D31V28, continuous
D31V29, continuous
D31V30, 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                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  3(2Q22.1) MUTATED                         9                       0
  DEL PEAK  3(2Q22.1) WILD-TYPE                      26                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  3(2Q22.1) MUTATED                         3
  DEL PEAK  3(2Q22.1) WILD-TYPE                       5
D31V31, multiclass
                                     clus
vv                                    DEL PEAK  3(2Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       9
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    DEL PEAK  3(2Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        26
  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  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                                                7
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             18
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  3(2Q22.1) MUTATED                                                                                  14
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                                67
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  3(2Q22.1) MUTATED                                                                                             31
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                                           89
D31V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  3(2Q22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          31
                                                                                              clus
vv                                                                                             DEL PEAK  3(2Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V33, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   18 14
  DEL PEAK  3(2Q22.1) WILD-TYPE 52 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     18   14
  DEL PEAK  3(2Q22.1) WILD-TYPE   52   59
         clus
vv        DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  ABSENT                           18                            52
  PRESENT                          14                            59
[1] 2 2
[1] FALSE
D31V34, continuous
D31V35, continuous
D31V36, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   11 29
  DEL PEAK  3(2Q22.1) WILD-TYPE 37 87
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     11   29
  DEL PEAK  3(2Q22.1) WILD-TYPE   37   87
                                          clus
vv                                         DEL PEAK  3(2Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          29
                                          clus
vv                                         DEL PEAK  3(2Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            87
[1] 2 2
[1] FALSE
D31V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  3(2Q22.1) MUTATED              4          19         21
  DEL PEAK  3(2Q22.1) WILD-TYPE           11          34         63
D31V38, multiclass
              clus
vv             DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           19                            34
  NEVER USED                            21                            63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V39, continuous
D31V40, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   22  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 70 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     22    0
  DEL PEAK  3(2Q22.1) WILD-TYPE   70   17
         clus
vv        DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  ABSENT                           22                            70
  PRESENT                           0                            17
[1] 2 2
[1] FALSE
D31V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  3(2Q22.1) MUTATED      0   7   14    8  3   3    2    2   7  1   1
  DEL PEAK  3(2Q22.1) WILD-TYPE    1  27   55   22  3   7    5    7  29  1   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  3(2Q22.1) MUTATED     6  2   1  2
  DEL PEAK  3(2Q22.1) WILD-TYPE  11  6   0 14
D31V42, multiclass
      clus
vv     DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1A1                           0                             1
  T1B                            7                            27
  T1B1                          14                            55
  T1B2                           8                            22
  T2                             3                             3
  T2A                            3                             7
  T2A1                           2                             5
  T2A2                           2                             7
  T2B                            7                            29
  T3                             1                             1
  T3A                            1                             1
  T3B                            6                            11
  T4                             2                             6
  TIS                            1                             0
  TX                             2                            14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  3(2Q22.1) MUTATED         0        0         0         0        6
  DEL PEAK  3(2Q22.1) WILD-TYPE       5        1         1         1       27
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  3(2Q22.1) MUTATED          19         7        3         2
  DEL PEAK  3(2Q22.1) WILD-TYPE        58        29        1         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  3(2Q22.1) MUTATED            1          1         7         1
  DEL PEAK  3(2Q22.1) WILD-TYPE          4          6        36         0
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  3(2Q22.1) MUTATED            1          9         2         4
  DEL PEAK  3(2Q22.1) WILD-TYPE          2         33         5         8
D31V44, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             6                            27
  STAGE IB1                           19                            58
  STAGE IB2                            7                            29
  STAGE II                             3                             1
  STAGE IIA                            2                             6
  STAGE IIA1                           1                             4
  STAGE IIA2                           1                             6
  STAGE IIB                            7                            36
  STAGE III                            1                             0
  STAGE IIIA                           1                             2
  STAGE IIIB                           9                            33
  STAGE IVA                            2                             5
  STAGE IVB                            4                             8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK  4(2Q37.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.1) MUTATED    97  27
  DEL PEAK  4(2Q37.1) WILD-TYPE 116  38
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          124                           154 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                           27                            38 
$`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       210.67       134.33       155.77 
TCGA-C5-A7UH TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
      131.11        50.99        45.83         8.35        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       27.52        11.87         1.12        44.94        40.04        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        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A43B 
       12.36        30.90        13.05        25.02        24.56        26.01 
TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       12.66         7.46        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2R8 TCGA-EK-A2RD 
       45.96        26.27         1.51        19.27         1.45         0.03 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A69L 
        1.18         2.24         0.10         0.10         7.92        19.79 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A770 
        0.92        31.36         1.45         0.82         1.35         1.12 
TCGA-HM-A3JJ TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VL 
       21.67        29.85        36.36        27.42        21.44        15.58 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       21.11        30.31         7.99        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-MY-A5BF TCGA-MY-A913 
       13.35        22.52        17.82        11.38        20.84         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       15.58        16.41         9.04        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        12.16        10.03        40.50        37.78        26.43 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A953 
       18.05        59.51        11.51        57.93         4.73        15.68 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UC 
       48.07        50.14        45.34        44.94        42.41        22.72 
TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UU TCGA-VS-A9UY 
       19.69        40.96        27.25        41.42        14.53        18.25 
TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ 
       18.84        14.04        14.89        16.24        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZX-AA5X 
       67.59        19.13         0.69         3.91 

$`DEL PEAK  4(2Q37.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       12.39        49.48       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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF 
       44.22        73.45        83.05        38.43        33.24        17.85 
TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       20.42       154.32       101.82        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XJ 
       17.19        94.95         9.34        13.61         2.73       146.86 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZM TCGA-DS-A0VK 
       20.81        20.91        58.88        50.76        58.88        36.76 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       22.98        16.83        16.18        37.35        31.53        31.36 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO 
       14.50        26.40        14.50        12.82        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2PL 
       13.91        15.02        14.99        14.96         6.64         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         0.59         0.13        16.08         0.07         4.04 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 
        0.36        47.77         0.07         0.10         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70         8.32        15.55         1.22        23.84 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A57G 
        2.17        36.26         1.58         1.48         3.52         1.32 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         9.01        25.41        10.82        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B 
       78.71        81.96         3.29        24.56        20.48        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3X 
        8.28        18.15       195.85        11.28         0.89        20.28 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         9.17         8.52        13.87        34.62         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       54.81        35.05         2.96        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI 
       14.07        15.88         9.34        15.39        19.36        66.05 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM 
       19.96        32.15        46.03        36.13        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 
       36.26        16.64        24.39        39.78        50.86        50.63 
TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL 
       43.40        25.74        21.30        46.92         1.71        14.53 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V1 
       43.27        35.97        20.09         3.42        67.20         5.16 
TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        4.34        15.42         1.41         0.16 

  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                       210.67                        195.85 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                       19.640                        20.025 
[1] "0.0 - 210.7 (19.6)" "0.0 - 195.8 (20.0)"
[1] "hr=" "1.1"
D32V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  4(2Q37.1) MUTATED   65 25  9  3
  DEL PEAK  4(2Q37.1) WILD-TYPE 69 43 12  5
D32V3, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  T1                          65                            69
  T2                          25                            43
  T3                           9                            12
  T4                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   52 26
  DEL PEAK  4(2Q37.1) WILD-TYPE 75 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     52   26
  DEL PEAK  4(2Q37.1) WILD-TYPE   75   29
   clus
vv  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  0                          52                            75
  1                          26                            29
[1] 2 2
[1] FALSE
D32V5, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   51  2
  DEL PEAK  4(2Q37.1) WILD-TYPE 56  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     51    2
  DEL PEAK  4(2Q37.1) WILD-TYPE   56    8
   clus
vv  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  0                          51                            56
  1                           2                             8
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q37.1) MUTATED               1                              115
  DEL PEAK  4(2Q37.1) WILD-TYPE             4                              126
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  4(2Q37.1) MUTATED                                               2
  DEL PEAK  4(2Q37.1) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  4(2Q37.1) MUTATED                                     6
  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                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  4(2Q37.1) MUTATED                                              4
  DEL PEAK  4(2Q37.1) WILD-TYPE                                           11
D32V6, multiclass
                                               clus
vv                                              DEL PEAK  4(2Q37.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      115
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
                                               clus
vv                                              DEL PEAK  4(2Q37.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        126
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.1) MUTATED    13 115
  DEL PEAK  4(2Q37.1) WILD-TYPE  17 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     13  115
  DEL PEAK  4(2Q37.1) WILD-TYPE   17  147
     clus
vv    DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  NO                           13                            17
  YES                         115                           147
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.1) MUTATED                                  5    11
  DEL PEAK  4(2Q37.1) WILD-TYPE                                3     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(2Q37.1) MUTATED                          11
  DEL PEAK  4(2Q37.1) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(2Q37.1) MUTATED                                           1    87
  DEL PEAK  4(2Q37.1) WILD-TYPE                                         1   114
D32V10, multiclass
                                           clus
vv                                          DEL PEAK  4(2Q37.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    5
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              87
                                           clus
vv                                          DEL PEAK  4(2Q37.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            17
  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"
D32V11, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED    8 71
  DEL PEAK  4(2Q37.1) WILD-TYPE 15 90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED      8   71
  DEL PEAK  4(2Q37.1) WILD-TYPE   15   90
                        clus
vv                       DEL PEAK  4(2Q37.1) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       DEL PEAK  4(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                            90
[1] 2 2
[1] FALSE
D32V12, continuous
D32V13, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   59 17
  DEL PEAK  4(2Q37.1) WILD-TYPE 75 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     59   17
  DEL PEAK  4(2Q37.1) WILD-TYPE   75   24
            clus
vv           DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  TUMOR FREE                          59                            75
  WITH TUMOR                          17                            24
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  4(2Q37.1) MUTATED       27      3       0      5       3
  DEL PEAK  4(2Q37.1) WILD-TYPE     26      2       1      6       4
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  4(2Q37.1) MUTATED              82       8
  DEL PEAK  4(2Q37.1) WILD-TYPE           119       6
D32V14, multiclass
               clus
vv              DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  BRAZIL                                 27                            26
  CANADA                                  3                             2
  NIGERIA                                 0                             1
  RUSSIA                                  5                             6
  UKRAINE                                 3                             4
  UNITED STATES                          82                           119
  VIETNAM                                 8                             6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  4(2Q37.1) MUTATED    7 57 49  0 11
  DEL PEAK  4(2Q37.1) WILD-TYPE 11 72 64  1 13
D32V15, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  G1                           7                            11
  G2                          57                            72
  G3                          49                            64
  G4                           0                             1
  GX                          11                            13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V16, continuous
D32V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  4(2Q37.1) MUTATED                                            13
  DEL PEAK  4(2Q37.1) WILD-TYPE                                          24
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  4(2Q37.1) MUTATED                                        2
  DEL PEAK  4(2Q37.1) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  4(2Q37.1) MUTATED                                                 3
  DEL PEAK  4(2Q37.1) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  4(2Q37.1) MUTATED               26                  68
  DEL PEAK  4(2Q37.1) WILD-TYPE             36                  74
D32V18, multiclass
                                                 clus
vv                                                DEL PEAK  4(2Q37.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           3
  CURRENT SMOKER                                                           26
  LIFELONG NON-SMOKER                                                      68
                                                 clus
vv                                                DEL PEAK  4(2Q37.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             36
  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"
D32V19, continuous
D32V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  4(2Q37.1) MUTATED             7       48             6       11
  DEL PEAK  4(2Q37.1) WILD-TYPE          12       54             6       14
D32V21, multiclass
               clus
vv              DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               48                            54
  EXTERNAL BEAM                           6                             6
  INTERNAL                               11                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V22, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   10  2
  DEL PEAK  4(2Q37.1) WILD-TYPE 15  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     10    2
  DEL PEAK  4(2Q37.1) WILD-TYPE   15    1
                         clus
vv                        DEL PEAK  4(2Q37.1) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK  4(2Q37.1) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  4(2Q37.1) MUTATED                    1                2
  DEL PEAK  4(2Q37.1) WILD-TYPE                  1                0
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  4(2Q37.1) MUTATED                    20            16
  DEL PEAK  4(2Q37.1) WILD-TYPE                  16            17
D32V23, multiclass
                     clus
vv                    DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  DISTANT RECURRENCE                            1                             1
  LOCAL RECURRENCE                              2                             0
  PRIMARY TUMOR FIELD                          20                            16
  REGIONAL SITE                                16                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V24, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   29  3
  DEL PEAK  4(2Q37.1) WILD-TYPE 27  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     29    3
  DEL PEAK  4(2Q37.1) WILD-TYPE   27    2
     clus
vv    DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  CGY                          29                            27
  GY                            3                             2
[1] 2 2
[1] FALSE
D32V25, continuous
D32V26, continuous
D32V27, continuous
D32V28, continuous
D32V29, continuous
D32V30, 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                                     4
  DEL PEAK  4(2Q37.1) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  4(2Q37.1) MUTATED                        16                       1
  DEL PEAK  4(2Q37.1) WILD-TYPE                      19                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  4(2Q37.1) MUTATED                         2
  DEL PEAK  4(2Q37.1) WILD-TYPE                       6
D32V31, multiclass
                                     clus
vv                                    DEL PEAK  4(2Q37.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      16
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK  4(2Q37.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        19
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                               15
  DEL PEAK  4(2Q37.1) WILD-TYPE                                             10
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  4(2Q37.1) MUTATED                                                                                  32
  DEL PEAK  4(2Q37.1) WILD-TYPE                                                                                49
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  4(2Q37.1) MUTATED                                                                                             54
  DEL PEAK  4(2Q37.1) WILD-TYPE                                                                                           66
D32V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  4(2Q37.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     32
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          54
                                                                                              clus
vv                                                                                             DEL PEAK  4(2Q37.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       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"
D32V33, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   30 31
  DEL PEAK  4(2Q37.1) WILD-TYPE 40 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     30   31
  DEL PEAK  4(2Q37.1) WILD-TYPE   40   42
         clus
vv        DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  ABSENT                           30                            40
  PRESENT                          31                            42
[1] 2 2
[1] FALSE
D32V34, continuous
D32V35, continuous
D32V36, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   23 52
  DEL PEAK  4(2Q37.1) WILD-TYPE 25 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     23   52
  DEL PEAK  4(2Q37.1) WILD-TYPE   25   64
                                          clus
vv                                         DEL PEAK  4(2Q37.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          52
                                          clus
vv                                         DEL PEAK  4(2Q37.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            64
[1] 2 2
[1] FALSE
D32V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  4(2Q37.1) MUTATED              8          24         43
  DEL PEAK  4(2Q37.1) WILD-TYPE            7          29         41
D32V38, multiclass
              clus
vv             DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  CURRENT USER                           8                             7
  FORMER USER                           24                            29
  NEVER USED                            43                            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"
D32V39, continuous
D32V40, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   39  5
  DEL PEAK  4(2Q37.1) WILD-TYPE 53 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     39    5
  DEL PEAK  4(2Q37.1) WILD-TYPE   53   12
         clus
vv        DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  ABSENT                           39                            53
  PRESENT                           5                            12
[1] 2 2
[1] FALSE
D32V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  4(2Q37.1) MUTATED      0  17   36   12  2   4    1    5  13  0   1
  DEL PEAK  4(2Q37.1) WILD-TYPE    1  17   33   18  4   6    6    4  23  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  4(2Q37.1) MUTATED     8  3   1  7
  DEL PEAK  4(2Q37.1) WILD-TYPE   9  5   0  9
D32V42, multiclass
      clus
vv     DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  T1A1                           0                             1
  T1B                           17                            17
  T1B1                          36                            33
  T1B2                          12                            18
  T2                             2                             4
  T2A                            4                             6
  T2A1                           1                             6
  T2A2                           5                             4
  T2B                           13                            23
  T3                             0                             2
  T3A                            1                             1
  T3B                            8                             9
  T4                             3                             5
  TIS                            1                             0
  TX                             7                             9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  4(2Q37.1) MUTATED         2        0         0         0       18
  DEL PEAK  4(2Q37.1) WILD-TYPE       3        1         1         1       15
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  4(2Q37.1) MUTATED          36        14        3         3
  DEL PEAK  4(2Q37.1) WILD-TYPE        41        22        1         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  4(2Q37.1) MUTATED            0          3        18         0
  DEL PEAK  4(2Q37.1) WILD-TYPE          5          4        25         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  4(2Q37.1) MUTATED            1         19         4         3
  DEL PEAK  4(2Q37.1) WILD-TYPE          2         23         3         9
D32V44, multiclass
            clus
vv           DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            18                            15
  STAGE IB1                           36                            41
  STAGE IB2                           14                            22
  STAGE II                             3                             1
  STAGE IIA                            3                             5
  STAGE IIA1                           0                             5
  STAGE IIA2                           3                             4
  STAGE IIB                           18                            25
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          19                            23
  STAGE IVA                            4                             3
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  5(3P14.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P14.2) MUTATED    89  34
  DEL PEAK  5(3P14.2) WILD-TYPE 124  31
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                          123                           155 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           34                            31 
$`DEL PEAK  5(3P14.2) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI 
       12.39        49.48        23.67        11.44        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1MF 
      144.16       173.29         5.46        31.40        30.21        53.16 
TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD 
       35.61        20.91        40.93        73.18        83.05        52.01 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE 
      154.32       101.82       134.33        15.48       147.35       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ 
      131.11        94.95        13.61         2.73        45.83       146.86 
TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK 
       23.51        20.91        58.88        40.04        87.75        36.76 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HS 
      117.99       118.65        16.83        17.52        12.36        31.53 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E 
       13.05        25.02        24.56        14.50        12.66         7.46 
TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ 
       14.89        14.99        14.96        13.58         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM 
       45.96         6.64         1.51        19.27         0.43         0.59 
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-HG-A9SC 
       31.36         1.45         3.52         1.97        25.41        10.82 
TCGA-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ 
       21.67       147.39        78.71        29.85        24.56        21.44 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A5YI 
       18.15        21.11        30.31         9.17         8.52        34.62 
TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 
        5.49        16.41         9.04         9.34        19.36         3.88 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI 
       93.99        12.16        10.03        40.50        26.43        18.05 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        36.13        11.51        57.93        39.78 
TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 
       31.27         4.73        24.39        39.78        15.68        48.07 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH 
       45.34        44.94        43.40        25.74        19.69        46.92 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UV TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       14.53        27.25        43.27         3.42        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
       19.13         0.69         0.16 

$`DEL PEAK  5(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 
       33.24        18.02        17.85        20.42       210.67        20.35 
TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR 
       17.19         9.34        50.99         8.35        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM 
       20.81        11.87         1.12        50.76        44.94        58.88 
TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
        2.66        22.98        16.18         8.28        39.55        37.35 
TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA 
       30.90        31.36        14.50        26.40        26.01        12.82 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2R8 
       26.79        13.91        15.02        13.48        26.27         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        0.13        16.08         0.03         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
        0.10         0.07         0.10         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.92         2.17        36.26         1.58         1.48         0.82 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.35         1.32         1.12         9.01        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
        9.44       137.16        66.81       117.40        96.95        81.96 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        27.42         3.29        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
        8.28       195.85         7.99        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       19.56        11.38        13.87         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84         2.96        15.58        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PI 
       14.07        15.88        15.39        19.59        11.67        66.05 
TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A952 
       37.78        19.96        59.51        36.26        16.64        50.86 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UI 
       50.63        50.14        42.41        21.30        22.72        40.96 
TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UY 
        1.71        41.42        35.97        20.09        14.53        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        14.04        14.89         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       16.24        15.42        26.01         1.41         3.91 

  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                       173.29                        210.67 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                        23.67                         17.82 
[1] "0.1 - 173.3 (23.7)" "0.0 - 210.7 (17.8)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  5(3P14.2) MUTATED   51 23 14  5
  DEL PEAK  5(3P14.2) WILD-TYPE 83 45  7  3
D33V3, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  T1                          51                            83
  T2                          23                            45
  T3                          14                             7
  T4                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   42 30
  DEL PEAK  5(3P14.2) WILD-TYPE 85 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     42   30
  DEL PEAK  5(3P14.2) WILD-TYPE   85   25
   clus
vv  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  0                          42                            85
  1                          30                            25
[1] 2 2
[1] FALSE
D33V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   48  5
  DEL PEAK  5(3P14.2) WILD-TYPE 59  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     48    5
  DEL PEAK  5(3P14.2) WILD-TYPE   59    5
   clus
vv  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  0                          48                            59
  1                           5                             5
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(3P14.2) MUTATED               2                              123
  DEL PEAK  5(3P14.2) WILD-TYPE             3                              118
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  5(3P14.2) MUTATED                                               1
  DEL PEAK  5(3P14.2) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  5(3P14.2) MUTATED                                     2
  DEL PEAK  5(3P14.2) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  5(3P14.2) MUTATED                                           1
  DEL PEAK  5(3P14.2) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  5(3P14.2) MUTATED                                              3
  DEL PEAK  5(3P14.2) WILD-TYPE                                           12
D33V6, multiclass
                                               clus
vv                                              DEL PEAK  5(3P14.2) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              DEL PEAK  5(3P14.2) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        118
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P14.2) MUTATED    19 113
  DEL PEAK  5(3P14.2) WILD-TYPE  11 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     19  113
  DEL PEAK  5(3P14.2) WILD-TYPE   11  149
     clus
vv    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  NO                           19                            11
  YES                         113                           149
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P14.2) MUTATED                                  2     8
  DEL PEAK  5(3P14.2) WILD-TYPE                                6    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(3P14.2) MUTATED                          13
  DEL PEAK  5(3P14.2) WILD-TYPE                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(3P14.2) MUTATED                                           1    92
  DEL PEAK  5(3P14.2) WILD-TYPE                                         1   109
D33V10, multiclass
                                           clus
vv                                          DEL PEAK  5(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              92
                                           clus
vv                                          DEL PEAK  5(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            15
  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"
D33V11, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED    7 72
  DEL PEAK  5(3P14.2) WILD-TYPE 16 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED      7   72
  DEL PEAK  5(3P14.2) WILD-TYPE   16   89
                        clus
vv                       DEL PEAK  5(3P14.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          72
                        clus
vv                       DEL PEAK  5(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                            89
[1] 2 2
[1] FALSE
D33V12, continuous
D33V13, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   55 21
  DEL PEAK  5(3P14.2) WILD-TYPE 79 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     55   21
  DEL PEAK  5(3P14.2) WILD-TYPE   79   20
            clus
vv           DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  TUMOR FREE                          55                            79
  WITH TUMOR                          21                            20
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  5(3P14.2) MUTATED       27      2       0      6       2
  DEL PEAK  5(3P14.2) WILD-TYPE     26      3       1      5       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  5(3P14.2) MUTATED              89       6
  DEL PEAK  5(3P14.2) WILD-TYPE           112       8
D33V14, multiclass
               clus
vv              DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  BRAZIL                                 27                            26
  CANADA                                  2                             3
  NIGERIA                                 0                             1
  RUSSIA                                  6                             5
  UKRAINE                                 2                             5
  UNITED STATES                          89                           112
  VIETNAM                                 6                             8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  5(3P14.2) MUTATED    4 57 49  1 14
  DEL PEAK  5(3P14.2) WILD-TYPE 14 72 64  0 10
D33V15, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  G1                           4                            14
  G2                          57                            72
  G3                          49                            64
  G4                           1                             0
  GX                          14                            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"
D33V16, continuous
D33V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  5(3P14.2) MUTATED                                            16
  DEL PEAK  5(3P14.2) WILD-TYPE                                          21
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  5(3P14.2) MUTATED                                        2
  DEL PEAK  5(3P14.2) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  5(3P14.2) MUTATED                                                 3
  DEL PEAK  5(3P14.2) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  5(3P14.2) MUTATED               40                  52
  DEL PEAK  5(3P14.2) WILD-TYPE             22                  90
D33V18, multiclass
                                                 clus
vv                                                DEL PEAK  5(3P14.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           3
  CURRENT SMOKER                                                           40
  LIFELONG NON-SMOKER                                                      52
                                                 clus
vv                                                DEL PEAK  5(3P14.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             22
  LIFELONG NON-SMOKER                                                        90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V19, continuous
D33V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  5(3P14.2) MUTATED            12       48             7        8
  DEL PEAK  5(3P14.2) WILD-TYPE           7       54             5       17
D33V21, multiclass
               clus
vv              DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  COMBINATION                            12                             7
  EXTERNAL                               48                            54
  EXTERNAL BEAM                           7                             5
  INTERNAL                                8                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V22, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   16  2
  DEL PEAK  5(3P14.2) WILD-TYPE  9  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     16    2
  DEL PEAK  5(3P14.2) WILD-TYPE    9    1
                         clus
vv                        DEL PEAK  5(3P14.2) MUTATED
  COMPLETED AS PLANNED                             16
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK  5(3P14.2) WILD-TYPE
  COMPLETED AS PLANNED                                9
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  5(3P14.2) MUTATED                    1                2
  DEL PEAK  5(3P14.2) WILD-TYPE                  1                0
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  5(3P14.2) MUTATED                    17            17
  DEL PEAK  5(3P14.2) WILD-TYPE                  19            16
D33V23, multiclass
                     clus
vv                    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  DISTANT RECURRENCE                            1                             1
  LOCAL RECURRENCE                              2                             0
  PRIMARY TUMOR FIELD                          17                            19
  REGIONAL SITE                                17                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V24, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   28  2
  DEL PEAK  5(3P14.2) WILD-TYPE 28  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     28    2
  DEL PEAK  5(3P14.2) WILD-TYPE   28    3
     clus
vv    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CGY                          28                            28
  GY                            2                             3
[1] 2 2
[1] FALSE
D33V25, continuous
D33V26, continuous
D33V27, continuous
D33V28, continuous
D33V29, continuous
D33V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  5(3P14.2) MUTATED                                     0
  DEL PEAK  5(3P14.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  5(3P14.2) MUTATED                                     4
  DEL PEAK  5(3P14.2) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  5(3P14.2) MUTATED                        10                       1
  DEL PEAK  5(3P14.2) WILD-TYPE                      25                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  5(3P14.2) MUTATED                         5
  DEL PEAK  5(3P14.2) WILD-TYPE                       3
D33V31, multiclass
                                     clus
vv                                    DEL PEAK  5(3P14.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      10
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       5
                                     clus
vv                                    DEL PEAK  5(3P14.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        25
  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)
  DEL PEAK  5(3P14.2) MUTATED                                               1
  DEL PEAK  5(3P14.2) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  5(3P14.2) MUTATED                                               11
  DEL PEAK  5(3P14.2) WILD-TYPE                                             14
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  5(3P14.2) MUTATED                                                                                  33
  DEL PEAK  5(3P14.2) WILD-TYPE                                                                                48
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  5(3P14.2) MUTATED                                                                                             53
  DEL PEAK  5(3P14.2) WILD-TYPE                                                                                           67
D33V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  5(3P14.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          53
                                                                                              clus
vv                                                                                             DEL PEAK  5(3P14.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            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"
D33V33, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   17 36
  DEL PEAK  5(3P14.2) WILD-TYPE 53 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     17   36
  DEL PEAK  5(3P14.2) WILD-TYPE   53   37
         clus
vv        DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  ABSENT                           17                            53
  PRESENT                          36                            37
[1] 2 2
[1] FALSE
D33V34, continuous
D33V35, continuous
D33V36, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   25 52
  DEL PEAK  5(3P14.2) WILD-TYPE 23 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     25   52
  DEL PEAK  5(3P14.2) WILD-TYPE   23   64
                                          clus
vv                                         DEL PEAK  5(3P14.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          52
                                          clus
vv                                         DEL PEAK  5(3P14.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            64
[1] 2 2
[1] FALSE
D33V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  5(3P14.2) MUTATED              3          30         36
  DEL PEAK  5(3P14.2) WILD-TYPE           12          23         48
D33V38, multiclass
              clus
vv             DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           30                            23
  NEVER USED                            36                            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"
D33V39, continuous
D33V40, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   33  8
  DEL PEAK  5(3P14.2) WILD-TYPE 59  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     33    8
  DEL PEAK  5(3P14.2) WILD-TYPE   59    9
         clus
vv        DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  ABSENT                           33                            59
  PRESENT                           8                             9
[1] 2 2
[1] FALSE
D33V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  5(3P14.2) MUTATED      1  10   29   11  3   3    3    2  12  1   2
  DEL PEAK  5(3P14.2) WILD-TYPE    0  24   40   19  3   7    4    7  24  1   0
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  5(3P14.2) MUTATED    11  5   1 10
  DEL PEAK  5(3P14.2) WILD-TYPE   6  3   0  6
D33V42, multiclass
      clus
vv     DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  T1A1                           1                             0
  T1B                           10                            24
  T1B1                          29                            40
  T1B2                          11                            19
  T2                             3                             3
  T2A                            3                             7
  T2A1                           3                             4
  T2A2                           2                             7
  T2B                           12                            24
  T3                             1                             1
  T3A                            2                             0
  T3B                           11                             6
  T4                             5                             3
  TIS                            1                             0
  TX                            10                             6
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  5(3P14.2) MUTATED         3        0         1         0       15
  DEL PEAK  5(3P14.2) WILD-TYPE       2        1         0         1       18
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  5(3P14.2) MUTATED          31        12        1         4
  DEL PEAK  5(3P14.2) WILD-TYPE        46        24        3         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  5(3P14.2) MUTATED            3          0        23         0
  DEL PEAK  5(3P14.2) WILD-TYPE          2          7        20         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  5(3P14.2) MUTATED            3         22         6         5
  DEL PEAK  5(3P14.2) WILD-TYPE          0         20         1         7
D33V44, multiclass
            clus
vv           DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                             0                             1
  STAGE IA1                            1                             0
  STAGE IA2                            0                             1
  STAGE IB                            15                            18
  STAGE IB1                           31                            46
  STAGE IB2                           12                            24
  STAGE II                             1                             3
  STAGE IIA                            4                             4
  STAGE IIA1                           3                             2
  STAGE IIA2                           0                             7
  STAGE IIB                           23                            20
  STAGE III                            0                             1
  STAGE IIIA                           3                             0
  STAGE IIIB                          22                            20
  STAGE IVA                            6                             1
  STAGE IVB                            5                             7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK  6(4Q21.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4Q21.3) MUTATED    68  26
  DEL PEAK  6(4Q21.3) WILD-TYPE 145  39
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                           94                           184 
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                           26                            39 
$`DEL PEAK  6(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-A1ML TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD 
       35.61        20.91        73.18        73.45        83.05        52.01 
TCGA-C5-A3HE TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
       18.02       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK 
      131.11         9.34        13.61         2.73        45.83        99.91 
TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VN 
       27.52        20.91        58.88        40.04        87.75       118.65 
TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A556 
       12.36        24.56        14.50        26.01         7.46        14.89 
TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG 
       15.02        13.48         0.36        12.59        26.27         1.51 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
        0.59         0.59         1.45        16.08         1.18         2.24 
TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA 
        0.10        20.35         6.94         1.45         1.97         9.01 
TCGA-HM-A3JJ TCGA-JW-A5VK TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3X 
       21.67        20.48         7.99        11.28         0.89        20.28 
TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 
       17.82         9.17        11.38         5.49         2.96        16.41 
TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI 
       19.36        11.67        12.16        10.03        26.43        18.05 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       19.96        32.15        31.27        36.26        16.64         4.73 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       39.78        15.68        48.07        50.14        45.34        44.94 
TCGA-VS-A9U6 TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9V0 TCGA-VS-A9V2 
       43.40        46.92        14.53        41.42        18.84        14.04 
TCGA-VS-A9V4 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA 
        4.34        26.01        29.26         1.41 

$`DEL PEAK  6(4Q21.3) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VS TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       12.39        57.04        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 
       33.24        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ 
      155.77        94.95        50.99         8.35       146.86        23.51 
TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM 
       20.81        11.87         1.12        50.76        44.94        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-A3HR TCGA-EA-A3HS 
       17.52         8.28        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S 
       31.36        13.05        25.02        14.50        26.40        12.66 
TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.82        26.79        13.91        14.99        14.96        13.58 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RB 
       45.96         6.64        19.27         0.43         0.13         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        47.77         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.10         0.03         7.92        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.55         1.22        23.84         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.12        25.41        10.82        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       21.11       195.85        30.31        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI 
       13.35        22.52        19.56         8.52        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
        5.42        54.81        35.05        20.84        15.58        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC 
       15.39        19.59         3.88        93.99        66.05        40.50 
TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       37.78        59.51        46.03        36.13        11.51        57.93 
TCGA-VS-A8QH TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UA 
       39.78        24.39        50.86        50.63        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM 
       21.30        22.72        19.69        40.96         1.71        27.25 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       43.27        35.97        20.09        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       67.20         5.16        14.89        16.24        15.42        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         0.16         3.91 

  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                       147.35                        210.67 
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                       18.035                        20.600 
[1] "0.1 - 147.3 (18.0)" "0.0 - 210.7 (20.6)"
[1] "hr=" "1.5"
D34V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  6(4Q21.3) MUTATED   43 20  9  5
  DEL PEAK  6(4Q21.3) WILD-TYPE 91 48 12  3
D34V3, multiclass
    clus
vv   DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  T1                          43                            91
  T2                          20                            48
  T3                           9                            12
  T4                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   32 25
  DEL PEAK  6(4Q21.3) WILD-TYPE 95 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     32   25
  DEL PEAK  6(4Q21.3) WILD-TYPE   95   30
   clus
vv  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  0                          32                            95
  1                          25                            30
[1] 2 2
[1] FALSE
D34V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   34  6
  DEL PEAK  6(4Q21.3) WILD-TYPE 73  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     34    6
  DEL PEAK  6(4Q21.3) WILD-TYPE   73    4
   clus
vv  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  0                          34                            73
  1                           6                             4
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(4Q21.3) MUTATED               1                               91
  DEL PEAK  6(4Q21.3) WILD-TYPE             4                              150
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  6(4Q21.3) MUTATED                                               2
  DEL PEAK  6(4Q21.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  6(4Q21.3) MUTATED                                     1
  DEL PEAK  6(4Q21.3) WILD-TYPE                                  21
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  6(4Q21.3) MUTATED                                           1
  DEL PEAK  6(4Q21.3) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  6(4Q21.3) MUTATED                                              4
  DEL PEAK  6(4Q21.3) WILD-TYPE                                           11
D34V6, multiclass
                                               clus
vv                                              DEL PEAK  6(4Q21.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       91
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
                                               clus
vv                                              DEL PEAK  6(4Q21.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        150
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q21.3) MUTATED    12  88
  DEL PEAK  6(4Q21.3) WILD-TYPE  18 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     12   88
  DEL PEAK  6(4Q21.3) WILD-TYPE   18  174
     clus
vv    DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  NO                           12                            18
  YES                          88                           174
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(4Q21.3) MUTATED                                  1     7
  DEL PEAK  6(4Q21.3) WILD-TYPE                                7    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(4Q21.3) MUTATED                          15
  DEL PEAK  6(4Q21.3) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(4Q21.3) MUTATED                                           0    67
  DEL PEAK  6(4Q21.3) WILD-TYPE                                         2   134
D34V10, multiclass
                                           clus
vv                                          DEL PEAK  6(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              67
                                           clus
vv                                          DEL PEAK  6(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q21.3) MUTATED     8  54
  DEL PEAK  6(4Q21.3) WILD-TYPE  15 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED      8   54
  DEL PEAK  6(4Q21.3) WILD-TYPE   15  107
                        clus
vv                       DEL PEAK  6(4Q21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK  6(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           107
[1] 2 2
[1] FALSE
D34V12, continuous
D34V13, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   38 15
  DEL PEAK  6(4Q21.3) WILD-TYPE 96 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     38   15
  DEL PEAK  6(4Q21.3) WILD-TYPE   96   26
            clus
vv           DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  TUMOR FREE                          38                            96
  WITH TUMOR                          15                            26
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  6(4Q21.3) MUTATED       23      2       1      3       2
  DEL PEAK  6(4Q21.3) WILD-TYPE     30      3       0      8       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  6(4Q21.3) MUTATED              63       6
  DEL PEAK  6(4Q21.3) WILD-TYPE           138       8
D34V14, multiclass
               clus
vv              DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  BRAZIL                                 23                            30
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  3                             8
  UKRAINE                                 2                             5
  UNITED STATES                          63                           138
  VIETNAM                                 6                             8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  6(4Q21.3) MUTATED    2 39 50  0  7
  DEL PEAK  6(4Q21.3) WILD-TYPE 16 90 63  1 17
D34V15, multiclass
    clus
vv   DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  G1                           2                            16
  G2                          39                            90
  G3                          50                            63
  G4                           0                             1
  GX                           7                            17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V16, continuous
D34V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  6(4Q21.3) MUTATED                                            11
  DEL PEAK  6(4Q21.3) WILD-TYPE                                          26
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  6(4Q21.3) MUTATED                                        4
  DEL PEAK  6(4Q21.3) WILD-TYPE                                      5
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  6(4Q21.3) MUTATED                                                 3
  DEL PEAK  6(4Q21.3) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  6(4Q21.3) MUTATED               22                  41
  DEL PEAK  6(4Q21.3) WILD-TYPE             40                 101
D34V18, multiclass
                                                 clus
vv                                                DEL PEAK  6(4Q21.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           3
  CURRENT SMOKER                                                           22
  LIFELONG NON-SMOKER                                                      41
                                                 clus
vv                                                DEL PEAK  6(4Q21.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             40
  LIFELONG NON-SMOKER                                                       101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V19, continuous
D34V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  6(4Q21.3) MUTATED             7       35             4       11
  DEL PEAK  6(4Q21.3) WILD-TYPE          12       67             8       14
D34V21, multiclass
               clus
vv              DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               35                            67
  EXTERNAL BEAM                           4                             8
  INTERNAL                               11                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V22, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   10  1
  DEL PEAK  6(4Q21.3) WILD-TYPE 15  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     10    1
  DEL PEAK  6(4Q21.3) WILD-TYPE   15    2
                         clus
vv                        DEL PEAK  6(4Q21.3) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        DEL PEAK  6(4Q21.3) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  6(4Q21.3) MUTATED                    0                2
  DEL PEAK  6(4Q21.3) WILD-TYPE                  2                0
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  6(4Q21.3) MUTATED                    14            15
  DEL PEAK  6(4Q21.3) WILD-TYPE                  22            18
D34V23, multiclass
                     clus
vv                    DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              2                             0
  PRIMARY TUMOR FIELD                          14                            22
  REGIONAL SITE                                15                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V24, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   21  3
  DEL PEAK  6(4Q21.3) WILD-TYPE 35  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     21    3
  DEL PEAK  6(4Q21.3) WILD-TYPE   35    2
     clus
vv    DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  CGY                          21                            35
  GY                            3                             2
[1] 2 2
[1] FALSE
D34V25, continuous
D34V26, continuous
D34V27, continuous
D34V28, continuous
D34V29, continuous
D34V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  6(4Q21.3) MUTATED                                     0
  DEL PEAK  6(4Q21.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  6(4Q21.3) MUTATED                                     4
  DEL PEAK  6(4Q21.3) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  6(4Q21.3) MUTATED                        12                       1
  DEL PEAK  6(4Q21.3) WILD-TYPE                      23                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  6(4Q21.3) MUTATED                         1
  DEL PEAK  6(4Q21.3) WILD-TYPE                       7
D34V31, multiclass
                                     clus
vv                                    DEL PEAK  6(4Q21.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      12
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  6(4Q21.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        23
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  6(4Q21.3) MUTATED                                               0
  DEL PEAK  6(4Q21.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  6(4Q21.3) MUTATED                                                8
  DEL PEAK  6(4Q21.3) WILD-TYPE                                             17
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  6(4Q21.3) MUTATED                                                                                  24
  DEL PEAK  6(4Q21.3) WILD-TYPE                                                                                57
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  6(4Q21.3) MUTATED                                                                                             40
  DEL PEAK  6(4Q21.3) WILD-TYPE                                                                                           80
D34V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  6(4Q21.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     24
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          40
                                                                                              clus
vv                                                                                             DEL PEAK  6(4Q21.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V33, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   19 24
  DEL PEAK  6(4Q21.3) WILD-TYPE 51 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     19   24
  DEL PEAK  6(4Q21.3) WILD-TYPE   51   49
         clus
vv        DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  ABSENT                           19                            51
  PRESENT                          24                            49
[1] 2 2
[1] FALSE
D34V34, continuous
D34V35, continuous
D34V36, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   19 41
  DEL PEAK  6(4Q21.3) WILD-TYPE 29 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     19   41
  DEL PEAK  6(4Q21.3) WILD-TYPE   29   75
                                          clus
vv                                         DEL PEAK  6(4Q21.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          41
                                          clus
vv                                         DEL PEAK  6(4Q21.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            75
[1] 2 2
[1] FALSE
D34V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  6(4Q21.3) MUTATED              4          17         30
  DEL PEAK  6(4Q21.3) WILD-TYPE           11          36         54
D34V38, multiclass
              clus
vv             DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           17                            36
  NEVER USED                            30                            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"
D34V39, continuous
D34V40, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   23  7
  DEL PEAK  6(4Q21.3) WILD-TYPE 69 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     23    7
  DEL PEAK  6(4Q21.3) WILD-TYPE   69   10
         clus
vv        DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  ABSENT                           23                            69
  PRESENT                           7                            10
[1] 2 2
[1] FALSE
D34V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  6(4Q21.3) MUTATED      0  15   20    8  3   1    2    1  13  0   1
  DEL PEAK  6(4Q21.3) WILD-TYPE    1  19   49   22  3   9    5    8  23  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  6(4Q21.3) MUTATED     8  5   1  2
  DEL PEAK  6(4Q21.3) WILD-TYPE   9  3   0 14
D34V42, multiclass
      clus
vv     DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  T1A1                           0                             1
  T1B                           15                            19
  T1B1                          20                            49
  T1B2                           8                            22
  T2                             3                             3
  T2A                            1                             9
  T2A1                           2                             5
  T2A2                           1                             8
  T2B                           13                            23
  T3                             0                             2
  T3A                            1                             1
  T3B                            8                             9
  T4                             5                             3
  TIS                            1                             0
  TX                             2                            14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  6(4Q21.3) MUTATED         0        1         0         1       12
  DEL PEAK  6(4Q21.3) WILD-TYPE       5        0         1         0       21
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  6(4Q21.3) MUTATED          23        13        0         2
  DEL PEAK  6(4Q21.3) WILD-TYPE        54        23        4         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  6(4Q21.3) MUTATED            2          1        17         0
  DEL PEAK  6(4Q21.3) WILD-TYPE          3          6        26         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  6(4Q21.3) MUTATED            1         15         5         3
  DEL PEAK  6(4Q21.3) WILD-TYPE          2         27         2         9
D34V44, multiclass
            clus
vv           DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            12                            21
  STAGE IB1                           23                            54
  STAGE IB2                           13                            23
  STAGE II                             0                             4
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           1                             6
  STAGE IIB                           17                            26
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          15                            27
  STAGE IVA                            5                             2
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK  7(4Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q22.1) MUTATED    69  23
  DEL PEAK  7(4Q22.1) WILD-TYPE 144  42
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           92                           186 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           23                            42 
$`DEL PEAK  7(4Q22.1) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 
       12.39        49.48        23.67        11.44         5.46        31.40 
TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD 
       35.61        20.91        73.18        73.45        83.05        52.01 
TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
       18.02        15.48        20.35       147.35        17.19       131.11 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR 
        9.34        13.61         2.73        45.83        99.91        27.52 
TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-EA-A1QT TCGA-EA-A411 
       20.91        58.88        40.04        87.75        12.36        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.50        26.01        14.89        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       45.96        26.27         1.51         0.59         0.59         1.45 
TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 
       16.08         1.18         2.24         0.10        20.35         6.94 
TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3LK TCGA-JW-A5VK 
        1.45         1.97         9.01        21.67        29.85        20.48 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MY-A913 
        7.99        11.28         0.89        20.28        11.38         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB 
        2.96        16.41        19.36        11.67        12.16        10.03 
TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QF 
       40.50        26.43        18.05        19.96        32.15        57.93 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 
       31.27        36.26         4.73        39.78        15.68        48.07 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UH TCGA-VS-A9UL 
       50.14        45.34        44.94        43.40        46.92        14.53 
TCGA-VS-A9UO TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-WL-A834 TCGA-XS-A8TJ 
       41.42        18.84        14.04         4.34        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       67.59         1.41 

$`DEL PEAK  7(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 
       33.24        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
      134.33       155.77        94.95        50.99         8.35       146.86 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       23.51        20.81        11.87         1.12        50.76        44.94 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18        17.52         8.28        39.55        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        14.50 
TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       26.40        12.66        12.82         7.46        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PI 
       15.02        14.99        14.96        13.58         6.64        19.27 
TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.43         0.13         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
       47.77         0.07         0.10         0.10         0.03         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17        31.36        36.26         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.35         1.32         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       10.82        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL 
       66.81       117.40        96.95        78.71        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AX 
        8.28        18.15        21.11       195.85        30.31        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30         0.82        13.35        22.52        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        9.17         8.52        13.87        34.62         5.42        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       35.05        20.84        15.58        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
       17.56        14.07        15.88         9.34        15.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q9 
        3.88        93.99        66.05        37.78        59.51        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       36.13        11.51        39.78        16.64        24.39        50.86 
TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       50.63        42.41        25.74        21.30        22.72        19.69 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       40.96         1.71        27.25        43.27        35.97        20.09 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 
       14.53         3.42        18.25        67.20         5.16        14.89 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       16.24        15.42        19.13         0.69         0.16         3.91 

  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                       147.35                        210.67 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                       19.660                        19.825 
[1] "0.1 - 147.3 (19.7)" "0.0 - 210.7 (19.8)"
[1] "hr=" "1.3"
D35V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  7(4Q22.1) MUTATED   42 17 10  4
  DEL PEAK  7(4Q22.1) WILD-TYPE 92 51 11  4
D35V3, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  T1                          42                            92
  T2                          17                            51
  T3                          10                            11
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   32 21
  DEL PEAK  7(4Q22.1) WILD-TYPE 95 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     32   21
  DEL PEAK  7(4Q22.1) WILD-TYPE   95   34
   clus
vv  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  0                          32                            95
  1                          21                            34
[1] 2 2
[1] FALSE
D35V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   34  5
  DEL PEAK  7(4Q22.1) WILD-TYPE 73  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     34    5
  DEL PEAK  7(4Q22.1) WILD-TYPE   73    5
   clus
vv  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  0                          34                            73
  1                           5                             5
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(4Q22.1) MUTATED               1                               88
  DEL PEAK  7(4Q22.1) WILD-TYPE             4                              153
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  7(4Q22.1) MUTATED                                               2
  DEL PEAK  7(4Q22.1) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  7(4Q22.1) MUTATED                                     1
  DEL PEAK  7(4Q22.1) WILD-TYPE                                  21
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  7(4Q22.1) MUTATED                                           1
  DEL PEAK  7(4Q22.1) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  7(4Q22.1) MUTATED                                              4
  DEL PEAK  7(4Q22.1) WILD-TYPE                                           11
D35V6, multiclass
                                               clus
vv                                              DEL PEAK  7(4Q22.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       88
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
                                               clus
vv                                              DEL PEAK  7(4Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    11  86
  DEL PEAK  7(4Q22.1) WILD-TYPE  19 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     11   86
  DEL PEAK  7(4Q22.1) WILD-TYPE   19  176
     clus
vv    DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  NO                           11                            19
  YES                          86                           176
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(4Q22.1) MUTATED                                  1     5
  DEL PEAK  7(4Q22.1) WILD-TYPE                                7    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(4Q22.1) MUTATED                          14
  DEL PEAK  7(4Q22.1) WILD-TYPE                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(4Q22.1) MUTATED                                           0    67
  DEL PEAK  7(4Q22.1) WILD-TYPE                                         2   134
D35V10, multiclass
                                           clus
vv                                          DEL PEAK  7(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              67
                                           clus
vv                                          DEL PEAK  7(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED     6  52
  DEL PEAK  7(4Q22.1) WILD-TYPE  17 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED      6   52
  DEL PEAK  7(4Q22.1) WILD-TYPE   17  109
                        clus
vv                       DEL PEAK  7(4Q22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       DEL PEAK  7(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           109
[1] 2 2
[1] FALSE
D35V12, continuous
D35V13, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   39 13
  DEL PEAK  7(4Q22.1) WILD-TYPE 95 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     39   13
  DEL PEAK  7(4Q22.1) WILD-TYPE   95   28
            clus
vv           DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  TUMOR FREE                          39                            95
  WITH TUMOR                          13                            28
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  7(4Q22.1) MUTATED       24      2       1      4       2
  DEL PEAK  7(4Q22.1) WILD-TYPE     29      3       0      7       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  7(4Q22.1) MUTATED              60       4
  DEL PEAK  7(4Q22.1) WILD-TYPE           141      10
D35V14, multiclass
               clus
vv              DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  BRAZIL                                 24                            29
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  4                             7
  UKRAINE                                 2                             5
  UNITED STATES                          60                           141
  VIETNAM                                 4                            10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  7(4Q22.1) MUTATED    2 34 52  0  8
  DEL PEAK  7(4Q22.1) WILD-TYPE 16 95 61  1 16
D35V15, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  G1                           2                            16
  G2                          34                            95
  G3                          52                            61
  G4                           0                             1
  GX                           8                            16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V16, continuous
D35V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  7(4Q22.1) MUTATED                                            11
  DEL PEAK  7(4Q22.1) WILD-TYPE                                          26
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  7(4Q22.1) MUTATED                                        3
  DEL PEAK  7(4Q22.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  7(4Q22.1) MUTATED                                                 2
  DEL PEAK  7(4Q22.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  7(4Q22.1) MUTATED               22                  38
  DEL PEAK  7(4Q22.1) WILD-TYPE             40                 104
D35V18, multiclass
                                                 clus
vv                                                DEL PEAK  7(4Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           22
  LIFELONG NON-SMOKER                                                      38
                                                 clus
vv                                                DEL PEAK  7(4Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             40
  LIFELONG NON-SMOKER                                                       104
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V19, continuous
D35V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  7(4Q22.1) MUTATED             6       38             4       11
  DEL PEAK  7(4Q22.1) WILD-TYPE          13       64             8       14
D35V21, multiclass
               clus
vv              DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  COMBINATION                             6                            13
  EXTERNAL                               38                            64
  EXTERNAL BEAM                           4                             8
  INTERNAL                               11                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V22, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED    9  2
  DEL PEAK  7(4Q22.1) WILD-TYPE 16  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED      9    2
  DEL PEAK  7(4Q22.1) WILD-TYPE   16    1
                         clus
vv                        DEL PEAK  7(4Q22.1) MUTATED
  COMPLETED AS PLANNED                              9
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK  7(4Q22.1) WILD-TYPE
  COMPLETED AS PLANNED                               16
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  7(4Q22.1) MUTATED                    0                2
  DEL PEAK  7(4Q22.1) WILD-TYPE                  2                0
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  7(4Q22.1) MUTATED                    13            16
  DEL PEAK  7(4Q22.1) WILD-TYPE                  23            17
D35V23, multiclass
                     clus
vv                    DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              2                             0
  PRIMARY TUMOR FIELD                          13                            23
  REGIONAL SITE                                16                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V24, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   22  3
  DEL PEAK  7(4Q22.1) WILD-TYPE 34  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     22    3
  DEL PEAK  7(4Q22.1) WILD-TYPE   34    2
     clus
vv    DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  CGY                          22                            34
  GY                            3                             2
[1] 2 2
[1] FALSE
D35V25, continuous
D35V26, continuous
D35V27, continuous
D35V28, continuous
D35V29, continuous
D35V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  7(4Q22.1) MUTATED                                     0
  DEL PEAK  7(4Q22.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  7(4Q22.1) MUTATED                                     5
  DEL PEAK  7(4Q22.1) WILD-TYPE                                   2
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  7(4Q22.1) MUTATED                        10                       0
  DEL PEAK  7(4Q22.1) WILD-TYPE                      25                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  7(4Q22.1) MUTATED                         1
  DEL PEAK  7(4Q22.1) WILD-TYPE                       7
D35V31, multiclass
                                     clus
vv                                    DEL PEAK  7(4Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           5
  OTHER LOCATION, SPECIFY                                      10
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  7(4Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        25
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  7(4Q22.1) MUTATED                                               0
  DEL PEAK  7(4Q22.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  7(4Q22.1) MUTATED                                                9
  DEL PEAK  7(4Q22.1) WILD-TYPE                                             16
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  7(4Q22.1) MUTATED                                                                                  25
  DEL PEAK  7(4Q22.1) WILD-TYPE                                                                                56
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  7(4Q22.1) MUTATED                                                                                             38
  DEL PEAK  7(4Q22.1) WILD-TYPE                                                                                           82
D35V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  7(4Q22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          38
                                                                                              clus
vv                                                                                             DEL PEAK  7(4Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V33, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   16 23
  DEL PEAK  7(4Q22.1) WILD-TYPE 54 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     16   23
  DEL PEAK  7(4Q22.1) WILD-TYPE   54   50
         clus
vv        DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  ABSENT                           16                            54
  PRESENT                          23                            50
[1] 2 2
[1] FALSE
D35V34, continuous
D35V35, continuous
D35V36, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   15 40
  DEL PEAK  7(4Q22.1) WILD-TYPE 33 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     15   40
  DEL PEAK  7(4Q22.1) WILD-TYPE   33   76
                                          clus
vv                                         DEL PEAK  7(4Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          40
                                          clus
vv                                         DEL PEAK  7(4Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            76
[1] 2 2
[1] FALSE
D35V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  7(4Q22.1) MUTATED              4          15         31
  DEL PEAK  7(4Q22.1) WILD-TYPE           11          38         53
D35V38, multiclass
              clus
vv             DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           15                            38
  NEVER USED                            31                            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"
D35V39, continuous
D35V40, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   22  5
  DEL PEAK  7(4Q22.1) WILD-TYPE 70 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     22    5
  DEL PEAK  7(4Q22.1) WILD-TYPE   70   12
         clus
vv        DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  ABSENT                           22                            70
  PRESENT                           5                            12
[1] 2 2
[1] FALSE
D35V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  7(4Q22.1) MUTATED      0  14   18   10  2   1    2    1  11  0   1
  DEL PEAK  7(4Q22.1) WILD-TYPE    1  20   51   20  4   9    5    8  25  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  7(4Q22.1) MUTATED     9  4   1  3
  DEL PEAK  7(4Q22.1) WILD-TYPE   8  4   0 13
D35V42, multiclass
      clus
vv     DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  T1A1                           0                             1
  T1B                           14                            20
  T1B1                          18                            51
  T1B2                          10                            20
  T2                             2                             4
  T2A                            1                             9
  T2A1                           2                             5
  T2A2                           1                             8
  T2B                           11                            25
  T3                             0                             2
  T3A                            1                             1
  T3B                            9                             8
  T4                             4                             4
  TIS                            1                             0
  TX                             3                            13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  7(4Q22.1) MUTATED         0        1         0         1       11
  DEL PEAK  7(4Q22.1) WILD-TYPE       5        0         1         0       22
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  7(4Q22.1) MUTATED          21        14        0         2
  DEL PEAK  7(4Q22.1) WILD-TYPE        56        22        4         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  7(4Q22.1) MUTATED            2          1        17         0
  DEL PEAK  7(4Q22.1) WILD-TYPE          3          6        26         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  7(4Q22.1) MUTATED            1         16         3         3
  DEL PEAK  7(4Q22.1) WILD-TYPE          2         26         4         9
D35V44, multiclass
            clus
vv           DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            11                            22
  STAGE IB1                           21                            56
  STAGE IB2                           14                            22
  STAGE II                             0                             4
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           1                             6
  STAGE IIB                           17                            26
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          16                            26
  STAGE IVA                            3                             4
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK  8(4Q35.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q35.2) MUTATED    80  25
  DEL PEAK  8(4Q35.2) WILD-TYPE 133  40
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                          105                           173 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                           25                            40 
$`DEL PEAK  8(4Q35.2) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M5 
       12.39        57.04        23.67        11.44         5.46        67.46 
TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT 
       31.40        57.73        35.61        20.91        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CK TCGA-C5-A7CL 
       73.45        83.05        52.01        18.02       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
       20.35       147.35        17.19       131.11         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-C5-A907 
        2.73        45.83        99.91        27.52        20.91        11.87 
TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A1QT 
       58.88        40.04        87.75        16.83        39.55        12.36 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       31.36        13.05        24.56        14.50        26.01        12.66 
TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.89        14.99        14.96        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       45.96        26.27         1.51         0.59         0.59         1.45 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A8YF 
        1.18         2.24         0.10        20.35         6.94        15.55 
TCGA-FU-A2QG TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3LA 
        0.92         1.45         1.97         9.01        21.67       137.16 
TCGA-JW-A5VG TCGA-JW-A5VK TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       27.42        20.48        21.11         7.99        11.28         0.89 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 
       22.52        20.28        11.38         5.49         2.96        16.41 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB 
       15.39        19.36        19.59        11.67        12.16        10.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Y 
       26.43        18.05        32.15        31.27        36.26         4.73 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       39.78        15.68        48.07        45.34        44.94        43.40 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9V2 TCGA-VS-A9V4 
       22.72        46.92        14.53        41.42        14.04         4.34 
TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       26.01        67.59         1.41 

$`DEL PEAK  8(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        33.24        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC 
      210.67       154.32       101.82       155.77        94.95        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KK 
        8.35       146.86        23.51        20.81         1.12        50.76 
TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       44.94        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR 
       22.98        16.18        17.52         8.28        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E 
       31.53        25.02        14.50        26.40        12.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PI 
       26.79        13.91        15.02        13.58         6.64        19.27 
TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.43         0.13        16.08         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        47.77         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        19.79         8.32         1.22        23.84 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17        31.36        36.26         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
        3.52         1.35         1.32         1.12        25.41        10.82 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93         9.44       147.39        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH 
       96.95        78.71        81.96        29.85        36.36         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        15.58        28.37         8.28        18.15 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
      195.85        30.31        12.49         0.30         0.82        13.35 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI 
       17.82        19.56         9.17         8.52        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
        5.42        54.81        35.05        20.84        15.58        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ 
        3.88        93.99        66.05        40.50        37.78        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       59.51        46.03        36.13        11.51        57.93        39.78 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U7 
       16.64        24.39        50.86        50.63        50.14        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM 
       25.74        21.30        19.69        40.96         1.71        27.25 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       43.27        35.97        20.09        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       67.20        18.84         5.16        14.89        16.24        15.42 
TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        19.13         0.69         0.16         3.91 

  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                       147.35                        210.67 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                        19.36                         19.96 
[1] "0.1 - 147.3 (19.4)" "0.0 - 210.7 (20.0)"
[1] "hr=" "1.2"
D36V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  8(4Q35.2) MUTATED   53 18  9  4
  DEL PEAK  8(4Q35.2) WILD-TYPE 81 50 12  4
D36V3, multiclass
    clus
vv   DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  T1                          53                            81
  T2                          18                            50
  T3                           9                            12
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   42 23
  DEL PEAK  8(4Q35.2) WILD-TYPE 85 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     42   23
  DEL PEAK  8(4Q35.2) WILD-TYPE   85   32
   clus
vv  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  0                          42                            85
  1                          23                            32
[1] 2 2
[1] FALSE
D36V5, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   44  4
  DEL PEAK  8(4Q35.2) WILD-TYPE 63  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     44    4
  DEL PEAK  8(4Q35.2) WILD-TYPE   63    6
   clus
vv  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  0                          44                            63
  1                           4                             6
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(4Q35.2) MUTATED               1                              100
  DEL PEAK  8(4Q35.2) WILD-TYPE             4                              141
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  8(4Q35.2) MUTATED                                               2
  DEL PEAK  8(4Q35.2) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  8(4Q35.2) MUTATED                                     3
  DEL PEAK  8(4Q35.2) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  8(4Q35.2) MUTATED                                           2
  DEL PEAK  8(4Q35.2) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  8(4Q35.2) MUTATED                                              3
  DEL PEAK  8(4Q35.2) WILD-TYPE                                           12
D36V6, multiclass
                                               clus
vv                                              DEL PEAK  8(4Q35.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      100
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              DEL PEAK  8(4Q35.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        141
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q35.2) MUTATED    12  99
  DEL PEAK  8(4Q35.2) WILD-TYPE  18 163
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     12   99
  DEL PEAK  8(4Q35.2) WILD-TYPE   18  163
     clus
vv    DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  NO                           12                            18
  YES                          99                           163
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4Q35.2) MUTATED                                  2     7
  DEL PEAK  8(4Q35.2) WILD-TYPE                                6    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(4Q35.2) MUTATED                          13
  DEL PEAK  8(4Q35.2) WILD-TYPE                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(4Q35.2) MUTATED                                           0    80
  DEL PEAK  8(4Q35.2) WILD-TYPE                                         2   121
D36V10, multiclass
                                           clus
vv                                          DEL PEAK  8(4Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              80
                                           clus
vv                                          DEL PEAK  8(4Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  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"
D36V11, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED    6 66
  DEL PEAK  8(4Q35.2) WILD-TYPE 17 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED      6   66
  DEL PEAK  8(4Q35.2) WILD-TYPE   17   95
                        clus
vv                       DEL PEAK  8(4Q35.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          66
                        clus
vv                       DEL PEAK  8(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                            95
[1] 2 2
[1] FALSE
D36V12, continuous
D36V13, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   49 14
  DEL PEAK  8(4Q35.2) WILD-TYPE 85 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     49   14
  DEL PEAK  8(4Q35.2) WILD-TYPE   85   27
            clus
vv           DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  TUMOR FREE                          49                            85
  WITH TUMOR                          14                            27
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  8(4Q35.2) MUTATED       19      2       1      6       3
  DEL PEAK  8(4Q35.2) WILD-TYPE     34      3       0      5       4
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  8(4Q35.2) MUTATED              74       6
  DEL PEAK  8(4Q35.2) WILD-TYPE           127       8
D36V14, multiclass
               clus
vv              DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  BRAZIL                                 19                            34
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  6                             5
  UKRAINE                                 3                             4
  UNITED STATES                          74                           127
  VIETNAM                                 6                             8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  8(4Q35.2) MUTATED    4 41 55  0  9
  DEL PEAK  8(4Q35.2) WILD-TYPE 14 88 58  1 15
D36V15, multiclass
    clus
vv   DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  G1                           4                            14
  G2                          41                            88
  G3                          55                            58
  G4                           0                             1
  GX                           9                            15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V16, continuous
D36V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  8(4Q35.2) MUTATED                                            11
  DEL PEAK  8(4Q35.2) WILD-TYPE                                          26
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  8(4Q35.2) MUTATED                                        3
  DEL PEAK  8(4Q35.2) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  8(4Q35.2) MUTATED                                                 2
  DEL PEAK  8(4Q35.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  8(4Q35.2) MUTATED               26                  49
  DEL PEAK  8(4Q35.2) WILD-TYPE             36                  93
D36V18, multiclass
                                                 clus
vv                                                DEL PEAK  8(4Q35.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           26
  LIFELONG NON-SMOKER                                                      49
                                                 clus
vv                                                DEL PEAK  8(4Q35.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             36
  LIFELONG NON-SMOKER                                                        93
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V19, continuous
D36V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  8(4Q35.2) MUTATED             8       43             4       10
  DEL PEAK  8(4Q35.2) WILD-TYPE          11       59             8       15
D36V21, multiclass
               clus
vv              DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  COMBINATION                             8                            11
  EXTERNAL                               43                            59
  EXTERNAL BEAM                           4                             8
  INTERNAL                               10                            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V22, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   10  2
  DEL PEAK  8(4Q35.2) WILD-TYPE 15  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     10    2
  DEL PEAK  8(4Q35.2) WILD-TYPE   15    1
                         clus
vv                        DEL PEAK  8(4Q35.2) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK  8(4Q35.2) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  8(4Q35.2) MUTATED                    0                2
  DEL PEAK  8(4Q35.2) WILD-TYPE                  2                0
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  8(4Q35.2) MUTATED                    16            13
  DEL PEAK  8(4Q35.2) WILD-TYPE                  20            20
D36V23, multiclass
                     clus
vv                    DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              2                             0
  PRIMARY TUMOR FIELD                          16                            20
  REGIONAL SITE                                13                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V24, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   20  4
  DEL PEAK  8(4Q35.2) WILD-TYPE 36  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     20    4
  DEL PEAK  8(4Q35.2) WILD-TYPE   36    1
     clus
vv    DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  CGY                          20                            36
  GY                            4                             1
[1] 2 2
[1] FALSE
D36V25, continuous
D36V26, continuous
D36V27, continuous
D36V28, continuous
D36V29, continuous
D36V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  8(4Q35.2) MUTATED                                     0
  DEL PEAK  8(4Q35.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  8(4Q35.2) MUTATED                                     4
  DEL PEAK  8(4Q35.2) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  8(4Q35.2) MUTATED                        11                       0
  DEL PEAK  8(4Q35.2) WILD-TYPE                      24                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  8(4Q35.2) MUTATED                         1
  DEL PEAK  8(4Q35.2) WILD-TYPE                       7
D36V31, multiclass
                                     clus
vv                                    DEL PEAK  8(4Q35.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      11
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  8(4Q35.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        24
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  8(4Q35.2) MUTATED                                               1
  DEL PEAK  8(4Q35.2) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  8(4Q35.2) MUTATED                                               13
  DEL PEAK  8(4Q35.2) WILD-TYPE                                             12
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  8(4Q35.2) MUTATED                                                                                  28
  DEL PEAK  8(4Q35.2) WILD-TYPE                                                                                53
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  8(4Q35.2) MUTATED                                                                                             42
  DEL PEAK  8(4Q35.2) WILD-TYPE                                                                                           78
D36V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  8(4Q35.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          42
                                                                                              clus
vv                                                                                             DEL PEAK  8(4Q35.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V33, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   23 28
  DEL PEAK  8(4Q35.2) WILD-TYPE 47 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     23   28
  DEL PEAK  8(4Q35.2) WILD-TYPE   47   45
         clus
vv        DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  ABSENT                           23                            47
  PRESENT                          28                            45
[1] 2 2
[1] FALSE
D36V34, continuous
D36V35, continuous
D36V36, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   23 47
  DEL PEAK  8(4Q35.2) WILD-TYPE 25 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     23   47
  DEL PEAK  8(4Q35.2) WILD-TYPE   25   69
                                          clus
vv                                         DEL PEAK  8(4Q35.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          47
                                          clus
vv                                         DEL PEAK  8(4Q35.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            69
[1] 2 2
[1] FALSE
D36V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  8(4Q35.2) MUTATED              4          19         36
  DEL PEAK  8(4Q35.2) WILD-TYPE           11          34         48
D36V38, multiclass
              clus
vv             DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           19                            34
  NEVER USED                            36                            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"
D36V39, continuous
D36V40, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   31  4
  DEL PEAK  8(4Q35.2) WILD-TYPE 61 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     31    4
  DEL PEAK  8(4Q35.2) WILD-TYPE   61   13
         clus
vv        DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  ABSENT                           31                            61
  PRESENT                           4                            13
[1] 2 2
[1] FALSE
D36V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  8(4Q35.2) MUTATED      0  17   27    9  2   2    3    1  10  0   1
  DEL PEAK  8(4Q35.2) WILD-TYPE    1  17   42   21  4   8    4    8  26  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  8(4Q35.2) MUTATED     8  4   1  3
  DEL PEAK  8(4Q35.2) WILD-TYPE   9  4   0 13
D36V42, multiclass
      clus
vv     DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  T1A1                           0                             1
  T1B                           17                            17
  T1B1                          27                            42
  T1B2                           9                            21
  T2                             2                             4
  T2A                            2                             8
  T2A1                           3                             4
  T2A2                           1                             8
  T2B                           10                            26
  T3                             0                             2
  T3A                            1                             1
  T3B                            8                             9
  T4                             4                             4
  TIS                            1                             0
  TX                             3                            13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  8(4Q35.2) MUTATED         1        1         0         1       15
  DEL PEAK  8(4Q35.2) WILD-TYPE       4        0         1         0       18
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  8(4Q35.2) MUTATED          29        14        0         3
  DEL PEAK  8(4Q35.2) WILD-TYPE        48        22        4         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  8(4Q35.2) MUTATED            2          0        16         0
  DEL PEAK  8(4Q35.2) WILD-TYPE          3          7        27         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  8(4Q35.2) MUTATED            1         17         4         3
  DEL PEAK  8(4Q35.2) WILD-TYPE          2         25         3         9
D36V44, multiclass
            clus
vv           DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            15                            18
  STAGE IB1                           29                            48
  STAGE IB2                           14                            22
  STAGE II                             0                             4
  STAGE IIA                            3                             5
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           16                            27
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          17                            25
  STAGE IVA                            4                             3
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(5Q12.1) MUTATED    50  21
  DEL PEAK  9(5Q12.1) WILD-TYPE 163  44
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           71                           207 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           21                            44 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BN 
       12.39        11.44        68.84       144.16       177.04         5.46 
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MN 
       31.40        30.21        35.01        38.99        35.61        40.93 
TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-DG-A2KJ 
       18.02       154.32        17.19         9.34        45.83        58.88 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QS TCGA-EA-A1QT 
       87.75        36.76         2.66       117.99        39.55        12.36 
TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A97N 
       30.90        24.56        14.50        14.89        14.96         0.36 
TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2RJ TCGA-EK-A2RM 
       12.59         6.64        19.27         0.43         1.18         2.24 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY 
        0.10         0.03        20.35        23.84         0.92        31.36 
TCGA-FU-A3NI TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-JW-A5VI 
        1.45         1.97        25.41        10.82        21.67        24.56 
TCGA-LP-A4AW TCGA-MA-AA3Z TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-VS-A8EH 
        0.89        19.56         5.49        15.95         9.04        26.43 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A958 
       18.05        19.96        57.93        39.78         4.73        50.14 
TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP 
       44.94        19.69        40.96        14.53        41.42        43.27 
TCGA-VS-A9UU TCGA-VS-A9V4 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
       14.53         4.34        26.01        29.26        19.13 

$`DEL PEAK  9(5Q12.1) 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-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91         3.58        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48        20.35       147.35       155.77       131.11        94.95 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61         2.73        50.99         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        11.87         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ 
       50.76        44.94        40.04        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        17.52         8.28        37.35        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B 
       31.36        13.05        25.02        14.50        26.40        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.66        12.82         7.46        26.79        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG 
       14.99        13.58        13.48        45.96        26.27         1.51 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        4.04         0.03         0.36        47.77         0.10         0.07 
TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.10         7.92         6.94        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
       15.55         1.22         2.17        36.26         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.35         1.32         1.12         9.01 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       11.28        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       20.28        17.82         9.17         8.52        11.38        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62         5.42        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        16.41        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        15.39        19.36        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        66.05        10.03        40.50        37.78 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM 
       59.51        32.15        46.03        36.13        11.51        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       36.26        16.64        24.39        39.78        50.86        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.63        48.07        45.34        43.40        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UQ 
       21.30        22.72        46.92         1.71        27.25        35.97 
TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       20.09         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 
       14.04        14.89        16.24        15.42        67.59         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       177.04                        210.67 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                        19.69                         19.86 
[1] "0.0 - 177.0 (19.7)" "0.0 - 210.7 (19.9)"
[1] "hr=" "1.5"
D37V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  9(5Q12.1) MUTATED   35 14  7  1
  DEL PEAK  9(5Q12.1) WILD-TYPE 99 54 14  7
D37V3, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T1                          35                            99
  T2                          14                            54
  T3                           7                            14
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   28 16
  DEL PEAK  9(5Q12.1) WILD-TYPE 99 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     28   16
  DEL PEAK  9(5Q12.1) WILD-TYPE   99   39
   clus
vv  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  0                          28                            99
  1                          16                            39
[1] 2 2
[1] FALSE
D37V5, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   27  2
  DEL PEAK  9(5Q12.1) WILD-TYPE 80  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     27    2
  DEL PEAK  9(5Q12.1) WILD-TYPE   80    8
   clus
vv  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  0                          27                            80
  1                           2                             8
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(5Q12.1) MUTATED               1                               66
  DEL PEAK  9(5Q12.1) WILD-TYPE             4                              175
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  9(5Q12.1) MUTATED                                               1
  DEL PEAK  9(5Q12.1) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  9(5Q12.1) MUTATED                                     2
  DEL PEAK  9(5Q12.1) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  9(5Q12.1) MUTATED                                           1
  DEL PEAK  9(5Q12.1) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  9(5Q12.1) MUTATED                                              4
  DEL PEAK  9(5Q12.1) WILD-TYPE                                           11
D37V6, multiclass
                                               clus
vv                                              DEL PEAK  9(5Q12.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       66
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
                                               clus
vv                                              DEL PEAK  9(5Q12.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        175
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    12  63
  DEL PEAK  9(5Q12.1) WILD-TYPE  18 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     12   63
  DEL PEAK  9(5Q12.1) WILD-TYPE   18  199
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                           12                            18
  YES                          63                           199
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(5Q12.1) MUTATED                                  1     4
  DEL PEAK  9(5Q12.1) WILD-TYPE                                7    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(5Q12.1) MUTATED                           7
  DEL PEAK  9(5Q12.1) WILD-TYPE                        21
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(5Q12.1) MUTATED                                           1    56
  DEL PEAK  9(5Q12.1) WILD-TYPE                                         1   145
D37V10, multiclass
                                           clus
vv                                          DEL PEAK  9(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              56
                                           clus
vv                                          DEL PEAK  9(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               145
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED     4  44
  DEL PEAK  9(5Q12.1) WILD-TYPE  19 117
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      4   44
  DEL PEAK  9(5Q12.1) WILD-TYPE   19  117
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           117
[1] 2 2
[1] FALSE
D37V12, continuous
D37V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    31  14
  DEL PEAK  9(5Q12.1) WILD-TYPE 103  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     31   14
  DEL PEAK  9(5Q12.1) WILD-TYPE  103   27
            clus
vv           DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  TUMOR FREE                          31                           103
  WITH TUMOR                          14                            27
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  9(5Q12.1) MUTATED       16      1       0      6       1
  DEL PEAK  9(5Q12.1) WILD-TYPE     37      4       1      5       6
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  9(5Q12.1) MUTATED              48       3
  DEL PEAK  9(5Q12.1) WILD-TYPE           153      11
D37V14, multiclass
               clus
vv              DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  BRAZIL                                 16                            37
  CANADA                                  1                             4
  NIGERIA                                 0                             1
  RUSSIA                                  6                             5
  UKRAINE                                 1                             6
  UNITED STATES                          48                           153
  VIETNAM                                 3                            11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  9(5Q12.1) MUTATED    2 31 33  0  6
  DEL PEAK  9(5Q12.1) WILD-TYPE 16 98 80  1 18
D37V15, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  G1                           2                            16
  G2                          31                            98
  G3                          33                            80
  G4                           0                             1
  GX                           6                            18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V16, continuous
D37V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  9(5Q12.1) MUTATED                                             7
  DEL PEAK  9(5Q12.1) WILD-TYPE                                          30
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  9(5Q12.1) MUTATED                                        2
  DEL PEAK  9(5Q12.1) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  9(5Q12.1) MUTATED                                                 2
  DEL PEAK  9(5Q12.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  9(5Q12.1) MUTATED               15                  35
  DEL PEAK  9(5Q12.1) WILD-TYPE             47                 107
D37V18, multiclass
                                                 clus
vv                                                DEL PEAK  9(5Q12.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           15
  LIFELONG NON-SMOKER                                                      35
                                                 clus
vv                                                DEL PEAK  9(5Q12.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             47
  LIFELONG NON-SMOKER                                                       107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V19, continuous
D37V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  9(5Q12.1) MUTATED             7       21             5        5
  DEL PEAK  9(5Q12.1) WILD-TYPE          12       81             7       20
D37V21, multiclass
               clus
vv              DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               21                            81
  EXTERNAL BEAM                           5                             7
  INTERNAL                                5                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V22, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   11  1
  DEL PEAK  9(5Q12.1) WILD-TYPE 14  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     11    1
  DEL PEAK  9(5Q12.1) WILD-TYPE   14    2
                         clus
vv                        DEL PEAK  9(5Q12.1) MUTATED
  COMPLETED AS PLANNED                             11
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        DEL PEAK  9(5Q12.1) WILD-TYPE
  COMPLETED AS PLANNED                               14
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK  9(5Q12.1) MUTATED                    0                2
  DEL PEAK  9(5Q12.1) WILD-TYPE                  2                0
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK  9(5Q12.1) MUTATED                    10             7
  DEL PEAK  9(5Q12.1) WILD-TYPE                  26            26
D37V23, multiclass
                     clus
vv                    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              2                             0
  PRIMARY TUMOR FIELD                          10                            26
  REGIONAL SITE                                 7                            26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V24, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   16  1
  DEL PEAK  9(5Q12.1) WILD-TYPE 40  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     16    1
  DEL PEAK  9(5Q12.1) WILD-TYPE   40    4
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  CGY                          16                            40
  GY                            1                             4
[1] 2 2
[1] FALSE
D37V25, continuous
D37V26, continuous
D37V27, continuous
D37V28, continuous
D37V29, continuous
D37V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  9(5Q12.1) MUTATED                                     0
  DEL PEAK  9(5Q12.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  9(5Q12.1) MUTATED                                     3
  DEL PEAK  9(5Q12.1) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  9(5Q12.1) MUTATED                        10                       0
  DEL PEAK  9(5Q12.1) WILD-TYPE                      25                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  9(5Q12.1) MUTATED                         1
  DEL PEAK  9(5Q12.1) WILD-TYPE                       7
D37V31, multiclass
                                     clus
vv                                    DEL PEAK  9(5Q12.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                      10
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  9(5Q12.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                        25
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  9(5Q12.1) MUTATED                                               1
  DEL PEAK  9(5Q12.1) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  9(5Q12.1) MUTATED                                                8
  DEL PEAK  9(5Q12.1) WILD-TYPE                                             17
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  9(5Q12.1) MUTATED                                                                                  21
  DEL PEAK  9(5Q12.1) WILD-TYPE                                                                                60
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  9(5Q12.1) MUTATED                                                                                             29
  DEL PEAK  9(5Q12.1) WILD-TYPE                                                                                           91
D37V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  9(5Q12.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          29
                                                                                              clus
vv                                                                                             DEL PEAK  9(5Q12.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V33, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   13 22
  DEL PEAK  9(5Q12.1) WILD-TYPE 57 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     13   22
  DEL PEAK  9(5Q12.1) WILD-TYPE   57   51
         clus
vv        DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  ABSENT                           13                            57
  PRESENT                          22                            51
[1] 2 2
[1] FALSE
D37V34, continuous
D37V35, continuous
D37V36, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   12 34
  DEL PEAK  9(5Q12.1) WILD-TYPE 36 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     12   34
  DEL PEAK  9(5Q12.1) WILD-TYPE   36   82
                                          clus
vv                                         DEL PEAK  9(5Q12.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          34
                                          clus
vv                                         DEL PEAK  9(5Q12.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            82
[1] 2 2
[1] FALSE
D37V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  9(5Q12.1) MUTATED              3          15         22
  DEL PEAK  9(5Q12.1) WILD-TYPE           12          38         62
D37V38, multiclass
              clus
vv             DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           15                            38
  NEVER USED                            22                            62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V39, continuous
D37V40, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   22  4
  DEL PEAK  9(5Q12.1) WILD-TYPE 70 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     22    4
  DEL PEAK  9(5Q12.1) WILD-TYPE   70   13
         clus
vv        DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  ABSENT                           22                            70
  PRESENT                           4                            13
[1] 2 2
[1] FALSE
D37V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK  9(5Q12.1) MUTATED      0   8   18    9  0   2    2    0  10  0   1
  DEL PEAK  9(5Q12.1) WILD-TYPE    1  26   51   21  6   8    5    9  26  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  9(5Q12.1) MUTATED     6  1   1  6
  DEL PEAK  9(5Q12.1) WILD-TYPE  11  7   0 10
D37V42, multiclass
      clus
vv     DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T1A1                           0                             1
  T1B                            8                            26
  T1B1                          18                            51
  T1B2                           9                            21
  T2                             0                             6
  T2A                            2                             8
  T2A1                           2                             5
  T2A2                           0                             9
  T2B                           10                            26
  T3                             0                             2
  T3A                            1                             1
  T3B                            6                            11
  T4                             1                             7
  TIS                            1                             0
  TX                             6                            10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  9(5Q12.1) MUTATED         2        1         0         1        8
  DEL PEAK  9(5Q12.1) WILD-TYPE       3        0         1         0       25
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  9(5Q12.1) MUTATED          15        11        1         2
  DEL PEAK  9(5Q12.1) WILD-TYPE        62        25        3         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  9(5Q12.1) MUTATED            2          0        15         0
  DEL PEAK  9(5Q12.1) WILD-TYPE          3          7        28         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  9(5Q12.1) MUTATED            1         13         1         0
  DEL PEAK  9(5Q12.1) WILD-TYPE          2         29         6        12
D37V44, multiclass
            clus
vv           DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             8                            25
  STAGE IB1                           15                            62
  STAGE IB2                           11                            25
  STAGE II                             1                             3
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           15                            28
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          13                            29
  STAGE IVA                            1                             6
  STAGE IVB                            0                            12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK 10(5Q35.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q35.2) MUTATED    51  17
  DEL PEAK 10(5Q35.2) WILD-TYPE 162  48
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                           68                           210 
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                           17                            48 
$`DEL PEAK 10(5Q35.2) MUTATED`
TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 
       12.39        11.44       144.16       173.29         5.46        31.40 
TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A3HE TCGA-C5-A7CH 
       35.01        38.99        35.61        40.93        18.02       154.32 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL 
       17.19       155.77        58.88        87.75        36.76         2.66 
TCGA-DS-A0VM TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3Y4 TCGA-EA-A411 
      117.99        39.55        12.36        30.90        14.50        24.56 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2IP 
       14.50        14.89        14.96         0.36        12.59         6.64 
TCGA-EK-A2PL TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 
        0.43         0.03         1.18         2.24         0.10        20.35 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A2PA 
       23.84         0.92        31.36         1.35         1.97        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-JW-A5VI TCGA-LP-A4AW TCGA-LP-A5U3 
       10.82        21.67       137.16        24.56         0.89         0.82 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       22.52        17.82        19.56         5.49        15.95         9.04 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A9U5 
       26.43        18.05        57.93        39.78         4.73        44.94 
TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9UU TCGA-VS-A9V4 TCGA-WL-A834 TCGA-XS-A8TJ 
       19.69        14.53        14.53         4.34        26.01        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       19.13         1.41 

$`DEL PEAK 10(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-A1ML TCGA-C5-A1MP 
       57.73        53.16         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43        33.24        52.01        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UH 
      101.82       134.33        15.48        20.35       147.35       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       94.95         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91        11.87         1.12        50.76        44.94        40.04 
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        17.52 
TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        8.28        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       26.40        26.01        12.66        12.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       13.91        15.02        14.99        13.58        13.48        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         1.51        19.27         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL 
        0.13        16.08         0.07         4.04         0.36        47.77 
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-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO 
       14.70        19.79         8.32        15.55         1.22         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.32         1.12         9.01        20.78        14.93         9.44 
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-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
       29.85        36.36        27.42         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        28.37         8.28        18.15        21.11       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU 
       30.31         7.99        11.28        12.49         0.30        13.35 
TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       20.28         9.17         8.52        11.38        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        54.81        35.05        20.84         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       16.41        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ 
       12.16        66.05        10.03        40.50        37.78        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM 
       59.51        32.15        46.03        36.13        11.51        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       36.26        16.64        24.39        39.78        50.86        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 
       50.63        48.07        50.14        45.34        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       25.74        21.30        22.72        46.92        40.96         1.71 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV 
       27.25        41.42        43.27        35.97        20.09         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        14.04        14.89 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       16.24        15.42        67.59         0.69         0.16         3.91 

  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                       173.29                        210.67 
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                       18.035                        20.315 
[1] "0.0 - 173.3 (18.0)" "0.0 - 210.7 (20.3)"
[1] "hr=" "1.2"
D38V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 10(5Q35.2) MUTATED   37 10  6  1
  DEL PEAK 10(5Q35.2) WILD-TYPE 97 58 15  7
D38V3, multiclass
    clus
vv   DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  T1                          37                            97
  T2                          10                            58
  T3                           6                            15
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   30 15
  DEL PEAK 10(5Q35.2) WILD-TYPE 97 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     30   15
  DEL PEAK 10(5Q35.2) WILD-TYPE   97   40
   clus
vv  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  0                          30                            97
  1                          15                            40
[1] 2 2
[1] FALSE
D38V5, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   31  1
  DEL PEAK 10(5Q35.2) WILD-TYPE 76  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     31    1
  DEL PEAK 10(5Q35.2) WILD-TYPE   76    9
   clus
vv  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  0                          31                            76
  1                           1                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(5Q35.2) MUTATED               1                               62
  DEL PEAK 10(5Q35.2) WILD-TYPE             4                              179
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 10(5Q35.2) MUTATED                                               1
  DEL PEAK 10(5Q35.2) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 10(5Q35.2) MUTATED                                     3
  DEL PEAK 10(5Q35.2) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 10(5Q35.2) MUTATED                                           2
  DEL PEAK 10(5Q35.2) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 10(5Q35.2) MUTATED                                              2
  DEL PEAK 10(5Q35.2) WILD-TYPE                                           13
D38V6, multiclass
                                               clus
vv                                              DEL PEAK 10(5Q35.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       62
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              DEL PEAK 10(5Q35.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        179
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q35.2) MUTATED    11  60
  DEL PEAK 10(5Q35.2) WILD-TYPE  19 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     11   60
  DEL PEAK 10(5Q35.2) WILD-TYPE   19  202
     clus
vv    DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  NO                           11                            19
  YES                          60                           202
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(5Q35.2) MUTATED                                  2     5
  DEL PEAK 10(5Q35.2) WILD-TYPE                                6    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(5Q35.2) MUTATED                           6
  DEL PEAK 10(5Q35.2) WILD-TYPE                        22
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(5Q35.2) MUTATED                                           1    53
  DEL PEAK 10(5Q35.2) WILD-TYPE                                         1   148
D38V10, multiclass
                                           clus
vv                                          DEL PEAK 10(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              53
                                           clus
vv                                          DEL PEAK 10(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               148
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q35.2) MUTATED     6  44
  DEL PEAK 10(5Q35.2) WILD-TYPE  17 117
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED      6   44
  DEL PEAK 10(5Q35.2) WILD-TYPE   17  117
                        clus
vv                       DEL PEAK 10(5Q35.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK 10(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           117
[1] 2 2
[1] FALSE
D38V12, continuous
D38V13, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q35.2) MUTATED    32  12
  DEL PEAK 10(5Q35.2) WILD-TYPE 102  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     32   12
  DEL PEAK 10(5Q35.2) WILD-TYPE  102   29
            clus
vv           DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  TUMOR FREE                          32                           102
  WITH TUMOR                          12                            29
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 10(5Q35.2) MUTATED       11      1       0      6       2
  DEL PEAK 10(5Q35.2) WILD-TYPE     42      4       1      5       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 10(5Q35.2) MUTATED              47       4
  DEL PEAK 10(5Q35.2) WILD-TYPE           154      10
D38V14, multiclass
               clus
vv              DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  BRAZIL                                 11                            42
  CANADA                                  1                             4
  NIGERIA                                 0                             1
  RUSSIA                                  6                             5
  UKRAINE                                 2                             5
  UNITED STATES                          47                           154
  VIETNAM                                 4                            10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK 10(5Q35.2) MUTATED     2  26  36   0   5
  DEL PEAK 10(5Q35.2) WILD-TYPE  16 103  77   1  19
D38V15, multiclass
    clus
vv   DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  G1                           2                            16
  G2                          26                           103
  G3                          36                            77
  G4                           0                             1
  GX                           5                            19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V16, continuous
D38V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 10(5Q35.2) MUTATED                                             7
  DEL PEAK 10(5Q35.2) WILD-TYPE                                          30
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 10(5Q35.2) MUTATED                                        2
  DEL PEAK 10(5Q35.2) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 10(5Q35.2) MUTATED                                                 2
  DEL PEAK 10(5Q35.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 10(5Q35.2) MUTATED               15                  33
  DEL PEAK 10(5Q35.2) WILD-TYPE             47                 109
D38V18, multiclass
                                                 clus
vv                                                DEL PEAK 10(5Q35.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           15
  LIFELONG NON-SMOKER                                                      33
                                                 clus
vv                                                DEL PEAK 10(5Q35.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             47
  LIFELONG NON-SMOKER                                                       109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V19, continuous
D38V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 10(5Q35.2) MUTATED             7       21             4        3
  DEL PEAK 10(5Q35.2) WILD-TYPE          12       81             8       22
D38V21, multiclass
               clus
vv              DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               21                            81
  EXTERNAL BEAM                           4                             8
  INTERNAL                                3                            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"
D38V22, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   10  1
  DEL PEAK 10(5Q35.2) WILD-TYPE 15  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     10    1
  DEL PEAK 10(5Q35.2) WILD-TYPE   15    2
                         clus
vv                        DEL PEAK 10(5Q35.2) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        DEL PEAK 10(5Q35.2) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 10(5Q35.2) MUTATED                    0                2
  DEL PEAK 10(5Q35.2) WILD-TYPE                  2                0
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 10(5Q35.2) MUTATED                     9             4
  DEL PEAK 10(5Q35.2) WILD-TYPE                  27            29
D38V23, multiclass
                     clus
vv                    DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              2                             0
  PRIMARY TUMOR FIELD                           9                            27
  REGIONAL SITE                                 4                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V24, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   12  1
  DEL PEAK 10(5Q35.2) WILD-TYPE 44  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     12    1
  DEL PEAK 10(5Q35.2) WILD-TYPE   44    4
     clus
vv    DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  CGY                          12                            44
  GY                            1                             4
[1] 2 2
[1] FALSE
D38V25, continuous
D38V26, continuous
D38V27, continuous
D38V28, continuous
D38V29, continuous
D38V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 10(5Q35.2) MUTATED                                     0
  DEL PEAK 10(5Q35.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 10(5Q35.2) MUTATED                                     3
  DEL PEAK 10(5Q35.2) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 10(5Q35.2) MUTATED                         6                       0
  DEL PEAK 10(5Q35.2) WILD-TYPE                      29                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 10(5Q35.2) MUTATED                         1
  DEL PEAK 10(5Q35.2) WILD-TYPE                       7
D38V31, multiclass
                                     clus
vv                                    DEL PEAK 10(5Q35.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                       6
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK 10(5Q35.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                        29
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 10(5Q35.2) MUTATED                                               0
  DEL PEAK 10(5Q35.2) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 10(5Q35.2) MUTATED                                                6
  DEL PEAK 10(5Q35.2) WILD-TYPE                                             19
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 10(5Q35.2) MUTATED                                                                                  21
  DEL PEAK 10(5Q35.2) WILD-TYPE                                                                                60
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 10(5Q35.2) MUTATED                                                                                             31
  DEL PEAK 10(5Q35.2) WILD-TYPE                                                                                           89
D38V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 10(5Q35.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          31
                                                                                              clus
vv                                                                                             DEL PEAK 10(5Q35.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V33, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   14 23
  DEL PEAK 10(5Q35.2) WILD-TYPE 56 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     14   23
  DEL PEAK 10(5Q35.2) WILD-TYPE   56   50
         clus
vv        DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  ABSENT                           14                            56
  PRESENT                          23                            50
[1] 2 2
[1] FALSE
D38V34, continuous
D38V35, continuous
D38V36, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   10 37
  DEL PEAK 10(5Q35.2) WILD-TYPE 38 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     10   37
  DEL PEAK 10(5Q35.2) WILD-TYPE   38   79
                                          clus
vv                                         DEL PEAK 10(5Q35.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          37
                                          clus
vv                                         DEL PEAK 10(5Q35.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            79
[1] 2 2
[1] FALSE
D38V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 10(5Q35.2) MUTATED              3          15         20
  DEL PEAK 10(5Q35.2) WILD-TYPE           12          38         64
D38V38, multiclass
              clus
vv             DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           15                            38
  NEVER USED                            20                            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V39, continuous
D38V40, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   25  4
  DEL PEAK 10(5Q35.2) WILD-TYPE 67 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     25    4
  DEL PEAK 10(5Q35.2) WILD-TYPE   67   13
         clus
vv        DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  ABSENT                           25                            67
  PRESENT                           4                            13
[1] 2 2
[1] FALSE
D38V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 10(5Q35.2) MUTATED      0   7   21    9  0   1    3    0   6  0   1
  DEL PEAK 10(5Q35.2) WILD-TYPE    1  27   48   21  6   9    4    9  30  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 10(5Q35.2) MUTATED     5  1   1  5
  DEL PEAK 10(5Q35.2) WILD-TYPE  12  7   0 11
D38V42, multiclass
      clus
vv     DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  T1A1                           0                             1
  T1B                            7                            27
  T1B1                          21                            48
  T1B2                           9                            21
  T2                             0                             6
  T2A                            1                             9
  T2A1                           3                             4
  T2A2                           0                             9
  T2B                            6                            30
  T3                             0                             2
  T3A                            1                             1
  T3B                            5                            12
  T4                             1                             7
  TIS                            1                             0
  TX                             5                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 10(5Q35.2) MUTATED         2        1         0         1        9
  DEL PEAK 10(5Q35.2) WILD-TYPE       3        0         1         0       24
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 10(5Q35.2) MUTATED          19        10        1         1
  DEL PEAK 10(5Q35.2) WILD-TYPE        58        26        3         7
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 10(5Q35.2) MUTATED            2          0        11         0
  DEL PEAK 10(5Q35.2) WILD-TYPE          3          7        32         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 10(5Q35.2) MUTATED            1         10         1         0
  DEL PEAK 10(5Q35.2) WILD-TYPE          2         32         6        12
D38V44, multiclass
            clus
vv           DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             9                            24
  STAGE IB1                           19                            58
  STAGE IB2                           10                            26
  STAGE II                             1                             3
  STAGE IIA                            1                             7
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           11                            32
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          10                            32
  STAGE IVA                            1                             6
  STAGE IVB                            0                            12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK 11(6P24.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(6P24.2) MUTATED    32  12
  DEL PEAK 11(6P24.2) WILD-TYPE 181  53
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                           44                           234 
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                           12                            53 
$`DEL PEAK 11(6P24.2) MUTATED`
TCGA-4J-AA1J TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7CO 
       12.39        19.86        30.21        73.18       210.67       147.35 
TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KK 
        9.34        45.83        23.51        27.52         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3QE 
       44.94        40.04        36.76       117.99        22.98        25.02 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2PI TCGA-EK-A2RC 
       12.66        14.89        14.96        13.58        19.27         4.04 
TCGA-EK-A2RN TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-HG-A2PA TCGA-IR-A3L7 TCGA-JW-A5VJ 
        0.10         7.92        31.36        25.41       147.39        21.44 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-UC-A7PF 
       21.11         7.99        19.56         9.17         8.52        93.99 
TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A9UU TCGA-VS-A9UY 
       12.16        59.51         4.73        48.07        14.53        18.25 
TCGA-VS-A9V3 TCGA-ZX-AA5X 
       14.89         3.91 

$`DEL PEAK 11(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-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        3.58        44.22        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC 
      154.32       101.82       134.33        15.48        20.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      155.77       131.11        94.95        13.61         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
        8.35       146.86        99.91        20.81        20.91        11.87 
TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        87.75        58.88         2.66       118.65        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        12.36        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
       30.90        31.53        31.36        13.05        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       24.56        14.50        26.01        12.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       13.91        15.02        14.99        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
       45.96        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RD 
        0.59         1.45         0.13        16.08         0.07         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36         1.18        47.77         2.24         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.03        20.35         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        8.32        15.55         1.22        23.84         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC 
        1.35         1.32         1.97         1.12         9.01        10.82 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
       21.67        20.78        14.93         9.44       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
        8.28        18.15       195.85        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       12.49         0.30         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
       17.82        11.38        13.87        34.62         5.42        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       35.05        20.84         5.49         2.96        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        15.39        19.36        19.59         3.88        11.67 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       66.05        10.03        40.50        37.78        26.43        18.05 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        32.15        46.03        36.13        11.51        57.93 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 
       39.78        31.27        36.26        16.64        24.39        39.78 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       50.86        15.68        50.63        50.14        45.34        44.94 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       43.40        42.41        25.74        21.30        22.72        19.69 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       46.92        40.96         1.71        14.53        27.25        41.42 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 
       43.27        35.97        20.09         3.42        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        14.04         4.34        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.69         1.41         0.16 

  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                       210.67                        195.85 
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                       20.485                        19.740 
[1] "0.1 - 210.7 (20.5)" "0.0 - 195.8 (19.7)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 11(6P24.2) MUTATED    25  10   2   1
  DEL PEAK 11(6P24.2) WILD-TYPE 109  58  19   7
D39V3, multiclass
    clus
vv   DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  T1                          25                           109
  T2                          10                            58
  T3                           2                            19
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P24.2) MUTATED    18  12
  DEL PEAK 11(6P24.2) WILD-TYPE 109  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     18   12
  DEL PEAK 11(6P24.2) WILD-TYPE  109   43
   clus
vv  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  0                          18                           109
  1                          12                            43
[1] 2 2
[1] FALSE
D39V5, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED   24  1
  DEL PEAK 11(6P24.2) WILD-TYPE 83  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     24    1
  DEL PEAK 11(6P24.2) WILD-TYPE   83    9
   clus
vv  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  0                          24                            83
  1                           1                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(6P24.2) MUTATED               1                               43
  DEL PEAK 11(6P24.2) WILD-TYPE             4                              198
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 11(6P24.2) MUTATED                                               0
  DEL PEAK 11(6P24.2) WILD-TYPE                                             6
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 11(6P24.2) MUTATED                                     1
  DEL PEAK 11(6P24.2) WILD-TYPE                                  21
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 11(6P24.2) MUTATED                                           1
  DEL PEAK 11(6P24.2) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 11(6P24.2) MUTATED                                              0
  DEL PEAK 11(6P24.2) WILD-TYPE                                           15
D39V6, multiclass
                                               clus
vv                                              DEL PEAK 11(6P24.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       43
  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 11(6P24.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        198
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P24.2) MUTATED     3  43
  DEL PEAK 11(6P24.2) WILD-TYPE  27 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED      3   43
  DEL PEAK 11(6P24.2) WILD-TYPE   27  219
     clus
vv    DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  NO                            3                            27
  YES                          43                           219
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(6P24.2) MUTATED                                  1     2
  DEL PEAK 11(6P24.2) WILD-TYPE                                7    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(6P24.2) MUTATED                           1
  DEL PEAK 11(6P24.2) WILD-TYPE                        27
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(6P24.2) MUTATED                                           0    31
  DEL PEAK 11(6P24.2) WILD-TYPE                                         2   170
D39V10, multiclass
                                           clus
vv                                          DEL PEAK 11(6P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              31
                                           clus
vv                                          DEL PEAK 11(6P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P24.2) MUTATED     4  21
  DEL PEAK 11(6P24.2) WILD-TYPE  19 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED      4   21
  DEL PEAK 11(6P24.2) WILD-TYPE   19  140
                        clus
vv                       DEL PEAK 11(6P24.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          21
                        clus
vv                       DEL PEAK 11(6P24.2) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           140
[1] 2 2
[1] FALSE
D39V12, continuous
D39V13, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P24.2) MUTATED    21   6
  DEL PEAK 11(6P24.2) WILD-TYPE 113  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     21    6
  DEL PEAK 11(6P24.2) WILD-TYPE  113   35
            clus
vv           DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  TUMOR FREE                          21                           113
  WITH TUMOR                           6                            35
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 11(6P24.2) MUTATED        6      4       0      3       1
  DEL PEAK 11(6P24.2) WILD-TYPE     47      1       1      8       6
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 11(6P24.2) MUTATED              30       2
  DEL PEAK 11(6P24.2) WILD-TYPE           171      12
D39V14, multiclass
               clus
vv              DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  BRAZIL                                  6                            47
  CANADA                                  4                             1
  NIGERIA                                 0                             1
  RUSSIA                                  3                             8
  UKRAINE                                 1                             6
  UNITED STATES                          30                           171
  VIETNAM                                 2                            12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK 11(6P24.2) MUTATED     4  19  18   0   3
  DEL PEAK 11(6P24.2) WILD-TYPE  14 110  95   1  21
D39V15, multiclass
    clus
vv   DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  G1                           4                            14
  G2                          19                           110
  G3                          18                            95
  G4                           0                             1
  GX                           3                            21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V16, continuous
D39V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 11(6P24.2) MUTATED                                             6
  DEL PEAK 11(6P24.2) WILD-TYPE                                          31
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 11(6P24.2) MUTATED                                        2
  DEL PEAK 11(6P24.2) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 11(6P24.2) MUTATED                                                 0
  DEL PEAK 11(6P24.2) WILD-TYPE                                               3
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 11(6P24.2) MUTATED               11                  22
  DEL PEAK 11(6P24.2) WILD-TYPE             51                 120
D39V18, multiclass
                                                 clus
vv                                                DEL PEAK 11(6P24.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           11
  LIFELONG NON-SMOKER                                                      22
                                                 clus
vv                                                DEL PEAK 11(6P24.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             3
  CURRENT SMOKER                                                             51
  LIFELONG NON-SMOKER                                                       120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V19, continuous
D39V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 11(6P24.2) MUTATED             0       13             4        6
  DEL PEAK 11(6P24.2) WILD-TYPE          19       89             8       19
D39V21, multiclass
               clus
vv              DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  COMBINATION                             0                            19
  EXTERNAL                               13                            89
  EXTERNAL BEAM                           4                             8
  INTERNAL                                6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V22, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED    3  0
  DEL PEAK 11(6P24.2) WILD-TYPE 22  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED      3    0
  DEL PEAK 11(6P24.2) WILD-TYPE   22    3
                         clus
vv                        DEL PEAK 11(6P24.2) MUTATED
  COMPLETED AS PLANNED                              3
  TREATMENT NOT COMPLETED                           0
                         clus
vv                        DEL PEAK 11(6P24.2) WILD-TYPE
  COMPLETED AS PLANNED                               22
  TREATMENT NOT COMPLETED                             3
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 11(6P24.2) MUTATED                    0                0
  DEL PEAK 11(6P24.2) WILD-TYPE                  2                2
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 11(6P24.2) MUTATED                     8             5
  DEL PEAK 11(6P24.2) WILD-TYPE                  28            28
D39V23, multiclass
                     clus
vv                    DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              0                             2
  PRIMARY TUMOR FIELD                           8                            28
  REGIONAL SITE                                 5                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V24, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED   11  0
  DEL PEAK 11(6P24.2) WILD-TYPE 45  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     11    0
  DEL PEAK 11(6P24.2) WILD-TYPE   45    5
     clus
vv    DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  CGY                          11                            45
  GY                            0                             5
[1] 2 2
[1] FALSE
D39V25, continuous
D39V26, continuous
D39V27, continuous
D39V28, continuous
D39V29, continuous
D39V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 11(6P24.2) MUTATED                                     0
  DEL PEAK 11(6P24.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 11(6P24.2) MUTATED                                     0
  DEL PEAK 11(6P24.2) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 11(6P24.2) MUTATED                         7                       0
  DEL PEAK 11(6P24.2) WILD-TYPE                      28                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 11(6P24.2) MUTATED                         2
  DEL PEAK 11(6P24.2) WILD-TYPE                       6
D39V31, multiclass
                                     clus
vv                                    DEL PEAK 11(6P24.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       7
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK 11(6P24.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        28
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 11(6P24.2) MUTATED                                               1
  DEL PEAK 11(6P24.2) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 11(6P24.2) MUTATED                                                2
  DEL PEAK 11(6P24.2) WILD-TYPE                                             23
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 11(6P24.2) MUTATED                                                                                  11
  DEL PEAK 11(6P24.2) WILD-TYPE                                                                                70
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 11(6P24.2) MUTATED                                                                                             21
  DEL PEAK 11(6P24.2) WILD-TYPE                                                                                           99
D39V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 11(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)                                     11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          21
                                                                                              clus
vv                                                                                             DEL PEAK 11(6P24.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V33, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED   10 15
  DEL PEAK 11(6P24.2) WILD-TYPE 60 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     10   15
  DEL PEAK 11(6P24.2) WILD-TYPE   60   58
         clus
vv        DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  ABSENT                           10                            60
  PRESENT                          15                            58
[1] 2 2
[1] FALSE
D39V34, continuous
D39V35, continuous
D39V36, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED   10 19
  DEL PEAK 11(6P24.2) WILD-TYPE 38 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     10   19
  DEL PEAK 11(6P24.2) WILD-TYPE   38   97
                                          clus
vv                                         DEL PEAK 11(6P24.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          19
                                          clus
vv                                         DEL PEAK 11(6P24.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            97
[1] 2 2
[1] FALSE
D39V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 11(6P24.2) MUTATED              4          10         12
  DEL PEAK 11(6P24.2) WILD-TYPE           11          43         72
D39V38, multiclass
              clus
vv             DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           10                            43
  NEVER USED                            12                            72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V39, continuous
D39V40, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED   18  2
  DEL PEAK 11(6P24.2) WILD-TYPE 74 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     18    2
  DEL PEAK 11(6P24.2) WILD-TYPE   74   15
         clus
vv        DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  ABSENT                           18                            74
  PRESENT                           2                            15
[1] 2 2
[1] FALSE
D39V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 11(6P24.2) MUTATED      0   6   14    5  1   1    0    1   7  0   0
  DEL PEAK 11(6P24.2) WILD-TYPE    1  28   55   25  5   9    7    8  29  2   2
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 11(6P24.2) MUTATED     2  1   0  1
  DEL PEAK 11(6P24.2) WILD-TYPE  15  7   1 15
D39V42, multiclass
      clus
vv     DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  T1A1                           0                             1
  T1B                            6                            28
  T1B1                          14                            55
  T1B2                           5                            25
  T2                             1                             5
  T2A                            1                             9
  T2A1                           0                             7
  T2A2                           1                             8
  T2B                            7                            29
  T3                             0                             2
  T3A                            0                             2
  T3B                            2                            15
  T4                             1                             7
  TIS                            0                             1
  TX                             1                            15
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 11(6P24.2) MUTATED         0        0         0         0        7
  DEL PEAK 11(6P24.2) WILD-TYPE       5        1         1         1       26
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 11(6P24.2) MUTATED          14         5        0         1
  DEL PEAK 11(6P24.2) WILD-TYPE        63        31        4         7
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 11(6P24.2) MUTATED            0          0         7         0
  DEL PEAK 11(6P24.2) WILD-TYPE          5          7        36         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 11(6P24.2) MUTATED            0          9         0         2
  DEL PEAK 11(6P24.2) WILD-TYPE          3         33         7        10
D39V44, multiclass
            clus
vv           DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             7                            26
  STAGE IB1                           14                            63
  STAGE IB2                            5                            31
  STAGE II                             0                             4
  STAGE IIA                            1                             7
  STAGE IIA1                           0                             5
  STAGE IIA2                           0                             7
  STAGE IIB                            7                            36
  STAGE III                            0                             1
  STAGE IIIA                           0                             3
  STAGE IIIB                           9                            33
  STAGE IVA                            0                             7
  STAGE IVB                            2                            10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = DEL PEAK 12(6Q26) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q26) MUTATED    72  18
  DEL PEAK 12(6Q26) WILD-TYPE 141  47
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         90                         188 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         18                          47 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM 
       12.39        49.48        23.67        36.56       173.29        82.85 
TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LT TCGA-C5-A2LV 
       67.46        30.21        35.01        57.73        73.18        73.45 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH 
      100.14        38.43        52.01        17.85       210.67       154.32 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XK 
      147.35       131.11        94.95         9.34        50.99        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM 
       23.51        27.52         1.12        58.88        44.94        40.04 
TCGA-DS-A0VM TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
      117.99        12.36        25.02        14.50        26.01        12.66 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PI 
       14.89        14.96        13.58        12.59         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RM TCGA-EK-A2RN 
        0.43         0.59         0.07         4.04         2.24         0.10 
TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3HY 
        0.10         7.92        14.70        15.55        23.84        31.36 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LC 
        3.52         1.35         1.32        20.78       147.39       117.40 
TCGA-IR-A3LH TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX TCGA-MA-AA42 
       78.71        21.44        21.11         7.99        12.49         8.52 
TCGA-MU-A5YI TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PD 
       34.62         5.49        16.41         9.04        19.59        11.67 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF 
       12.16        10.03        19.96        59.51        11.51        57.93 
TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UC 
        4.73        39.78        48.07        45.34        44.94        22.72 
TCGA-VS-A9UU TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
       14.53        18.84        14.04        14.89        29.26        19.13 

$`DEL PEAK 12(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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL 
       44.22        83.05        78.35        33.24        18.02        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48        20.35        17.19       155.77 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YT 
       13.61         2.73        45.83         8.35       146.86        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       20.91        11.87        50.76        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        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        39.55        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E 
       13.05        14.50        26.40        24.56        12.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N 
       26.79        13.91        15.02        14.99        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       45.96        26.27         6.64         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO 
       16.08         0.03         0.36         1.18        47.77         0.07 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M 
        0.10         0.03        20.35         6.94        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        1.22         0.92         2.17        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        1.48         0.82         1.97         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
       10.82        21.67        14.93         9.44       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 
      195.85        30.31        11.28         0.89         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       13.35        22.52        20.28        17.82        19.56         9.17 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       11.38        13.87         5.42        54.81        35.05        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        2.96        15.58        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF 
       15.88         9.34        15.39        19.36         3.88        93.99 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 
       66.05        40.50        37.78        26.43        18.05        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       46.03        36.13        39.78        31.27        36.26        16.64 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U6 
       24.39        50.86        15.68        50.63        50.14        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       42.41        25.74        21.30        19.69        46.92        40.96 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        41.42        43.27        35.97 
TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V4 
       20.09         3.42        18.25        67.20         5.16         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       16.24        15.42        26.01        67.59         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     210.67                      195.85 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     20.945                      19.625 
[1] "0.1 - 210.7 (20.9)" "0.0 - 195.8 (19.6)"
[1] "hr=" "1.5"
D40V2, continuous
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK 12(6Q26) MUTATED   43 22  6  1
  DEL PEAK 12(6Q26) WILD-TYPE 91 46 15  7
D40V3, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T1                        43                          91
  T2                        22                          46
  T3                         6                          15
  T4                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   38 19
  DEL PEAK 12(6Q26) WILD-TYPE 89 36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     38   19
  DEL PEAK 12(6Q26) WILD-TYPE   89   36
   clus
vv  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  0                        38                          89
  1                        19                          36
[1] 2 2
[1] FALSE
D40V5, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   39  4
  DEL PEAK 12(6Q26) WILD-TYPE 68  6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     39    4
  DEL PEAK 12(6Q26) WILD-TYPE   68    6
   clus
vv  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  0                        39                          68
  1                         4                           6
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(6Q26) MUTATED               1                               87
  DEL PEAK 12(6Q26) WILD-TYPE             4                              154
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 12(6Q26) MUTATED                                               1
  DEL PEAK 12(6Q26) WILD-TYPE                                             5
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 12(6Q26) MUTATED                                     8
  DEL PEAK 12(6Q26) WILD-TYPE                                  14
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 12(6Q26) MUTATED                                           1
  DEL PEAK 12(6Q26) WILD-TYPE                                         2
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 12(6Q26) MUTATED                                              2
  DEL PEAK 12(6Q26) WILD-TYPE                                           13
D40V6, multiclass
                                               clus
vv                                              DEL PEAK 12(6Q26) MUTATED
  ADENOSQUAMOUS                                                         1
  CERVICAL SQUAMOUS CELL CARCINOMA                                     87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          2
                                               clus
vv                                              DEL PEAK 12(6Q26) WILD-TYPE
  ADENOSQUAMOUS                                                           4
  CERVICAL SQUAMOUS CELL CARCINOMA                                      154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED     9  91
  DEL PEAK 12(6Q26) WILD-TYPE  21 171
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED      9   91
  DEL PEAK 12(6Q26) WILD-TYPE   21  171
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  NO                          9                          21
  YES                        91                         171
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6Q26) MUTATED                                  2     4
  DEL PEAK 12(6Q26) WILD-TYPE                                6    14
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(6Q26) MUTATED                          11
  DEL PEAK 12(6Q26) WILD-TYPE                        17
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(6Q26) MUTATED                                           2    68
  DEL PEAK 12(6Q26) WILD-TYPE                                         0   133
D40V10, multiclass
                                           clus
vv                                          DEL PEAK 12(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             4
  BLACK OR AFRICAN AMERICAN                                        11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            68
                                           clus
vv                                          DEL PEAK 12(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                          17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             133
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED     5  55
  DEL PEAK 12(6Q26) WILD-TYPE  18 106
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED      5   55
  DEL PEAK 12(6Q26) WILD-TYPE   18  106
                        clus
vv                       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             5                          18
  NOT HISPANIC OR LATINO                        55                         106
[1] 2 2
[1] FALSE
D40V12, continuous
D40V13, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   42 14
  DEL PEAK 12(6Q26) WILD-TYPE 92 27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     42   14
  DEL PEAK 12(6Q26) WILD-TYPE   92   27
            clus
vv           DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  TUMOR FREE                        42                          92
  WITH TUMOR                        14                          27
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 12(6Q26) MUTATED       16      4       0      4       2
  DEL PEAK 12(6Q26) WILD-TYPE     37      1       1      7       5
                             vv
clus                          UNITED STATES VIETNAM
  DEL PEAK 12(6Q26) MUTATED              70       4
  DEL PEAK 12(6Q26) WILD-TYPE           131      10
D40V14, multiclass
               clus
vv              DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  BRAZIL                               16                          37
  CANADA                                4                           1
  NIGERIA                               0                           1
  RUSSIA                                4                           7
  UKRAINE                               2                           5
  UNITED STATES                        70                         131
  VIETNAM                               4                          10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  DEL PEAK 12(6Q26) MUTATED    7 36 46  1  5
  DEL PEAK 12(6Q26) WILD-TYPE 11 93 67  0 19
D40V15, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  G1                         7                          11
  G2                        36                          93
  G3                        46                          67
  G4                         1                           0
  GX                         5                          19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V16, continuous
D40V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 12(6Q26) MUTATED                                            13
  DEL PEAK 12(6Q26) WILD-TYPE                                          24
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 12(6Q26) MUTATED                                        2
  DEL PEAK 12(6Q26) WILD-TYPE                                      7
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 12(6Q26) MUTATED                                                 2
  DEL PEAK 12(6Q26) WILD-TYPE                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 12(6Q26) MUTATED               21                  44
  DEL PEAK 12(6Q26) WILD-TYPE             41                  98
D40V18, multiclass
                                                 clus
vv                                                DEL PEAK 12(6Q26) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                            13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         2
  CURRENT SMOKER                                                         21
  LIFELONG NON-SMOKER                                                    44
                                                 clus
vv                                                DEL PEAK 12(6Q26) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           41
  LIFELONG NON-SMOKER                                                      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"
D40V19, continuous
D40V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 12(6Q26) MUTATED             6       34             4        9
  DEL PEAK 12(6Q26) WILD-TYPE          13       68             8       16
D40V21, multiclass
               clus
vv              DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  COMBINATION                           6                          13
  EXTERNAL                             34                          68
  EXTERNAL BEAM                         4                           8
  INTERNAL                              9                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V22, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED    8  0
  DEL PEAK 12(6Q26) WILD-TYPE 17  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED      8    0
  DEL PEAK 12(6Q26) WILD-TYPE   17    3
                         clus
vv                        DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  COMPLETED AS PLANNED                            8                          17
  TREATMENT NOT COMPLETED                         0                           3
[1] 2 2
[1] FALSE
                             vv
clus                          DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 12(6Q26) MUTATED                    0                0
  DEL PEAK 12(6Q26) WILD-TYPE                  2                2
                             vv
clus                          PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 12(6Q26) MUTATED                    16             9
  DEL PEAK 12(6Q26) WILD-TYPE                  20            24
D40V23, multiclass
                     clus
vv                    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  DISTANT RECURRENCE                          0                           2
  LOCAL RECURRENCE                            0                           2
  PRIMARY TUMOR FIELD                        16                          20
  REGIONAL SITE                               9                          24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V24, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   18  3
  DEL PEAK 12(6Q26) WILD-TYPE 38  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     18    3
  DEL PEAK 12(6Q26) WILD-TYPE   38    2
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  CGY                        18                          38
  GY                          3                           2
[1] 2 2
[1] FALSE
D40V25, continuous
D40V26, continuous
D40V27, continuous
D40V28, continuous
D40V29, continuous
D40V30, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 12(6Q26) MUTATED                                     1
  DEL PEAK 12(6Q26) WILD-TYPE                                   1
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 12(6Q26) MUTATED                                     1
  DEL PEAK 12(6Q26) WILD-TYPE                                   6
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 12(6Q26) MUTATED                        15                       0
  DEL PEAK 12(6Q26) WILD-TYPE                      20                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  DEL PEAK 12(6Q26) MUTATED                         3
  DEL PEAK 12(6Q26) WILD-TYPE                       5
D40V31, multiclass
                                     clus
vv                                    DEL PEAK 12(6Q26) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  OTHER LOCATION, SPECIFY                                    15
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     3
                                     clus
vv                                    DEL PEAK 12(6Q26) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           6
  OTHER LOCATION, SPECIFY                                      20
  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 12(6Q26) MUTATED                                               2
  DEL PEAK 12(6Q26) WILD-TYPE                                             0
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 12(6Q26) MUTATED                                                8
  DEL PEAK 12(6Q26) WILD-TYPE                                             17
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 12(6Q26) MUTATED                                                                                  24
  DEL PEAK 12(6Q26) WILD-TYPE                                                                                57
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 12(6Q26) MUTATED                                                                                             39
  DEL PEAK 12(6Q26) WILD-TYPE                                                                                           81
D40V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 12(6Q26) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   24
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        39
                                                                                              clus
vv                                                                                             DEL PEAK 12(6Q26) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V33, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   21 25
  DEL PEAK 12(6Q26) WILD-TYPE 49 48
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     21   25
  DEL PEAK 12(6Q26) WILD-TYPE   49   48
         clus
vv        DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  ABSENT                         21                          49
  PRESENT                        25                          48
[1] 2 2
[1] FALSE
D40V34, continuous
D40V35, continuous
D40V36, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   16 36
  DEL PEAK 12(6Q26) WILD-TYPE 32 80
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     16   36
  DEL PEAK 12(6Q26) WILD-TYPE   32   80
                                          clus
vv                                         DEL PEAK 12(6Q26) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        36
                                          clus
vv                                         DEL PEAK 12(6Q26) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          80
[1] 2 2
[1] FALSE
D40V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  DEL PEAK 12(6Q26) MUTATED              5          19         24
  DEL PEAK 12(6Q26) WILD-TYPE           10          34         60
D40V38, multiclass
              clus
vv             DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  CURRENT USER                         5                          10
  FORMER USER                         19                          34
  NEVER USED                          24                          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"
D40V39, continuous
D40V40, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   33  5
  DEL PEAK 12(6Q26) WILD-TYPE 59 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     33    5
  DEL PEAK 12(6Q26) WILD-TYPE   59   12
         clus
vv        DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  ABSENT                         33                          59
  PRESENT                         5                          12
[1] 2 2
[1] FALSE
D40V41, continuous
                             vv
clus                          T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 12(6Q26) MUTATED      1  15   22    5  1   1    5    1  14  0   1
  DEL PEAK 12(6Q26) WILD-TYPE    0  19   47   25  5   9    2    8  22  2   1
                             vv
clus                          T3B T4 TIS TX
  DEL PEAK 12(6Q26) MUTATED     5  1   1  5
  DEL PEAK 12(6Q26) WILD-TYPE  12  7   0 11
D40V42, multiclass
      clus
vv     DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T1A1                         1                           0
  T1B                         15                          19
  T1B1                        22                          47
  T1B2                         5                          25
  T2                           1                           5
  T2A                          1                           9
  T2A1                         5                           2
  T2A2                         1                           8
  T2B                         14                          22
  T3                           0                           2
  T3A                          1                           1
  T3B                          5                          12
  T4                           1                           7
  TIS                          1                           0
  TX                           5                          11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 12(6Q26) MUTATED         2        0         1         1       15
  DEL PEAK 12(6Q26) WILD-TYPE       3        1         0         0       18
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  DEL PEAK 12(6Q26) MUTATED          27         7        0         3          3
  DEL PEAK 12(6Q26) WILD-TYPE        50        29        4         5          2
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  DEL PEAK 12(6Q26) MUTATED            1        15         0          1
  DEL PEAK 12(6Q26) WILD-TYPE          6        28         1          2
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 12(6Q26) MUTATED           16         1         3
  DEL PEAK 12(6Q26) WILD-TYPE         26         6         9
D40V44, multiclass
            clus
vv           DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  STAGE I                            2                           3
  STAGE IA                           0                           1
  STAGE IA1                          1                           0
  STAGE IA2                          1                           0
  STAGE IB                          15                          18
  STAGE IB1                         27                          50
  STAGE IB2                          7                          29
  STAGE II                           0                           4
  STAGE IIA                          3                           5
  STAGE IIA1                         3                           2
  STAGE IIA2                         1                           6
  STAGE IIB                         15                          28
  STAGE III                          0                           1
  STAGE IIIA                         1                           2
  STAGE IIIB                        16                          26
  STAGE IVA                          1                           6
  STAGE IVB                          3                           9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 13(7Q34) MUTATION ANALYSIS
D41V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(7Q34) MUTATED    40  19
  DEL PEAK 13(7Q34) WILD-TYPE 173  46
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                         59                         219 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                         19                          46 
$`DEL PEAK 13(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-C5-A8XH 
       52.01       154.32        15.48        20.35        13.61        45.83 
TCGA-DG-A2KJ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A5ZF 
       58.88        17.52        39.55        31.36        14.50        14.96 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2RD TCGA-EK-A2RE 
       13.48         0.36        45.96        26.27         0.03         0.36 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A40J TCGA-FU-A5XV 
        2.24         0.10        20.35         0.92         1.35         1.97 
TCGA-HM-A3JJ TCGA-JW-A5VG TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MU-A51Y 
       21.67        27.42        30.31        13.35        22.52        13.87 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-RA-A741 TCGA-UC-A7PF 
       20.84         5.49        16.41         9.04         3.88        93.99 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A957 TCGA-VS-A9U7 TCGA-VS-A9UL 
       26.43        18.05        32.15        48.07        42.41        14.53 
TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9UY TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       41.42        20.09        18.25        67.59         1.41 

$`DEL PEAK 13(7Q34) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI 
       12.39        49.48        57.04        23.67        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M7 
      144.16       177.04       173.29        82.85        19.86        46.32 
TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       30.21        57.73        53.16         0.46         2.43        20.91 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 
        3.58        44.22        73.18        78.35        38.43        33.24 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99         8.35       146.86        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52        20.81        20.91        11.87         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI 
      117.99       118.65        22.98        16.83        16.18         8.28 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36        37.35        30.90        31.53        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50        26.40        24.56        26.01        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        13.91        15.02        14.99 
TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
       13.58        12.59         6.64         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        4.04         1.18        47.77         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03         7.92         6.94        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55         1.22        23.84         2.17        31.36        36.26 
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-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12         9.01        25.41        10.82        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        29.85        36.36         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85         7.99        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
        0.30         0.82        20.28        17.82        19.56         9.17 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.52        11.38        34.62         5.42        54.81        35.05 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        2.96        15.58        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD 
       15.88         9.34        15.39        19.36        19.59        11.67 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ 
       12.16        66.05        10.03        40.50        37.78        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       59.51        46.03        36.13        11.51        57.93        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        36.26        16.64         4.73        24.39        39.78 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       50.86        15.68        50.63        50.14        45.34        44.94 
TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       43.40        25.74        21.30        22.72        19.69        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU 
       40.96         1.71        27.25        43.27        35.97        14.53 
TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
        3.42        67.20        18.84         5.16        14.04        14.89 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
        4.34        16.24        15.42        26.01        29.26        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         0.16         3.91 

  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                       0.03                        0.03 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                     154.32                      210.67 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                      20.84                       19.56 
[1] "0.0 - 154.3 (20.8)" "0.0 - 210.7 (19.6)"
[1] "hr=" "1.5"
D41V2, continuous
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 13(7Q34) MUTATED    28  11   4   0
  DEL PEAK 13(7Q34) WILD-TYPE 106  57  17   8
D41V3, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  T1                        28                         106
  T2                        11                          57
  T3                         4                          17
  T4                         0                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED    21  14
  DEL PEAK 13(7Q34) WILD-TYPE 106  41
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     21   14
  DEL PEAK 13(7Q34) WILD-TYPE  106   41
   clus
vv  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  0                        21                         106
  1                        14                          41
[1] 2 2
[1] FALSE
D41V5, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   18  1
  DEL PEAK 13(7Q34) WILD-TYPE 89  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     18    1
  DEL PEAK 13(7Q34) WILD-TYPE   89    9
   clus
vv  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  0                        18                          89
  1                         1                           9
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(7Q34) MUTATED               0                               50
  DEL PEAK 13(7Q34) WILD-TYPE             5                              191
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 13(7Q34) MUTATED                                               2
  DEL PEAK 13(7Q34) WILD-TYPE                                             4
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 13(7Q34) MUTATED                                     6
  DEL PEAK 13(7Q34) WILD-TYPE                                  16
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 13(7Q34) MUTATED                                           0
  DEL PEAK 13(7Q34) WILD-TYPE                                         3
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 13(7Q34) MUTATED                                              2
  DEL PEAK 13(7Q34) WILD-TYPE                                           13
D41V6, multiclass
                                               clus
vv                                              DEL PEAK 13(7Q34) MUTATED
  ADENOSQUAMOUS                                                         0
  CERVICAL SQUAMOUS CELL CARCINOMA                                     50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          2
                                               clus
vv                                              DEL PEAK 13(7Q34) WILD-TYPE
  ADENOSQUAMOUS                                                           5
  CERVICAL SQUAMOUS CELL CARCINOMA                                      191
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED    13  47
  DEL PEAK 13(7Q34) WILD-TYPE  17 215
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     13   47
  DEL PEAK 13(7Q34) WILD-TYPE   17  215
     clus
vv    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  NO                         13                          17
  YES                        47                         215
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(7Q34) MUTATED                                  2     5
  DEL PEAK 13(7Q34) WILD-TYPE                                6    13
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(7Q34) MUTATED                           6
  DEL PEAK 13(7Q34) WILD-TYPE                        22
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(7Q34) MUTATED                                           0    43
  DEL PEAK 13(7Q34) WILD-TYPE                                         2   158
D41V10, multiclass
                                           clus
vv                                          DEL PEAK 13(7Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                         6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            43
                                           clus
vv                                          DEL PEAK 13(7Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                          22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                             158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     4  39
  DEL PEAK 13(7Q34) WILD-TYPE  19 122
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      4   39
  DEL PEAK 13(7Q34) WILD-TYPE   19  122
                        clus
vv                       DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             4                          19
  NOT HISPANIC OR LATINO                        39                         122
[1] 2 2
[1] FALSE
D41V12, continuous
D41V13, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED    25  12
  DEL PEAK 13(7Q34) WILD-TYPE 109  29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     25   12
  DEL PEAK 13(7Q34) WILD-TYPE  109   29
            clus
vv           DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  TUMOR FREE                        25                         109
  WITH TUMOR                        12                          29
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 13(7Q34) MUTATED        9      1       0      2       1
  DEL PEAK 13(7Q34) WILD-TYPE     44      4       1      9       6
                             vv
clus                          UNITED STATES VIETNAM
  DEL PEAK 13(7Q34) MUTATED              43       4
  DEL PEAK 13(7Q34) WILD-TYPE           158      10
D41V14, multiclass
               clus
vv              DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  BRAZIL                                9                          44
  CANADA                                1                           4
  NIGERIA                               0                           1
  RUSSIA                                2                           9
  UKRAINE                               1                           6
  UNITED STATES                        43                         158
  VIETNAM                               4                          10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           G1  G2  G3  G4  GX
  DEL PEAK 13(7Q34) MUTATED     2  25  27   0   5
  DEL PEAK 13(7Q34) WILD-TYPE  16 104  86   1  19
D41V15, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  G1                         2                          16
  G2                        25                         104
  G3                        27                          86
  G4                         0                           1
  GX                         5                          19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V16, continuous
D41V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 13(7Q34) MUTATED                                             5
  DEL PEAK 13(7Q34) WILD-TYPE                                          32
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 13(7Q34) MUTATED                                        3
  DEL PEAK 13(7Q34) WILD-TYPE                                      6
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 13(7Q34) MUTATED                                                 1
  DEL PEAK 13(7Q34) WILD-TYPE                                               2
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 13(7Q34) MUTATED               13                  29
  DEL PEAK 13(7Q34) WILD-TYPE             49                 113
D41V18, multiclass
                                                 clus
vv                                                DEL PEAK 13(7Q34) 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                                                         13
  LIFELONG NON-SMOKER                                                    29
                                                 clus
vv                                                DEL PEAK 13(7Q34) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           49
  LIFELONG NON-SMOKER                                                     113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V19, continuous
D41V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 13(7Q34) MUTATED             9       18             4        5
  DEL PEAK 13(7Q34) WILD-TYPE          10       84             8       20
D41V21, multiclass
               clus
vv              DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  COMBINATION                           9                          10
  EXTERNAL                             18                          84
  EXTERNAL BEAM                         4                           8
  INTERNAL                              5                          20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V22, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   11  2
  DEL PEAK 13(7Q34) WILD-TYPE 14  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     11    2
  DEL PEAK 13(7Q34) WILD-TYPE   14    1
                         clus
vv                        DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  COMPLETED AS PLANNED                           11                          14
  TREATMENT NOT COMPLETED                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                          DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 13(7Q34) MUTATED                    0                2
  DEL PEAK 13(7Q34) WILD-TYPE                  2                0
                             vv
clus                          PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 13(7Q34) MUTATED                     6             9
  DEL PEAK 13(7Q34) WILD-TYPE                  30            24
D41V23, multiclass
                     clus
vv                    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  DISTANT RECURRENCE                          0                           2
  LOCAL RECURRENCE                            2                           0
  PRIMARY TUMOR FIELD                         6                          30
  REGIONAL SITE                               9                          24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V24, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   13  2
  DEL PEAK 13(7Q34) WILD-TYPE 43  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     13    2
  DEL PEAK 13(7Q34) WILD-TYPE   43    3
     clus
vv    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  CGY                        13                          43
  GY                          2                           3
[1] 2 2
[1] FALSE
D41V25, continuous
D41V26, continuous
D41V27, continuous
D41V28, continuous
D41V29, continuous
D41V30, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 13(7Q34) MUTATED                                     0
  DEL PEAK 13(7Q34) WILD-TYPE                                   2
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 13(7Q34) MUTATED                                     2
  DEL PEAK 13(7Q34) WILD-TYPE                                   5
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 13(7Q34) MUTATED                         5                       0
  DEL PEAK 13(7Q34) WILD-TYPE                      30                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  DEL PEAK 13(7Q34) MUTATED                         1
  DEL PEAK 13(7Q34) WILD-TYPE                       7
D41V31, multiclass
                                     clus
vv                                    DEL PEAK 13(7Q34) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         2
  OTHER LOCATION, SPECIFY                                     5
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     1
                                     clus
vv                                    DEL PEAK 13(7Q34) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           5
  OTHER LOCATION, SPECIFY                                      30
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 13(7Q34) MUTATED                                               1
  DEL PEAK 13(7Q34) WILD-TYPE                                             1
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 13(7Q34) MUTATED                                                6
  DEL PEAK 13(7Q34) WILD-TYPE                                             19
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 13(7Q34) MUTATED                                                                                  17
  DEL PEAK 13(7Q34) WILD-TYPE                                                                                64
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 13(7Q34) MUTATED                                                                                             23
  DEL PEAK 13(7Q34) WILD-TYPE                                                                                           97
D41V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 13(7Q34) 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)                                   17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        23
                                                                                              clus
vv                                                                                             DEL PEAK 13(7Q34) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V33, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   11 18
  DEL PEAK 13(7Q34) WILD-TYPE 59 55
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     11   18
  DEL PEAK 13(7Q34) WILD-TYPE   59   55
         clus
vv        DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  ABSENT                         11                          59
  PRESENT                        18                          55
[1] 2 2
[1] FALSE
D41V34, continuous
D41V35, continuous
D41V36, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   13 24
  DEL PEAK 13(7Q34) WILD-TYPE 35 92
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     13   24
  DEL PEAK 13(7Q34) WILD-TYPE   35   92
                                          clus
vv                                         DEL PEAK 13(7Q34) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        24
                                          clus
vv                                         DEL PEAK 13(7Q34) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          92
[1] 2 2
[1] FALSE
D41V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  DEL PEAK 13(7Q34) MUTATED              2          12         15
  DEL PEAK 13(7Q34) WILD-TYPE           13          41         69
D41V38, multiclass
              clus
vv             DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  CURRENT USER                         2                          13
  FORMER USER                         12                          41
  NEVER USED                          15                          69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V39, continuous
D41V40, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   18  4
  DEL PEAK 13(7Q34) WILD-TYPE 74 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     18    4
  DEL PEAK 13(7Q34) WILD-TYPE   74   13
         clus
vv        DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  ABSENT                         18                          74
  PRESENT                         4                          13
[1] 2 2
[1] FALSE
D41V41, continuous
                             vv
clus                          T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 13(7Q34) MUTATED      0   9   14    5  2   2    3    2   2  0   0
  DEL PEAK 13(7Q34) WILD-TYPE    1  25   55   25  4   8    4    7  34  2   2
                             vv
clus                          T3B T4 TIS TX
  DEL PEAK 13(7Q34) MUTATED     4  0   1  2
  DEL PEAK 13(7Q34) WILD-TYPE  13  8   0 14
D41V42, multiclass
      clus
vv     DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  T1A1                         0                           1
  T1B                          9                          25
  T1B1                        14                          55
  T1B2                         5                          25
  T2                           2                           4
  T2A                          2                           8
  T2A1                         3                           4
  T2A2                         2                           7
  T2B                          2                          34
  T3                           0                           2
  T3A                          0                           2
  T3B                          4                          13
  T4                           0                           8
  TIS                          1                           0
  TX                           2                          14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 13(7Q34) MUTATED         1        0         0         0        5
  DEL PEAK 13(7Q34) WILD-TYPE       4        1         1         1       28
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  DEL PEAK 13(7Q34) MUTATED          18         7        1         4          2
  DEL PEAK 13(7Q34) WILD-TYPE        59        29        3         4          3
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  DEL PEAK 13(7Q34) MUTATED            1         9         0          0
  DEL PEAK 13(7Q34) WILD-TYPE          6        34         1          3
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 13(7Q34) MUTATED            9         0         2
  DEL PEAK 13(7Q34) WILD-TYPE         33         7        10
D41V44, multiclass
            clus
vv           DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                           0                           1
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           5                          28
  STAGE IB1                         18                          59
  STAGE IB2                          7                          29
  STAGE II                           1                           3
  STAGE IIA                          4                           4
  STAGE IIA1                         2                           3
  STAGE IIA2                         1                           6
  STAGE IIB                          9                          34
  STAGE III                          0                           1
  STAGE IIIA                         0                           3
  STAGE IIIB                         9                          33
  STAGE IVA                          0                           7
  STAGE IVB                          2                          10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.3) MUTATED    67  32
  DEL PEAK 14(8P23.3) WILD-TYPE 146  33
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           99                           179 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           32                            33 
$`DEL PEAK 14(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-A1ML TCGA-C5-A1MN 
       35.01        57.73        53.16         2.43        20.91        40.93 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CK 
       73.18        73.45        78.35        33.24        52.01       134.33 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      131.11        94.95        13.61         2.73        50.99        45.83 
TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VK 
       99.91        27.52        11.87         1.12        58.88        36.76 
TCGA-DS-A0VN TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A43B 
      118.65         8.28        12.36        30.90        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PI TCGA-EK-A2RM 
       12.66        14.89        12.59        45.96        19.27         2.24 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A23K 
        0.07         0.10         0.03         6.94         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA 
       23.84         1.45         0.82         1.32         1.12         9.01 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LH TCGA-IR-A3LK 
       25.41        21.67        14.93       137.16        78.71        29.85 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-LP-A7HU 
       15.58         8.28        30.31         0.89         0.82        13.35 
TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MY-A913 TCGA-PN-A8MA 
       17.82         9.17         8.52        34.62         5.49         2.96 
TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB 
        9.04         9.34        19.36        19.59        11.67        10.03 
TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       40.50        19.96        59.51        36.13        57.93        39.78 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM 
        4.73        24.39        19.69        40.96        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V4 
       41.42        35.97         3.42        18.25        18.84         4.34 
TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       15.42        67.59         1.41 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI 
       12.39        49.48        23.67        11.44        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX 
       38.99        35.61         0.46         3.58        44.22        83.05 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
      100.14        38.43        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      154.32       101.82        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YT 
      155.77         9.34         8.35       146.86        23.51        20.81 
TCGA-C5-A8ZZ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       20.91        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99        22.98        16.83        16.18        17.52 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       39.55        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       14.50        26.40        24.56        12.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
        0.36        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK 
        0.03         0.36         1.18        47.77         0.10         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG 
       20.35         7.92        14.70        19.79        15.55         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ 
        2.17        31.36        36.26         1.58         1.48         3.52 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.35         1.97        10.82        20.78         9.44       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        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH 
        3.29        24.56        21.44        20.48        28.37        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 
       21.11       195.85         7.99        11.28        12.49         0.30 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A8JM 
       22.52        20.28        19.56        11.38        13.87         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       54.81        35.05        20.84        15.58        16.41        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 
       16.14        17.56        14.07        15.88        15.39         3.88 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       93.99        12.16        66.05        37.78        26.43        18.05 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       32.15        46.03        11.51        31.27        36.26        16.64 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       39.78        50.86        15.68        50.63        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       45.34        44.94        43.40        42.41        25.74        21.30 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UU 
       22.72        46.92         1.71        43.27        20.09        14.53 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 
       67.20         5.16        14.04        14.89        16.24        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        19.13         0.69         0.16         3.91 

  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       137.16                        210.67 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                        19.59                         20.09 
[1] "0.0 - 137.2 (19.6)" "0.0 - 210.7 (20.1)"
[1] "hr=" "1.8"
D42V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 14(8P23.3) MUTATED   48 23  6  2
  DEL PEAK 14(8P23.3) WILD-TYPE 86 45 15  6
D42V3, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  T1                          48                            86
  T2                          23                            45
  T3                           6                            15
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   46 17
  DEL PEAK 14(8P23.3) WILD-TYPE 81 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     46   17
  DEL PEAK 14(8P23.3) WILD-TYPE   81   38
   clus
vv  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  0                          46                            81
  1                          17                            38
[1] 2 2
[1] FALSE
D42V5, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   36  4
  DEL PEAK 14(8P23.3) WILD-TYPE 71  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     36    4
  DEL PEAK 14(8P23.3) WILD-TYPE   71    6
   clus
vv  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  0                          36                            71
  1                           4                             6
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(8P23.3) MUTATED               2                               84
  DEL PEAK 14(8P23.3) WILD-TYPE             3                              157
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 14(8P23.3) MUTATED                                               2
  DEL PEAK 14(8P23.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 14(8P23.3) MUTATED                                     7
  DEL PEAK 14(8P23.3) WILD-TYPE                                  15
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 14(8P23.3) MUTATED                                           2
  DEL PEAK 14(8P23.3) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 14(8P23.3) MUTATED                                              6
  DEL PEAK 14(8P23.3) WILD-TYPE                                            9
D42V6, multiclass
                                               clus
vv                                              DEL PEAK 14(8P23.3) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
                                               clus
vv                                              DEL PEAK 14(8P23.3) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        157
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED    15  88
  DEL PEAK 14(8P23.3) WILD-TYPE  15 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     15   88
  DEL PEAK 14(8P23.3) WILD-TYPE   15  174
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  NO                           15                            15
  YES                          88                           174
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(8P23.3) MUTATED                                  3     5
  DEL PEAK 14(8P23.3) WILD-TYPE                                5    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(8P23.3) MUTATED                          12
  DEL PEAK 14(8P23.3) WILD-TYPE                        16
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(8P23.3) MUTATED                                           1    75
  DEL PEAK 14(8P23.3) WILD-TYPE                                         1   126
D42V10, multiclass
                                           clus
vv                                          DEL PEAK 14(8P23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              75
                                           clus
vv                                          DEL PEAK 14(8P23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               126
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     8  58
  DEL PEAK 14(8P23.3) WILD-TYPE  15 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      8   58
  DEL PEAK 14(8P23.3) WILD-TYPE   15  103
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           103
[1] 2 2
[1] FALSE
D42V12, continuous
D42V13, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   40 18
  DEL PEAK 14(8P23.3) WILD-TYPE 94 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     40   18
  DEL PEAK 14(8P23.3) WILD-TYPE   94   23
            clus
vv           DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  TUMOR FREE                          40                            94
  WITH TUMOR                          18                            23
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 14(8P23.3) MUTATED       20      2       1      3       2
  DEL PEAK 14(8P23.3) WILD-TYPE     33      3       0      8       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 14(8P23.3) MUTATED              71       4
  DEL PEAK 14(8P23.3) WILD-TYPE           130      10
D42V14, multiclass
               clus
vv              DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  BRAZIL                                 20                            33
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  3                             8
  UKRAINE                                 2                             5
  UNITED STATES                          71                           130
  VIETNAM                                 4                            10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 14(8P23.3) MUTATED    4 43 44  1  9
  DEL PEAK 14(8P23.3) WILD-TYPE 14 86 69  0 15
D42V15, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  G1                           4                            14
  G2                          43                            86
  G3                          44                            69
  G4                           1                             0
  GX                           9                            15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V16, continuous
D42V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 14(8P23.3) MUTATED                                            17
  DEL PEAK 14(8P23.3) WILD-TYPE                                          20
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 14(8P23.3) MUTATED                                        4
  DEL PEAK 14(8P23.3) WILD-TYPE                                      5
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 14(8P23.3) MUTATED                                                 2
  DEL PEAK 14(8P23.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 14(8P23.3) MUTATED               21                  45
  DEL PEAK 14(8P23.3) WILD-TYPE             41                  97
D42V18, multiclass
                                                 clus
vv                                                DEL PEAK 14(8P23.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           21
  LIFELONG NON-SMOKER                                                      45
                                                 clus
vv                                                DEL PEAK 14(8P23.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             41
  LIFELONG NON-SMOKER                                                        97
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V19, continuous
D42V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 14(8P23.3) MUTATED             9       37             7        7
  DEL PEAK 14(8P23.3) WILD-TYPE          10       65             5       18
D42V21, multiclass
               clus
vv              DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  COMBINATION                             9                            10
  EXTERNAL                               37                            65
  EXTERNAL BEAM                           7                             5
  INTERNAL                                7                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V22, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   12  2
  DEL PEAK 14(8P23.3) WILD-TYPE 13  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     12    2
  DEL PEAK 14(8P23.3) WILD-TYPE   13    1
                         clus
vv                        DEL PEAK 14(8P23.3) MUTATED
  COMPLETED AS PLANNED                             12
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK 14(8P23.3) WILD-TYPE
  COMPLETED AS PLANNED                               13
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 14(8P23.3) MUTATED                    0                1
  DEL PEAK 14(8P23.3) WILD-TYPE                  2                1
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 14(8P23.3) MUTATED                    16            10
  DEL PEAK 14(8P23.3) WILD-TYPE                  20            23
D42V23, multiclass
                     clus
vv                    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              1                             1
  PRIMARY TUMOR FIELD                          16                            20
  REGIONAL SITE                                10                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V24, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   20  3
  DEL PEAK 14(8P23.3) WILD-TYPE 36  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     20    3
  DEL PEAK 14(8P23.3) WILD-TYPE   36    2
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  CGY                          20                            36
  GY                            3                             2
[1] 2 2
[1] FALSE
D42V25, continuous
D42V26, continuous
D42V27, continuous
D42V28, continuous
D42V29, continuous
D42V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 14(8P23.3) MUTATED                                     1
  DEL PEAK 14(8P23.3) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 14(8P23.3) MUTATED                                     1
  DEL PEAK 14(8P23.3) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 14(8P23.3) MUTATED                        16                       0
  DEL PEAK 14(8P23.3) WILD-TYPE                      19                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 14(8P23.3) MUTATED                         3
  DEL PEAK 14(8P23.3) WILD-TYPE                       5
D42V31, multiclass
                                     clus
vv                                    DEL PEAK 14(8P23.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                      16
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    DEL PEAK 14(8P23.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                        19
  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 14(8P23.3) MUTATED                                               1
  DEL PEAK 14(8P23.3) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 14(8P23.3) MUTATED                                                8
  DEL PEAK 14(8P23.3) WILD-TYPE                                             17
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 14(8P23.3) MUTATED                                                                                  27
  DEL PEAK 14(8P23.3) WILD-TYPE                                                                                54
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 14(8P23.3) MUTATED                                                                                             45
  DEL PEAK 14(8P23.3) WILD-TYPE                                                                                           75
D42V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 14(8P23.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          45
                                                                                              clus
vv                                                                                             DEL PEAK 14(8P23.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V33, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   27 19
  DEL PEAK 14(8P23.3) WILD-TYPE 43 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     27   19
  DEL PEAK 14(8P23.3) WILD-TYPE   43   54
         clus
vv        DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  ABSENT                           27                            43
  PRESENT                          19                            54
[1] 2 2
[1] FALSE
D42V34, continuous
D42V35, continuous
D42V36, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   19 36
  DEL PEAK 14(8P23.3) WILD-TYPE 29 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     19   36
  DEL PEAK 14(8P23.3) WILD-TYPE   29   80
                                          clus
vv                                         DEL PEAK 14(8P23.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          36
                                          clus
vv                                         DEL PEAK 14(8P23.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            80
[1] 2 2
[1] FALSE
D42V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 14(8P23.3) MUTATED              5          23         28
  DEL PEAK 14(8P23.3) WILD-TYPE           10          30         56
D42V38, multiclass
              clus
vv             DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  CURRENT USER                           5                            10
  FORMER USER                           23                            30
  NEVER USED                            28                            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V39, continuous
D42V40, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   33  5
  DEL PEAK 14(8P23.3) WILD-TYPE 59 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     33    5
  DEL PEAK 14(8P23.3) WILD-TYPE   59   12
         clus
vv        DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  ABSENT                           33                            59
  PRESENT                           5                            12
[1] 2 2
[1] FALSE
D42V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 14(8P23.3) MUTATED      1  16   20   11  2   2    4    4  11  0   1
  DEL PEAK 14(8P23.3) WILD-TYPE    0  18   49   19  4   8    3    5  25  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 14(8P23.3) MUTATED     5  2   1  5
  DEL PEAK 14(8P23.3) WILD-TYPE  12  6   0 11
D42V42, multiclass
      clus
vv     DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  T1A1                           1                             0
  T1B                           16                            18
  T1B1                          20                            49
  T1B2                          11                            19
  T2                             2                             4
  T2A                            2                             8
  T2A1                           4                             3
  T2A2                           4                             5
  T2B                           11                            25
  T3                             0                             2
  T3A                            1                             1
  T3B                            5                            12
  T4                             2                             6
  TIS                            1                             0
  TX                             5                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 14(8P23.3) MUTATED         2        1         1         1       13
  DEL PEAK 14(8P23.3) WILD-TYPE       3        0         0         0       20
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 14(8P23.3) MUTATED          23        12        2         2
  DEL PEAK 14(8P23.3) WILD-TYPE        54        24        2         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 14(8P23.3) MUTATED            4          2        18         0
  DEL PEAK 14(8P23.3) WILD-TYPE          1          5        25         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 14(8P23.3) MUTATED            1         14         3         3
  DEL PEAK 14(8P23.3) WILD-TYPE          2         28         4         9
D42V44, multiclass
            clus
vv           DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            1                             0
  STAGE IA2                            1                             0
  STAGE IB                            13                            20
  STAGE IB1                           23                            54
  STAGE IB2                           12                            24
  STAGE II                             2                             2
  STAGE IIA                            2                             6
  STAGE IIA1                           4                             1
  STAGE IIA2                           2                             5
  STAGE IIB                           18                            25
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          14                            28
  STAGE IVA                            3                             4
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 15(8P23.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P23.1) MUTATED    64  28
  DEL PEAK 15(8P23.1) WILD-TYPE 149  37
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                           92                           186 
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                           28                            37 
$`DEL PEAK 15(8P23.1) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       57.04        68.84        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT 
       57.73        53.16         2.43        20.91        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       73.45        78.35        94.95        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VK 
       45.83        99.91        11.87         1.12        58.88        36.76 
TCGA-DS-A0VN TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A43B 
      118.65         8.28        12.36        30.90        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PI TCGA-EK-A2PM 
       12.66        14.89        12.59        45.96        19.27         0.59 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69M 
        2.24         0.07         0.10         0.03         6.94         8.32 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A57G TCGA-FU-A770 
        1.22        23.84         1.45         0.82         1.32         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LH TCGA-IR-A3LK 
        9.01        25.41        21.67       137.16        78.71        29.85 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3Y TCGA-MA-AA41 
       15.58         8.28         0.82        13.35        17.82         9.17 
TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73Q 
        8.52        34.62         5.49         2.96         9.04         9.34 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EC 
       19.36        19.59         3.88        11.67        10.03        40.50 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y 
       19.96        59.51        36.13        57.93        39.78         4.73 
TCGA-VS-A94Z TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       24.39        19.69        40.96        14.53        27.25        41.42 
TCGA-VS-A9UQ TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-VS-AA62 
       35.97         3.42        18.25        18.84         4.34        15.42 
TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       67.59         1.41 

$`DEL PEAK 15(8P23.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI 
       12.39        49.48        23.67        11.44        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS 
       67.46        38.99        35.61         0.46         3.58        44.22 
TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        9.34         8.35       146.86        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       20.91        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99        22.98        16.83        16.18        17.52 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       39.55        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       14.50        26.40        24.56        12.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 
        0.36        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H5 
        0.36         1.18        47.77         0.10         0.10        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92        14.70        19.79        15.55         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J 
       31.36        36.26         1.58         1.48         3.52         1.35 
TCGA-FU-A5XV TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.97        10.82        20.78        14.93         9.44       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        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH 
        3.29        24.56        21.44        20.48        28.37        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       195.85        30.31         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA43 
       12.49         0.30        22.52        20.28        19.56        11.38 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       13.87         5.42        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73R TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH 
       15.39        93.99        12.16        66.05        37.78        26.43 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W 
       18.05        32.15        46.03        11.51        31.27        36.26 
TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       16.64        39.78        50.86        15.68        50.63        48.07 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        45.34        44.94        43.40        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UP TCGA-VS-A9UR 
       21.30        22.72        46.92         1.71        43.27        20.09 
TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 
       14.53        67.20         5.16        14.04        14.89        16.24 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       26.01        29.26        19.13         0.69         0.16         3.91 

  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                       137.16                        210.67 
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                       19.055                        20.350 
[1] "0.0 - 137.2 (19.1)" "0.0 - 210.7 (20.4)"
[1] "hr=" "1.8"
D43V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 15(8P23.1) MUTATED   44 23  6  2
  DEL PEAK 15(8P23.1) WILD-TYPE 90 45 15  6
D43V3, multiclass
    clus
vv   DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  T1                          44                            90
  T2                          23                            45
  T3                           6                            15
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   43 16
  DEL PEAK 15(8P23.1) WILD-TYPE 84 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     43   16
  DEL PEAK 15(8P23.1) WILD-TYPE   84   39
   clus
vv  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  0                          43                            84
  1                          16                            39
[1] 2 2
[1] FALSE
D43V5, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   34  4
  DEL PEAK 15(8P23.1) WILD-TYPE 73  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     34    4
  DEL PEAK 15(8P23.1) WILD-TYPE   73    6
   clus
vv  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  0                          34                            73
  1                           4                             6
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(8P23.1) MUTATED               2                               79
  DEL PEAK 15(8P23.1) WILD-TYPE             3                              162
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 15(8P23.1) MUTATED                                               2
  DEL PEAK 15(8P23.1) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 15(8P23.1) MUTATED                                     5
  DEL PEAK 15(8P23.1) WILD-TYPE                                  17
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 15(8P23.1) MUTATED                                           2
  DEL PEAK 15(8P23.1) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 15(8P23.1) MUTATED                                              6
  DEL PEAK 15(8P23.1) WILD-TYPE                                            9
D43V6, multiclass
                                               clus
vv                                              DEL PEAK 15(8P23.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       79
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
                                               clus
vv                                              DEL PEAK 15(8P23.1) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        162
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.1) MUTATED    13  83
  DEL PEAK 15(8P23.1) WILD-TYPE  17 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     13   83
  DEL PEAK 15(8P23.1) WILD-TYPE   17  179
     clus
vv    DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  NO                           13                            17
  YES                          83                           179
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(8P23.1) MUTATED                                  3     3
  DEL PEAK 15(8P23.1) WILD-TYPE                                5    15
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(8P23.1) MUTATED                          12
  DEL PEAK 15(8P23.1) WILD-TYPE                        16
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(8P23.1) MUTATED                                           1    70
  DEL PEAK 15(8P23.1) WILD-TYPE                                         1   131
D43V10, multiclass
                                           clus
vv                                          DEL PEAK 15(8P23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              70
                                           clus
vv                                          DEL PEAK 15(8P23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               131
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.1) MUTATED     8  51
  DEL PEAK 15(8P23.1) WILD-TYPE  15 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED      8   51
  DEL PEAK 15(8P23.1) WILD-TYPE   15  110
                        clus
vv                       DEL PEAK 15(8P23.1) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       DEL PEAK 15(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           110
[1] 2 2
[1] FALSE
D43V12, continuous
D43V13, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   36 17
  DEL PEAK 15(8P23.1) WILD-TYPE 98 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     36   17
  DEL PEAK 15(8P23.1) WILD-TYPE   98   24
            clus
vv           DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  TUMOR FREE                          36                            98
  WITH TUMOR                          17                            24
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 15(8P23.1) MUTATED       20      2       1      3       2
  DEL PEAK 15(8P23.1) WILD-TYPE     33      3       0      8       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 15(8P23.1) MUTATED              65       3
  DEL PEAK 15(8P23.1) WILD-TYPE           136      11
D43V14, multiclass
               clus
vv              DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  BRAZIL                                 20                            33
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  3                             8
  UKRAINE                                 2                             5
  UNITED STATES                          65                           136
  VIETNAM                                 3                            11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 15(8P23.1) MUTATED    3 40 40  1 10
  DEL PEAK 15(8P23.1) WILD-TYPE 15 89 73  0 14
D43V15, multiclass
    clus
vv   DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  G1                           3                            15
  G2                          40                            89
  G3                          40                            73
  G4                           1                             0
  GX                          10                            14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V16, continuous
D43V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 15(8P23.1) MUTATED                                            16
  DEL PEAK 15(8P23.1) WILD-TYPE                                          21
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 15(8P23.1) MUTATED                                        3
  DEL PEAK 15(8P23.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 15(8P23.1) MUTATED                                                 1
  DEL PEAK 15(8P23.1) WILD-TYPE                                               2
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 15(8P23.1) MUTATED               20                  41
  DEL PEAK 15(8P23.1) WILD-TYPE             42                 101
D43V18, multiclass
                                                 clus
vv                                                DEL PEAK 15(8P23.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           20
  LIFELONG NON-SMOKER                                                      41
                                                 clus
vv                                                DEL PEAK 15(8P23.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             42
  LIFELONG NON-SMOKER                                                       101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V19, continuous
D43V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 15(8P23.1) MUTATED             7       36             7        6
  DEL PEAK 15(8P23.1) WILD-TYPE          12       66             5       19
D43V21, multiclass
               clus
vv              DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               36                            66
  EXTERNAL BEAM                           7                             5
  INTERNAL                                6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V22, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   10  2
  DEL PEAK 15(8P23.1) WILD-TYPE 15  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     10    2
  DEL PEAK 15(8P23.1) WILD-TYPE   15    1
                         clus
vv                        DEL PEAK 15(8P23.1) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK 15(8P23.1) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 15(8P23.1) MUTATED                    0                1
  DEL PEAK 15(8P23.1) WILD-TYPE                  2                1
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 15(8P23.1) MUTATED                    14             9
  DEL PEAK 15(8P23.1) WILD-TYPE                  22            24
D43V23, multiclass
                     clus
vv                    DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  DISTANT RECURRENCE                            0                             2
  LOCAL RECURRENCE                              1                             1
  PRIMARY TUMOR FIELD                          14                            22
  REGIONAL SITE                                 9                            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V24, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   19  3
  DEL PEAK 15(8P23.1) WILD-TYPE 37  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     19    3
  DEL PEAK 15(8P23.1) WILD-TYPE   37    2
     clus
vv    DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  CGY                          19                            37
  GY                            3                             2
[1] 2 2
[1] FALSE
D43V25, continuous
D43V26, continuous
D43V27, continuous
D43V28, continuous
D43V29, continuous
D43V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 15(8P23.1) MUTATED                                     1
  DEL PEAK 15(8P23.1) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 15(8P23.1) MUTATED                                     1
  DEL PEAK 15(8P23.1) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 15(8P23.1) MUTATED                        15                       0
  DEL PEAK 15(8P23.1) WILD-TYPE                      20                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 15(8P23.1) MUTATED                         3
  DEL PEAK 15(8P23.1) WILD-TYPE                       5
D43V31, multiclass
                                     clus
vv                                    DEL PEAK 15(8P23.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                      15
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    DEL PEAK 15(8P23.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                        20
  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 15(8P23.1) MUTATED                                               1
  DEL PEAK 15(8P23.1) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 15(8P23.1) MUTATED                                                7
  DEL PEAK 15(8P23.1) WILD-TYPE                                             18
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 15(8P23.1) MUTATED                                                                                  27
  DEL PEAK 15(8P23.1) WILD-TYPE                                                                                54
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 15(8P23.1) MUTATED                                                                                             43
  DEL PEAK 15(8P23.1) WILD-TYPE                                                                                           77
D43V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 15(8P23.1) 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)                                     27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          43
                                                                                              clus
vv                                                                                             DEL PEAK 15(8P23.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V33, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   26 17
  DEL PEAK 15(8P23.1) WILD-TYPE 44 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     26   17
  DEL PEAK 15(8P23.1) WILD-TYPE   44   56
         clus
vv        DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  ABSENT                           26                            44
  PRESENT                          17                            56
[1] 2 2
[1] FALSE
D43V34, continuous
D43V35, continuous
D43V36, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   18 36
  DEL PEAK 15(8P23.1) WILD-TYPE 30 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     18   36
  DEL PEAK 15(8P23.1) WILD-TYPE   30   80
                                          clus
vv                                         DEL PEAK 15(8P23.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          36
                                          clus
vv                                         DEL PEAK 15(8P23.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            80
[1] 2 2
[1] FALSE
D43V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 15(8P23.1) MUTATED              5          18         27
  DEL PEAK 15(8P23.1) WILD-TYPE           10          35         57
D43V38, multiclass
              clus
vv             DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  CURRENT USER                           5                            10
  FORMER USER                           18                            35
  NEVER USED                            27                            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"
D43V39, continuous
D43V40, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   31  5
  DEL PEAK 15(8P23.1) WILD-TYPE 61 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     31    5
  DEL PEAK 15(8P23.1) WILD-TYPE   61   12
         clus
vv        DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  ABSENT                           31                            61
  PRESENT                           5                            12
[1] 2 2
[1] FALSE
D43V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 15(8P23.1) MUTATED      1  14   19   10  2   2    4    4  11  0   1
  DEL PEAK 15(8P23.1) WILD-TYPE    0  20   50   20  4   8    3    5  25  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 15(8P23.1) MUTATED     5  2   1  5
  DEL PEAK 15(8P23.1) WILD-TYPE  12  6   0 11
D43V42, multiclass
      clus
vv     DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  T1A1                           1                             0
  T1B                           14                            20
  T1B1                          19                            50
  T1B2                          10                            20
  T2                             2                             4
  T2A                            2                             8
  T2A1                           4                             3
  T2A2                           4                             5
  T2B                           11                            25
  T3                             0                             2
  T3A                            1                             1
  T3B                            5                            12
  T4                             2                             6
  TIS                            1                             0
  TX                             5                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 15(8P23.1) MUTATED         2        0         1         1       12
  DEL PEAK 15(8P23.1) WILD-TYPE       3        1         0         0       21
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 15(8P23.1) MUTATED          22        10        2         2
  DEL PEAK 15(8P23.1) WILD-TYPE        55        26        2         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 15(8P23.1) MUTATED            4          2        19         0
  DEL PEAK 15(8P23.1) WILD-TYPE          1          5        24         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 15(8P23.1) MUTATED            1         12         2         3
  DEL PEAK 15(8P23.1) WILD-TYPE          2         30         5         9
D43V44, multiclass
            clus
vv           DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IA1                            1                             0
  STAGE IA2                            1                             0
  STAGE IB                            12                            21
  STAGE IB1                           22                            55
  STAGE IB2                           10                            26
  STAGE II                             2                             2
  STAGE IIA                            2                             6
  STAGE IIA1                           4                             1
  STAGE IIA2                           2                             5
  STAGE IIB                           19                            24
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          12                            30
  STAGE IVA                            2                             5
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 16(10Q23.31) MUTATED    58  23
  DEL PEAK 16(10Q23.31) WILD-TYPE 155  42
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             81                             197 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             23                              42 
$`DEL PEAK 16(10Q23.31) MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       57.04        23.67        11.44       173.29        82.85        19.86 
TCGA-C5-A1M6 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A2LT 
       31.40        38.99        35.61         0.46        20.91        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK 
       73.45        83.05        20.42       210.67       154.32       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A7X8 
       15.48        20.35       147.35        17.19        13.61         2.73 
TCGA-C5-A8XJ TCGA-C5-A8YR TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VK TCGA-EA-A439 
      146.86        27.52        58.88        44.94        36.76        14.50 
TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       14.96        13.48        12.59        26.27         6.64        19.27 
TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 
        0.59         1.18        47.77         2.24         0.10        20.35 
TCGA-FU-A2QG TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A40J TCGA-GH-A9DA TCGA-HM-A3JJ 
        0.92         1.58         1.48         1.35         9.01        21.67 
TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VK 
       20.78         9.44        66.81        78.71        36.36        20.48 
TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MY-A913 
       28.37        30.31        12.49         8.52        11.38         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EH 
        2.96        16.41         9.04        12.16        66.05        26.43 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A9U5 
       19.96        59.51         4.73        39.78        50.63        44.94 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UR 
       19.69        46.92        40.96        14.53        43.27        20.09 
TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-ZJ-AAX4 
       18.84         4.34         0.69 

$`DEL PEAK 16(10Q23.31) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       12.39        49.48        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
      177.04         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        33.24        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       155.77       131.11        94.95         9.34 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT 
       50.99        45.83         8.35        99.91        23.51        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        11.87         1.12        50.76        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        12.36        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        26.01        12.66        12.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89        26.79        13.91        15.02        14.99        13.58 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
        0.36        45.96         1.51         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.10         0.10         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ 
        2.17        31.36        36.26         1.45         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41        10.82        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        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 
       27.42         3.29        24.56        21.44        15.58         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       18.15        21.11       195.85         7.99        11.28         0.89 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
       19.56         9.17        13.87        34.62         5.42        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       35.05        20.84        15.58        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        15.39        19.36        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        3.88        11.67        93.99        10.03        40.50        37.78 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       18.05        32.15        46.03        36.13        11.51        57.93 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        36.26        16.64        24.39        50.86 
TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 
       15.68        48.07        50.14        45.34        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO 
       25.74        21.30        22.72         1.71        27.25        41.42 
TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 
       35.97        14.53         3.42        18.25        67.20         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       14.04        14.89        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         210.67                          195.85 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                          20.35                           19.13 
[1] "0.1 - 210.7 (20.4)" "0.0 - 195.8 (19.1)"
[1] "hr=" "1.2"
D44V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 16(10Q23.31) MUTATED    32  23   8   2
  DEL PEAK 16(10Q23.31) WILD-TYPE 102  45  13   6
D44V3, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T1                            32                             102
  T2                            23                              45
  T3                             8                              13
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   29 17
  DEL PEAK 16(10Q23.31) WILD-TYPE 98 38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     29   17
  DEL PEAK 16(10Q23.31) WILD-TYPE   98   38
   clus
vv  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  0                            29                              98
  1                            17                              38
[1] 2 2
[1] FALSE
D44V5, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   26  3
  DEL PEAK 16(10Q23.31) WILD-TYPE 81  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     26    3
  DEL PEAK 16(10Q23.31) WILD-TYPE   81    7
   clus
vv  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  0                            26                              81
  1                             3                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 16(10Q23.31) MUTATED               1
  DEL PEAK 16(10Q23.31) WILD-TYPE             4
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(10Q23.31) MUTATED                                 70
  DEL PEAK 16(10Q23.31) WILD-TYPE                              171
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 16(10Q23.31) MUTATED                                               2
  DEL PEAK 16(10Q23.31) WILD-TYPE                                             4
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 16(10Q23.31) MUTATED                                     7
  DEL PEAK 16(10Q23.31) WILD-TYPE                                  15
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 16(10Q23.31) MUTATED                                           1
  DEL PEAK 16(10Q23.31) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 16(10Q23.31) MUTATED                                              5
  DEL PEAK 16(10Q23.31) WILD-TYPE                                           10
D44V6, multiclass
                                               clus
vv                                              DEL PEAK 16(10Q23.31) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         70
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
                                               clus
vv                                              DEL PEAK 16(10Q23.31) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          171
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               10
[1] 6 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 16(10Q23.31) MUTATED    13  73
  DEL PEAK 16(10Q23.31) WILD-TYPE  17 189
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     13   73
  DEL PEAK 16(10Q23.31) WILD-TYPE   17  189
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  NO                             13                              17
  YES                            73                             189
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(10Q23.31) MUTATED                                  0     5
  DEL PEAK 16(10Q23.31) WILD-TYPE                                8    13
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(10Q23.31) MUTATED                          15
  DEL PEAK 16(10Q23.31) WILD-TYPE                        13
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 16(10Q23.31) MUTATED                                           0
  DEL PEAK 16(10Q23.31) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  DEL PEAK 16(10Q23.31) MUTATED      57
  DEL PEAK 16(10Q23.31) WILD-TYPE   144
D44V10, multiclass
                                           clus
vv                                          DEL PEAK 16(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                57
                                           clus
vv                                          DEL PEAK 16(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  WHITE                                                                 144
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED     6  46
  DEL PEAK 16(10Q23.31) WILD-TYPE  17 115
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      6   46
  DEL PEAK 16(10Q23.31) WILD-TYPE   17  115
                        clus
vv                       DEL PEAK 16(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            46
                        clus
vv                       DEL PEAK 16(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  17
  NOT HISPANIC OR LATINO                             115
[1] 2 2
[1] FALSE
D44V12, continuous
D44V13, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   38 14
  DEL PEAK 16(10Q23.31) WILD-TYPE 96 27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     38   14
  DEL PEAK 16(10Q23.31) WILD-TYPE   96   27
            clus
vv           DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  TUMOR FREE                            38                              96
  WITH TUMOR                            14                              27
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 16(10Q23.31) MUTATED       15      2       1      0       0
  DEL PEAK 16(10Q23.31) WILD-TYPE     38      3       0     11       7
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 16(10Q23.31) MUTATED              64       4
  DEL PEAK 16(10Q23.31) WILD-TYPE           137      10
D44V14, multiclass
               clus
vv              DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  BRAZIL                                   15                              38
  CANADA                                    2                               3
  NIGERIA                                   1                               0
  RUSSIA                                    0                              11
  UKRAINE                                   0                               7
  UNITED STATES                            64                             137
  VIETNAM                                   4                              10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               G1  G2  G3  G4  GX
  DEL PEAK 16(10Q23.31) MUTATED     3  29  46   1   6
  DEL PEAK 16(10Q23.31) WILD-TYPE  15 100  67   0  18
D44V15, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  G1                             3                              15
  G2                            29                             100
  G3                            46                              67
  G4                             1                               0
  GX                             6                              18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V16, continuous
D44V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 16(10Q23.31) MUTATED                                            14
  DEL PEAK 16(10Q23.31) WILD-TYPE                                          23
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 16(10Q23.31) MUTATED                                        4
  DEL PEAK 16(10Q23.31) WILD-TYPE                                      5
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 16(10Q23.31) MUTATED                                                 2
  DEL PEAK 16(10Q23.31) WILD-TYPE                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 16(10Q23.31) MUTATED               17                  32
  DEL PEAK 16(10Q23.31) WILD-TYPE             45                 110
D44V18, multiclass
                                                 clus
vv                                                DEL PEAK 16(10Q23.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             17
  LIFELONG NON-SMOKER                                                        32
                                                 clus
vv                                                DEL PEAK 16(10Q23.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               45
  LIFELONG NON-SMOKER                                                         110
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V19, continuous
D44V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 16(10Q23.31) MUTATED             7       31             6        4
  DEL PEAK 16(10Q23.31) WILD-TYPE          12       71             6       21
D44V21, multiclass
               clus
vv              DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  COMBINATION                               7                              12
  EXTERNAL                                 31                              71
  EXTERNAL BEAM                             6                               6
  INTERNAL                                  4                              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"
D44V22, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   11  1
  DEL PEAK 16(10Q23.31) WILD-TYPE 14  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     11    1
  DEL PEAK 16(10Q23.31) WILD-TYPE   14    2
                         clus
vv                        DEL PEAK 16(10Q23.31) MUTATED
  COMPLETED AS PLANNED                               11
  TREATMENT NOT COMPLETED                             1
                         clus
vv                        DEL PEAK 16(10Q23.31) WILD-TYPE
  COMPLETED AS PLANNED                                 14
  TREATMENT NOT COMPLETED                               2
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 16(10Q23.31) MUTATED                    0                2
  DEL PEAK 16(10Q23.31) WILD-TYPE                  2                0
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 16(10Q23.31) MUTATED                    14             9
  DEL PEAK 16(10Q23.31) WILD-TYPE                  22            24
D44V23, multiclass
                     clus
vv                    DEL PEAK 16(10Q23.31) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                2
  PRIMARY TUMOR FIELD                            14
  REGIONAL SITE                                   9
                     clus
vv                    DEL PEAK 16(10Q23.31) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  0
  PRIMARY TUMOR FIELD                              22
  REGIONAL SITE                                    24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V24, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   19  2
  DEL PEAK 16(10Q23.31) WILD-TYPE 37  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     19    2
  DEL PEAK 16(10Q23.31) WILD-TYPE   37    3
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CGY                            19                              37
  GY                              2                               3
[1] 2 2
[1] FALSE
D44V25, continuous
D44V26, continuous
D44V27, continuous
D44V28, continuous
D44V29, continuous
D44V30, 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                                   4
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 16(10Q23.31) MUTATED                         8
  DEL PEAK 16(10Q23.31) WILD-TYPE                      27
                                 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                         6
  DEL PEAK 16(10Q23.31) WILD-TYPE                       2
D44V31, multiclass
                                     clus
vv                                    DEL PEAK 16(10Q23.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                         8
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         6
                                     clus
vv                                    DEL PEAK 16(10Q23.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               4
  OTHER LOCATION, SPECIFY                                          27
  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 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                                                9
  DEL PEAK 16(10Q23.31) WILD-TYPE                                             16
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 16(10Q23.31) MUTATED                                                                                  30
  DEL PEAK 16(10Q23.31) WILD-TYPE                                                                                51
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 16(10Q23.31) MUTATED                                                                                             23
  DEL PEAK 16(10Q23.31) WILD-TYPE                                                                                           97
D44V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 16(10Q23.31) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            23
                                                                                              clus
vv                                                                                             DEL PEAK 16(10Q23.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V33, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   16 24
  DEL PEAK 16(10Q23.31) WILD-TYPE 54 49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     16   24
  DEL PEAK 16(10Q23.31) WILD-TYPE   54   49
         clus
vv        DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  ABSENT                             16                              54
  PRESENT                            24                              49
[1] 2 2
[1] FALSE
D44V34, continuous
D44V35, continuous
D44V36, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   19 29
  DEL PEAK 16(10Q23.31) WILD-TYPE 29 87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     19   29
  DEL PEAK 16(10Q23.31) WILD-TYPE   29   87
                                          clus
vv                                         DEL PEAK 16(10Q23.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            29
                                          clus
vv                                         DEL PEAK 16(10Q23.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              87
[1] 2 2
[1] FALSE
D44V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 16(10Q23.31) MUTATED              2          12         23
  DEL PEAK 16(10Q23.31) WILD-TYPE           13          41         61
D44V38, multiclass
              clus
vv             DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CURRENT USER                             2                              13
  FORMER USER                             12                              41
  NEVER USED                              23                              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"
D44V39, continuous
D44V40, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   22  5
  DEL PEAK 16(10Q23.31) WILD-TYPE 70 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     22    5
  DEL PEAK 16(10Q23.31) WILD-TYPE   70   12
         clus
vv        DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  ABSENT                             22                              70
  PRESENT                             5                              12
[1] 2 2
[1] FALSE
D44V41, continuous
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 16(10Q23.31) MUTATED      0   9   17    6  3   5    3    0  12  0
  DEL PEAK 16(10Q23.31) WILD-TYPE    1  25   52   24  3   5    4    9  24  2
                                 vv
clus                              T3A T3B T4 TIS TX
  DEL PEAK 16(10Q23.31) MUTATED     2   6  2   1  2
  DEL PEAK 16(10Q23.31) WILD-TYPE   0  11  6   0 14
D44V42, multiclass
      clus
vv     DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T1A1                             0                               1
  T1B                              9                              25
  T1B1                            17                              52
  T1B2                             6                              24
  T2                               3                               3
  T2A                              5                               5
  T2A1                             3                               4
  T2A2                             0                               9
  T2B                             12                              24
  T3                               0                               2
  T3A                              2                               0
  T3B                              6                              11
  T4                               2                               6
  TIS                              1                               0
  TX                               2                              14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 16(10Q23.31) MUTATED         1        0         0         1       13
  DEL PEAK 16(10Q23.31) WILD-TYPE       4        1         1         0       20
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 16(10Q23.31) MUTATED          17        11        1         5
  DEL PEAK 16(10Q23.31) WILD-TYPE        60        25        3         3
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 16(10Q23.31) MUTATED            2          1        12         0
  DEL PEAK 16(10Q23.31) WILD-TYPE          3          6        31         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 16(10Q23.31) MUTATED            2         14         3         2
  DEL PEAK 16(10Q23.31) WILD-TYPE          1         28         4        10
D44V44, multiclass
            clus
vv           DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                              13                              20
  STAGE IB1                             17                              60
  STAGE IB2                             11                              25
  STAGE II                               1                               3
  STAGE IIA                              5                               3
  STAGE IIA1                             2                               3
  STAGE IIA2                             1                               6
  STAGE IIB                             12                              31
  STAGE III                              0                               1
  STAGE IIIA                             2                               1
  STAGE IIIB                            14                              28
  STAGE IVA                              3                               4
  STAGE IVB                              2                              10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 17(11P15.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(11P15.1) MUTATED    71  25
  DEL PEAK 17(11P15.1) WILD-TYPE 142  40
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            96                            182 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            25                             40 
$`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-A1ML TCGA-C5-A2LV 
       30.21        38.99        35.61         0.46        20.91        73.45 
TCGA-C5-A2LZ TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A7UI 
      100.14       210.67       154.32        15.48       131.11        94.95 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
        2.73        50.99       146.86        99.91        23.51        27.52 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WI 
       40.04        87.75        36.76       117.99       118.65         8.28 
TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E 
       12.36        24.56        14.50        26.01        12.66         7.46 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2PL 
       14.99        14.96        13.48         0.36         1.51         0.43 
TCGA-EK-A2RA TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A69M TCGA-FU-A23L 
       16.08         2.24         0.10        20.35         8.32        23.84 
TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A770 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LK 
        1.45         0.82         1.12        66.81       117.40        29.85 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 
       24.56        21.44        20.48        11.28        12.49         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MY-A5BE TCGA-Q1-A5R2 
       13.35        22.52        20.28        11.38        35.05        16.41 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EB 
        9.04        17.56         9.34        19.59        12.16        10.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A94Y 
       26.43        18.05        19.96        46.03        57.93         4.73 
TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UI 
       39.78        48.07        45.34        44.94        19.69        40.96 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9V2 
       14.53        41.42        43.27        14.53         3.42        14.04 
TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       14.89        26.01        29.26         0.69         1.41         3.91 

$`DEL PEAK 17(11P15.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       12.39        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 
      144.16       173.29        82.85        67.46        31.40        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-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.18        83.05        78.35        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM 
       18.02        17.85        20.42       101.82       134.33        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH 
      147.35        17.19       155.77         9.34        13.61        45.83 
TCGA-C5-A8XI TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
        8.35        20.81        20.91        11.87         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ 
       50.76        44.94        58.88         2.66        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA 
       31.36        13.05        25.02        14.50        26.40        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2GZ 
       14.89        26.79        13.91        15.02        13.58        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96        26.27         6.64        19.27         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45         0.13         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
        1.18        47.77         0.10         0.07         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        7.92         6.94        14.70        19.79        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17        31.36        36.26         1.58         1.48 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       10.82        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      137.16        96.95        78.71        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
        3.29        15.58        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA3Y 
      195.85        30.31         7.99         0.89         0.30        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         9.17         8.52        13.87        34.62         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       54.81        20.84         5.49         2.96        15.58        15.95 
TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       16.14        14.07        15.88        15.39        19.36         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL 
       11.67        93.99        66.05        40.50        37.78        59.51 
TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       32.15        36.13        11.51        39.78        31.27        36.26 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 
       16.64        24.39        50.86        15.68        50.63        50.14 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH 
       43.40        42.41        25.74        21.30        22.72        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UY TCGA-VS-A9UZ 
        1.71        27.25        35.97        20.09        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       18.84         5.16         4.34        16.24        15.42        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       19.13         0.16 

  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                        210.67                         195.85 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                         20.12                          19.46 
[1] "0.1 - 210.7 (20.1)" "0.0 - 195.8 (19.5)"
[1] "hr=" "1.1"
D45V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 17(11P15.1) MUTATED   42 23 10  3
  DEL PEAK 17(11P15.1) WILD-TYPE 92 45 11  5
D45V3, multiclass
    clus
vv   DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  T1                           42                             92
  T2                           23                             45
  T3                           10                             11
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   37 19
  DEL PEAK 17(11P15.1) WILD-TYPE 90 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     37   19
  DEL PEAK 17(11P15.1) WILD-TYPE   90   36
   clus
vv  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  0                           37                             90
  1                           19                             36
[1] 2 2
[1] FALSE
D45V5, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   37  2
  DEL PEAK 17(11P15.1) WILD-TYPE 70  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     37    2
  DEL PEAK 17(11P15.1) WILD-TYPE   70    8
   clus
vv  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  0                           37                             70
  1                            2                              8
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(11P15.1) MUTATED               0                               92
  DEL PEAK 17(11P15.1) WILD-TYPE             5                              149
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 17(11P15.1) MUTATED                                               2
  DEL PEAK 17(11P15.1) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 17(11P15.1) MUTATED                                     4
  DEL PEAK 17(11P15.1) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 17(11P15.1) MUTATED                                           0
  DEL PEAK 17(11P15.1) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 17(11P15.1) MUTATED                                              3
  DEL PEAK 17(11P15.1) WILD-TYPE                                           12
D45V6, multiclass
                                               clus
vv                                              DEL PEAK 17(11P15.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        92
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             3
                                               clus
vv                                              DEL PEAK 17(11P15.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         149
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(11P15.1) MUTATED     8  93
  DEL PEAK 17(11P15.1) WILD-TYPE  22 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED      8   93
  DEL PEAK 17(11P15.1) WILD-TYPE   22  169
     clus
vv    DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  NO                             8                             22
  YES                           93                            169
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(11P15.1) MUTATED                                  2    11
  DEL PEAK 17(11P15.1) WILD-TYPE                                6     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(11P15.1) MUTATED                          10
  DEL PEAK 17(11P15.1) WILD-TYPE                        18
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 17(11P15.1) MUTATED                                           1
  DEL PEAK 17(11P15.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 17(11P15.1) MUTATED      68
  DEL PEAK 17(11P15.1) WILD-TYPE   133
D45V10, multiclass
                                           clus
vv                                          DEL PEAK 17(11P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               11
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               68
                                           clus
vv                                          DEL PEAK 17(11P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                  7
  BLACK OR AFRICAN AMERICAN                                             18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                133
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, binary
                                cls
clus                               0   1
  DEL PEAK 17(11P15.1) MUTATED     7  59
  DEL PEAK 17(11P15.1) WILD-TYPE  16 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED      7   59
  DEL PEAK 17(11P15.1) WILD-TYPE   16  102
                        clus
vv                       DEL PEAK 17(11P15.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK 17(11P15.1) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            102
[1] 2 2
[1] FALSE
D45V12, continuous
D45V13, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   44 19
  DEL PEAK 17(11P15.1) WILD-TYPE 90 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     44   19
  DEL PEAK 17(11P15.1) WILD-TYPE   90   22
            clus
vv           DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  TUMOR FREE                           44                             90
  WITH TUMOR                           19                             22
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 17(11P15.1) MUTATED       21      1       0      2       3
  DEL PEAK 17(11P15.1) WILD-TYPE     32      4       1      9       4
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 17(11P15.1) MUTATED              64      10
  DEL PEAK 17(11P15.1) WILD-TYPE           137       4
D45V14, multiclass
               clus
vv              DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  BRAZIL                                  21                             32
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   2                              9
  UKRAINE                                  3                              4
  UNITED STATES                           64                            137
  VIETNAM                                 10                              4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 17(11P15.1) MUTATED    3 39 48  0  8
  DEL PEAK 17(11P15.1) WILD-TYPE 15 90 65  1 16
D45V15, multiclass
    clus
vv   DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  G1                            3                             15
  G2                           39                             90
  G3                           48                             65
  G4                            0                              1
  GX                            8                             16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V16, continuous
D45V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 17(11P15.1) MUTATED                                            11
  DEL PEAK 17(11P15.1) WILD-TYPE                                          26
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 17(11P15.1) MUTATED                                        4
  DEL PEAK 17(11P15.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 17(11P15.1) MUTATED                                                 1
  DEL PEAK 17(11P15.1) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 17(11P15.1) MUTATED               25                  53
  DEL PEAK 17(11P15.1) WILD-TYPE             37                  89
D45V18, multiclass
                                                 clus
vv                                                DEL PEAK 17(11P15.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            25
  LIFELONG NON-SMOKER                                                       53
                                                 clus
vv                                                DEL PEAK 17(11P15.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              37
  LIFELONG NON-SMOKER                                                         89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V19, continuous
D45V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 17(11P15.1) MUTATED             5       41             3        7
  DEL PEAK 17(11P15.1) WILD-TYPE          14       61             9       18
D45V21, multiclass
               clus
vv              DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  COMBINATION                              5                             14
  EXTERNAL                                41                             61
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V22, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED    7  0
  DEL PEAK 17(11P15.1) WILD-TYPE 18  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED      7    0
  DEL PEAK 17(11P15.1) WILD-TYPE   18    3
                         clus
vv                        DEL PEAK 17(11P15.1) MUTATED
  COMPLETED AS PLANNED                               7
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 17(11P15.1) WILD-TYPE
  COMPLETED AS PLANNED                                18
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 17(11P15.1) MUTATED                    1                0
  DEL PEAK 17(11P15.1) WILD-TYPE                  1                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 17(11P15.1) MUTATED                    15            12
  DEL PEAK 17(11P15.1) WILD-TYPE                  21            21
D45V23, multiclass
                     clus
vv                    DEL PEAK 17(11P15.1) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                           15
  REGIONAL SITE                                 12
                     clus
vv                    DEL PEAK 17(11P15.1) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             21
  REGIONAL SITE                                   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"
D45V24, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   18  3
  DEL PEAK 17(11P15.1) WILD-TYPE 38  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     18    3
  DEL PEAK 17(11P15.1) WILD-TYPE   38    2
     clus
vv    DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  CGY                           18                             38
  GY                             3                              2
[1] 2 2
[1] FALSE
D45V25, continuous
D45V26, continuous
D45V27, continuous
D45V28, continuous
D45V29, continuous
D45V30, 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                                     3
  DEL PEAK 17(11P15.1) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 17(11P15.1) MUTATED                        13
  DEL PEAK 17(11P15.1) WILD-TYPE                      22
                                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                         2
  DEL PEAK 17(11P15.1) WILD-TYPE                       6
D45V31, multiclass
                                     clus
vv                                    DEL PEAK 17(11P15.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                       13
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 17(11P15.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                         22
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                               12
  DEL PEAK 17(11P15.1) WILD-TYPE                                             13
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 17(11P15.1) MUTATED                                                                                  35
  DEL PEAK 17(11P15.1) WILD-TYPE                                                                                46
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 17(11P15.1) MUTATED                                                                                             30
  DEL PEAK 17(11P15.1) WILD-TYPE                                                                                           90
D45V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 17(11P15.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           30
                                                                                              clus
vv                                                                                             DEL PEAK 17(11P15.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V33, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   25 21
  DEL PEAK 17(11P15.1) WILD-TYPE 45 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     25   21
  DEL PEAK 17(11P15.1) WILD-TYPE   45   52
         clus
vv        DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  ABSENT                            25                             45
  PRESENT                           21                             52
[1] 2 2
[1] FALSE
D45V34, continuous
D45V35, continuous
D45V36, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   15 41
  DEL PEAK 17(11P15.1) WILD-TYPE 33 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     15   41
  DEL PEAK 17(11P15.1) WILD-TYPE   33   75
                                          clus
vv                                         DEL PEAK 17(11P15.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           41
                                          clus
vv                                         DEL PEAK 17(11P15.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             75
[1] 2 2
[1] FALSE
D45V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 17(11P15.1) MUTATED              3          15         36
  DEL PEAK 17(11P15.1) WILD-TYPE           12          38         48
D45V38, multiclass
              clus
vv             DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                            15                             38
  NEVER USED                             36                             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"
D45V39, continuous
D45V40, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   31  6
  DEL PEAK 17(11P15.1) WILD-TYPE 61 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     31    6
  DEL PEAK 17(11P15.1) WILD-TYPE   61   11
         clus
vv        DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  ABSENT                            31                             61
  PRESENT                            6                             11
[1] 2 2
[1] FALSE
D45V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 17(11P15.1) MUTATED      0  12   24    6  3   2    2    5  11  0   2
  DEL PEAK 17(11P15.1) WILD-TYPE    1  22   45   24  3   8    5    4  25  2   0
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 17(11P15.1) MUTATED     8  3   0  8
  DEL PEAK 17(11P15.1) WILD-TYPE   9  5   1  8
D45V42, multiclass
      clus
vv     DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  T1A1                            0                              1
  T1B                            12                             22
  T1B1                           24                             45
  T1B2                            6                             24
  T2                              3                              3
  T2A                             2                              8
  T2A1                            2                              5
  T2A2                            5                              4
  T2B                            11                             25
  T3                              0                              2
  T3A                             2                              0
  T3B                             8                              9
  T4                              3                              5
  TIS                             0                              1
  TX                              8                              8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 17(11P15.1) MUTATED         3        0         0         1       15
  DEL PEAK 17(11P15.1) WILD-TYPE       2        1         1         0       18
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 17(11P15.1) MUTATED          26         7        2         2
  DEL PEAK 17(11P15.1) WILD-TYPE        51        29        2         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 17(11P15.1) MUTATED            2          3        13         0
  DEL PEAK 17(11P15.1) WILD-TYPE          3          4        30         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 17(11P15.1) MUTATED            2         18         2         1
  DEL PEAK 17(11P15.1) WILD-TYPE          1         24         5        11
D45V44, multiclass
            clus
vv           DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             15                             18
  STAGE IB1                            26                             51
  STAGE IB2                             7                             29
  STAGE II                              2                              2
  STAGE IIA                             2                              6
  STAGE IIA1                            2                              3
  STAGE IIA2                            3                              4
  STAGE IIB                            13                             30
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                           18                             24
  STAGE IVA                             2                              5
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 18(11Q23.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(11Q23.3) MUTATED   117  39
  DEL PEAK 18(11Q23.3) WILD-TYPE  96  26
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                           156                            122 
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                            39                             26 
$`DEL PEAK 18(11Q23.3) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 
       18.74       144.16       177.04       173.29        82.85        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-A1ML TCGA-C5-A2LV TCGA-C5-A2LX 
       35.61         0.46         2.43        20.91        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CH 
       78.35       100.14        33.24        52.01       210.67       154.32 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 
       15.48        20.35        17.19       131.11        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99        45.83       146.86        99.91        23.51        27.52 
TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       50.76        87.75        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD 
       22.98        16.83         8.28        12.36        30.90        13.05 
TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 
       25.02        24.56        14.50        26.01         7.46        13.91 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2IP 
       14.99        14.96        13.48         0.36        12.59         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD 
        1.51        19.27         0.59         0.13        16.08         0.03 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A3L1 
       47.77         2.24         0.07         0.10        20.35         6.94 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-HG-A9SC 
       19.79         8.32         1.45         1.58         0.82        10.82 
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-A3LL TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU 
       36.36        20.48        28.37        21.11         7.99        11.28 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA43 
       12.49         0.82        13.35        22.52        20.28        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       13.87        34.62        54.81        35.05        20.84         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q 
        2.96        16.41         9.04        17.56        15.88         9.34 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB 
       19.59         3.88        11.67        93.99        12.16        10.03 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       37.78        26.43        18.05        19.96        59.51        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 
       46.03        11.51        57.93        36.26        24.39        39.78 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       50.86        50.63        48.07        45.34        44.94        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO 
       42.41        25.74        19.69        40.96        14.53        41.42 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9V2 TCGA-VS-A9V3 
       43.27        35.97        14.53         3.42        14.04        14.89 
TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        29.26        19.13         0.69         0.16         3.91 

$`DEL PEAK 18(11Q23.3) WILD-TYPE`
TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A1MP 
       36.56         5.46        19.86        35.01        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       44.22        73.18        38.43        18.02        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
      101.82       134.33       147.35       155.77        94.95         9.34 
TCGA-C5-A8XI TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
        8.35        20.81        20.91        11.87         1.12        58.88 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
       44.94        40.04        58.88        16.18        17.52        39.55 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S 
       37.35        31.53        31.36        14.50        26.40        12.66 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2H0 
       12.82        14.89        26.79        15.02        13.58        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC 
       26.27         0.43         0.59         1.45         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70        15.55         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       31.36        36.26         1.48         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12         9.01        25.41        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH 
        9.44       147.39        96.95        29.85        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       24.56        21.44        15.58         8.28        18.15       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       30.31         0.89         0.30        17.82        19.56         9.17 
TCGA-MA-AA42 TCGA-MU-A8JM TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O 
        8.52         5.42        15.58        15.95        16.14        14.07 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8QA TCGA-VS-A8QH 
       15.39        19.36        66.05        40.50        36.13        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A953 TCGA-VS-A958 TCGA-VS-A9UB 
       31.27        16.64         4.73        15.68        50.14        21.30 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UR TCGA-VS-A9UY 
       22.72        46.92         1.71        27.25        20.09        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-WL-A834 
       67.20        18.84         5.16         4.34        16.24        26.01 
TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       67.59         1.41 

  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                        210.67                         195.85 
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                        21.010                         17.835 
[1] "0.0 - 210.7 (21.0)" "0.0 - 195.8 (17.8)"
[1] "hr=" "1.1"
D46V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 18(11Q23.3) MUTATED   73 35 13  4
  DEL PEAK 18(11Q23.3) WILD-TYPE 61 33  8  4
D46V3, multiclass
    clus
vv   DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  T1                           73                             61
  T2                           35                             33
  T3                           13                              8
  T4                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   67 30
  DEL PEAK 18(11Q23.3) WILD-TYPE 60 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     67   30
  DEL PEAK 18(11Q23.3) WILD-TYPE   60   25
   clus
vv  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  0                           67                             60
  1                           30                             25
[1] 2 2
[1] FALSE
D46V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   63  5
  DEL PEAK 18(11Q23.3) WILD-TYPE 44  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     63    5
  DEL PEAK 18(11Q23.3) WILD-TYPE   44    5
   clus
vv  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  0                           63                             44
  1                            5                              5
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(11Q23.3) MUTATED               1                              144
  DEL PEAK 18(11Q23.3) WILD-TYPE             4                               97
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 18(11Q23.3) MUTATED                                               1
  DEL PEAK 18(11Q23.3) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 18(11Q23.3) MUTATED                                     9
  DEL PEAK 18(11Q23.3) WILD-TYPE                                  13
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 18(11Q23.3) MUTATED                                           1
  DEL PEAK 18(11Q23.3) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 18(11Q23.3) MUTATED                                              5
  DEL PEAK 18(11Q23.3) WILD-TYPE                                           10
D46V6, multiclass
                                               clus
vv                                              DEL PEAK 18(11Q23.3) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       144
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             5
                                               clus
vv                                              DEL PEAK 18(11Q23.3) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          97
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              10
[1] 6 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 18(11Q23.3) MUTATED    20 141
  DEL PEAK 18(11Q23.3) WILD-TYPE  10 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     20  141
  DEL PEAK 18(11Q23.3) WILD-TYPE   10  121
     clus
vv    DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  NO                            20                             10
  YES                          141                            121
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(11Q23.3) MUTATED                                  3    11
  DEL PEAK 18(11Q23.3) WILD-TYPE                                5     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(11Q23.3) MUTATED                          20
  DEL PEAK 18(11Q23.3) WILD-TYPE                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 18(11Q23.3) MUTATED                                           2
  DEL PEAK 18(11Q23.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 18(11Q23.3) MUTATED     109
  DEL PEAK 18(11Q23.3) WILD-TYPE    92
D46V10, multiclass
                                           clus
vv                                          DEL PEAK 18(11Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               11
  BLACK OR AFRICAN AMERICAN                                           20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                              109
                                           clus
vv                                          DEL PEAK 18(11Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                  7
  BLACK OR AFRICAN AMERICAN                                              8
  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"
D46V11, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED    9 88
  DEL PEAK 18(11Q23.3) WILD-TYPE 14 73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED      9   88
  DEL PEAK 18(11Q23.3) WILD-TYPE   14   73
                        clus
vv                       DEL PEAK 18(11Q23.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       DEL PEAK 18(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                             73
[1] 2 2
[1] FALSE
D46V12, continuous
D46V13, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   78 26
  DEL PEAK 18(11Q23.3) WILD-TYPE 56 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     78   26
  DEL PEAK 18(11Q23.3) WILD-TYPE   56   15
            clus
vv           DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  TUMOR FREE                           78                             56
  WITH TUMOR                           26                             15
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 18(11Q23.3) MUTATED       33      1       1      5       3
  DEL PEAK 18(11Q23.3) WILD-TYPE     20      4       0      6       4
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 18(11Q23.3) MUTATED             109       9
  DEL PEAK 18(11Q23.3) WILD-TYPE            92       5
D46V14, multiclass
               clus
vv              DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  BRAZIL                                  33                             20
  CANADA                                   1                              4
  NIGERIA                                  1                              0
  RUSSIA                                   5                              6
  UKRAINE                                  3                              4
  UNITED STATES                          109                             92
  VIETNAM                                  9                              5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 18(11Q23.3) MUTATED    8 71 65  1 12
  DEL PEAK 18(11Q23.3) WILD-TYPE 10 58 48  0 12
D46V15, multiclass
    clus
vv   DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  G1                            8                             10
  G2                           71                             58
  G3                           65                             48
  G4                            1                              0
  GX                           12                             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"
D46V16, continuous
D46V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 18(11Q23.3) MUTATED                                            22
  DEL PEAK 18(11Q23.3) WILD-TYPE                                          15
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 18(11Q23.3) MUTATED                                        6
  DEL PEAK 18(11Q23.3) WILD-TYPE                                      3
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 18(11Q23.3) MUTATED                                                 2
  DEL PEAK 18(11Q23.3) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 18(11Q23.3) MUTATED               30                  80
  DEL PEAK 18(11Q23.3) WILD-TYPE             32                  62
D46V18, multiclass
                                                 clus
vv                                                DEL PEAK 18(11Q23.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            30
  LIFELONG NON-SMOKER                                                       80
                                                 clus
vv                                                DEL PEAK 18(11Q23.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              32
  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"
D46V19, continuous
D46V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 18(11Q23.3) MUTATED            15       55             6       16
  DEL PEAK 18(11Q23.3) WILD-TYPE           4       47             6        9
D46V21, multiclass
               clus
vv              DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  COMBINATION                             15                              4
  EXTERNAL                                55                             47
  EXTERNAL BEAM                            6                              6
  INTERNAL                                16                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V22, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   17  2
  DEL PEAK 18(11Q23.3) WILD-TYPE  8  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     17    2
  DEL PEAK 18(11Q23.3) WILD-TYPE    8    1
                         clus
vv                        DEL PEAK 18(11Q23.3) MUTATED
  COMPLETED AS PLANNED                              17
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        DEL PEAK 18(11Q23.3) WILD-TYPE
  COMPLETED AS PLANNED                                 8
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 18(11Q23.3) MUTATED                    1                2
  DEL PEAK 18(11Q23.3) WILD-TYPE                  1                0
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 18(11Q23.3) MUTATED                    20            21
  DEL PEAK 18(11Q23.3) WILD-TYPE                  16            12
D46V23, multiclass
                     clus
vv                    DEL PEAK 18(11Q23.3) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                           20
  REGIONAL SITE                                 21
                     clus
vv                    DEL PEAK 18(11Q23.3) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             16
  REGIONAL SITE                                   12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V24, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   34  4
  DEL PEAK 18(11Q23.3) WILD-TYPE 22  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     34    4
  DEL PEAK 18(11Q23.3) WILD-TYPE   22    1
     clus
vv    DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  CGY                           34                             22
  GY                             4                              1
[1] 2 2
[1] FALSE
D46V25, continuous
D46V26, continuous
D46V27, continuous
D46V28, continuous
D46V29, continuous
D46V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 18(11Q23.3) MUTATED                                     1
  DEL PEAK 18(11Q23.3) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 18(11Q23.3) MUTATED                                     4
  DEL PEAK 18(11Q23.3) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 18(11Q23.3) MUTATED                        22
  DEL PEAK 18(11Q23.3) WILD-TYPE                      13
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 18(11Q23.3) MUTATED                         1
  DEL PEAK 18(11Q23.3) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 18(11Q23.3) MUTATED                         5
  DEL PEAK 18(11Q23.3) WILD-TYPE                       3
D46V31, multiclass
                                     clus
vv                                    DEL PEAK 18(11Q23.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                       22
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        5
                                     clus
vv                                    DEL PEAK 18(11Q23.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              3
  OTHER LOCATION, SPECIFY                                         13
  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)
  DEL PEAK 18(11Q23.3) MUTATED                                               2
  DEL PEAK 18(11Q23.3) WILD-TYPE                                             0
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 18(11Q23.3) MUTATED                                               17
  DEL PEAK 18(11Q23.3) WILD-TYPE                                              8
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 18(11Q23.3) MUTATED                                                                                  53
  DEL PEAK 18(11Q23.3) WILD-TYPE                                                                                28
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 18(11Q23.3) MUTATED                                                                                             58
  DEL PEAK 18(11Q23.3) WILD-TYPE                                                                                           62
D46V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 18(11Q23.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           58
                                                                                              clus
vv                                                                                             DEL PEAK 18(11Q23.3) 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)                                        28
  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"
D46V33, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   34 46
  DEL PEAK 18(11Q23.3) WILD-TYPE 36 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     34   46
  DEL PEAK 18(11Q23.3) WILD-TYPE   36   27
         clus
vv        DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  ABSENT                            34                             36
  PRESENT                           46                             27
[1] 2 2
[1] FALSE
D46V34, continuous
D46V35, continuous
D46V36, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   28 64
  DEL PEAK 18(11Q23.3) WILD-TYPE 20 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     28   64
  DEL PEAK 18(11Q23.3) WILD-TYPE   20   52
                                          clus
vv                                         DEL PEAK 18(11Q23.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           64
                                          clus
vv                                         DEL PEAK 18(11Q23.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 20
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             52
[1] 2 2
[1] FALSE
D46V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 18(11Q23.3) MUTATED              7          28         50
  DEL PEAK 18(11Q23.3) WILD-TYPE            8          25         34
D46V38, multiclass
              clus
vv             DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  CURRENT USER                            7                              8
  FORMER USER                            28                             25
  NEVER USED                             50                             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"
D46V39, continuous
D46V40, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   49 12
  DEL PEAK 18(11Q23.3) WILD-TYPE 43  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     49   12
  DEL PEAK 18(11Q23.3) WILD-TYPE   43    5
         clus
vv        DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  ABSENT                            49                             43
  PRESENT                           12                              5
[1] 2 2
[1] FALSE
D46V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 18(11Q23.3) MUTATED      1  22   41    9  5   3    4    4  19  1   2
  DEL PEAK 18(11Q23.3) WILD-TYPE    0  12   28   21  1   7    3    5  17  1   0
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 18(11Q23.3) MUTATED    10  4   1 10
  DEL PEAK 18(11Q23.3) WILD-TYPE   7  4   0  6
D46V42, multiclass
      clus
vv     DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  T1A1                            1                              0
  T1B                            22                             12
  T1B1                           41                             28
  T1B2                            9                             21
  T2                              5                              1
  T2A                             3                              7
  T2A1                            4                              3
  T2A2                            4                              5
  T2B                            19                             17
  T3                              1                              1
  T3A                             2                              0
  T3B                            10                              7
  T4                              4                              4
  TIS                             1                              0
  TX                             10                              6
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 18(11Q23.3) MUTATED         4        0         1         1       26
  DEL PEAK 18(11Q23.3) WILD-TYPE       1        1         0         0        7
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 18(11Q23.3) MUTATED          42        13        3         2
  DEL PEAK 18(11Q23.3) WILD-TYPE        35        23        1         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 18(11Q23.3) MUTATED            4          4        25         0
  DEL PEAK 18(11Q23.3) WILD-TYPE          1          3        18         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 18(11Q23.3) MUTATED            3         22         3         4
  DEL PEAK 18(11Q23.3) WILD-TYPE          0         20         4         8
D46V44, multiclass
            clus
vv           DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                              0                              1
  STAGE IA1                             1                              0
  STAGE IA2                             1                              0
  STAGE IB                             26                              7
  STAGE IB1                            42                             35
  STAGE IB2                            13                             23
  STAGE II                              3                              1
  STAGE IIA                             2                              6
  STAGE IIA1                            4                              1
  STAGE IIA2                            4                              3
  STAGE IIB                            25                             18
  STAGE III                             0                              1
  STAGE IIIA                            3                              0
  STAGE IIIB                           22                             20
  STAGE IVA                             3                              4
  STAGE IVB                             4                              8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 19(11Q25) MUTATION ANALYSIS
D47V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 19(11Q25) MUTATED   113  41
  DEL PEAK 19(11Q25) WILD-TYPE 100  24
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                         154                          124 
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                          41                           24 
$`DEL PEAK 19(11Q25) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        30.21        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A2LV 
       38.99        35.61         0.46         2.43        20.91        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CG 
       83.05        78.35       100.14        33.24        52.01       210.67 
TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 
      154.32        15.48        20.35        17.19       131.11        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99        45.83       146.86        99.91        23.51 
TCGA-C5-A8YR TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       27.52        50.76        87.75        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT 
      118.65        22.98        16.83        17.52         8.28        12.36 
TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       30.90        13.05        25.02        24.56        14.50        26.01 
TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N 
        7.46        13.91        14.99        14.96        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R9 
       12.59         6.64         1.51        19.27         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ 
       16.08         0.03        47.77         2.24         0.07         0.10 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A3NI TCGA-FU-A3TQ 
       20.35         6.94        19.79         8.32         1.45         1.58 
TCGA-FU-A3WB TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
        0.82        10.82        21.67       137.16        66.81       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JX-A3PZ TCGA-JX-A5QV 
       78.71        81.96        36.36        20.48        21.11         7.99 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       11.28        12.49         0.82        13.35        22.52        20.28 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       11.38        13.87        34.62        54.81        35.05        20.84 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P 
        5.49         2.96        16.41         9.04        17.56        15.88 
TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
        9.34        19.59         3.88        11.67        93.99        12.16 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        37.78        26.43        18.05        19.96        59.51 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Z TCGA-VS-A950 
       32.15        46.03        11.51        57.93        24.39        39.78 
TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UD 
       50.86        48.07        44.94        43.40        42.41        19.69 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU 
       40.96        14.53        41.42        43.27        35.97        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-XS-A8TJ 
        3.42        18.25        14.04        14.89        15.42        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       19.13         0.69         1.41         0.16 

$`DEL PEAK 19(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-C5-A8XI 
      134.33       147.35       155.77        94.95         9.34         8.35 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL 
       20.81        20.91        11.87         1.12        58.88        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS 
       40.04        58.88        16.18        39.55        37.35        31.53 
TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 
       31.36        14.50        26.40        12.66        12.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PL 
       26.79        15.02        13.58        45.96        26.27         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         1.45         0.07         4.04         0.36         1.18 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A8YF 
        0.10         0.10         0.03         7.92        14.70        15.55 
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        31.36        36.26 
TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         3.52         1.35         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        9.01        25.41        20.78        14.93         9.44       147.39 
TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       96.95        29.85        27.42         3.29        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       15.58        28.37         8.28        18.15       195.85        30.31 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
        0.89         0.30        17.82        19.56         9.17         8.52 
TCGA-MU-A8JM TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73R 
        5.42        15.58        15.95        16.14        14.07        15.39 
TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM 
       19.36        66.05        40.50        36.13        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 
       36.26        16.64         4.73        15.68        50.63        50.14 
TCGA-VS-A959 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ 
       45.34        25.74        21.30        22.72        46.92         1.71 
TCGA-VS-A9UM TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 
       27.25        20.09        67.20        18.84         5.16         4.34 
TCGA-VS-A9V5 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZX-AA5X 
       16.24        26.01        67.59         3.91 

  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                        0.03                         0.03 
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                      210.67                       195.85 
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                      20.350                       18.495 
[1] "0.0 - 210.7 (20.4)" "0.0 - 195.8 (18.5)"
[1] "hr=" "1.1"
D47V2, continuous
                              vv
clus                           T1 T2 T3 T4
  DEL PEAK 19(11Q25) MUTATED   75 33 12  4
  DEL PEAK 19(11Q25) WILD-TYPE 59 35  9  4
D47V3, multiclass
    clus
vv   DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  T1                         75                           59
  T2                         33                           35
  T3                         12                            9
  T4                          4                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   69 30
  DEL PEAK 19(11Q25) WILD-TYPE 58 25
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     69   30
  DEL PEAK 19(11Q25) WILD-TYPE   58   25
   clus
vv  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  0                         69                           58
  1                         30                           25
[1] 2 2
[1] FALSE
D47V5, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   64  5
  DEL PEAK 19(11Q25) WILD-TYPE 43  5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     64    5
  DEL PEAK 19(11Q25) WILD-TYPE   43    5
   clus
vv  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  0                         64                           43
  1                          5                            5
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(11Q25) MUTATED               1                              142
  DEL PEAK 19(11Q25) WILD-TYPE             4                               99
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 19(11Q25) MUTATED                                               1
  DEL PEAK 19(11Q25) WILD-TYPE                                             5
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 19(11Q25) MUTATED                                     9
  DEL PEAK 19(11Q25) WILD-TYPE                                  13
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 19(11Q25) MUTATED                                           1
  DEL PEAK 19(11Q25) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 19(11Q25) MUTATED                                              5
  DEL PEAK 19(11Q25) WILD-TYPE                                           10
D47V6, multiclass
                                               clus
vv                                              DEL PEAK 19(11Q25) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                     142
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           5
                                               clus
vv                                              DEL PEAK 19(11Q25) WILD-TYPE
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        99
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            10
[1] 6 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 19(11Q25) MUTATED    21 138
  DEL PEAK 19(11Q25) WILD-TYPE   9 124
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     21  138
  DEL PEAK 19(11Q25) WILD-TYPE    9  124
     clus
vv    DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  NO                          21                            9
  YES                        138                          124
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(11Q25) MUTATED                                  3    11
  DEL PEAK 19(11Q25) WILD-TYPE                                5     7
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(11Q25) MUTATED                          20
  DEL PEAK 19(11Q25) WILD-TYPE                         8
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(11Q25) MUTATED                                           2   108
  DEL PEAK 19(11Q25) WILD-TYPE                                         0    93
D47V10, multiclass
                                           clus
vv                                          DEL PEAK 19(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   3
  ASIAN                                                             11
  BLACK OR AFRICAN AMERICAN                                         20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                            108
                                           clus
vv                                          DEL PEAK 19(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  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"
D47V11, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED    8 90
  DEL PEAK 19(11Q25) WILD-TYPE 15 71
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED      8   90
  DEL PEAK 19(11Q25) WILD-TYPE   15   71
                        clus
vv                       DEL PEAK 19(11Q25) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         90
                        clus
vv                       DEL PEAK 19(11Q25) WILD-TYPE
  HISPANIC OR LATINO                               15
  NOT HISPANIC OR LATINO                           71
[1] 2 2
[1] FALSE
D47V12, continuous
D47V13, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   74 26
  DEL PEAK 19(11Q25) WILD-TYPE 60 15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     74   26
  DEL PEAK 19(11Q25) WILD-TYPE   60   15
            clus
vv           DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  TUMOR FREE                         74                           60
  WITH TUMOR                         26                           15
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 19(11Q25) MUTATED       30      1       1      5       3
  DEL PEAK 19(11Q25) WILD-TYPE     23      4       0      6       4
                              vv
clus                           UNITED STATES VIETNAM
  DEL PEAK 19(11Q25) MUTATED             110       9
  DEL PEAK 19(11Q25) WILD-TYPE            91       5
D47V14, multiclass
               clus
vv              DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  BRAZIL                                30                           23
  CANADA                                 1                            4
  NIGERIA                                1                            0
  RUSSIA                                 5                            6
  UKRAINE                                3                            4
  UNITED STATES                        110                           91
  VIETNAM                                9                            5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           G1 G2 G3 G4 GX
  DEL PEAK 19(11Q25) MUTATED    8 71 64  1 11
  DEL PEAK 19(11Q25) WILD-TYPE 10 58 49  0 13
D47V15, multiclass
    clus
vv   DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  G1                          8                           10
  G2                         71                           58
  G3                         64                           49
  G4                          1                            0
  GX                         11                           13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V16, continuous
D47V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 19(11Q25) MUTATED                                            22
  DEL PEAK 19(11Q25) WILD-TYPE                                          15
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 19(11Q25) MUTATED                                        7
  DEL PEAK 19(11Q25) WILD-TYPE                                      2
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 19(11Q25) MUTATED                                                 2
  DEL PEAK 19(11Q25) WILD-TYPE                                               1
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 19(11Q25) MUTATED               31                  76
  DEL PEAK 19(11Q25) WILD-TYPE             31                  66
D47V18, multiclass
                                                 clus
vv                                                DEL PEAK 19(11Q25) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          2
  CURRENT SMOKER                                                          31
  LIFELONG NON-SMOKER                                                     76
                                                 clus
vv                                                DEL PEAK 19(11Q25) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            31
  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"
D47V19, continuous
D47V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 19(11Q25) MUTATED            16       54             6       16
  DEL PEAK 19(11Q25) WILD-TYPE           3       48             6        9
D47V21, multiclass
               clus
vv              DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  COMBINATION                           16                            3
  EXTERNAL                              54                           48
  EXTERNAL BEAM                          6                            6
  INTERNAL                              16                            9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V22, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   18  2
  DEL PEAK 19(11Q25) WILD-TYPE  7  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     18    2
  DEL PEAK 19(11Q25) WILD-TYPE    7    1
                         clus
vv                        DEL PEAK 19(11Q25) MUTATED
  COMPLETED AS PLANNED                            18
  TREATMENT NOT COMPLETED                          2
                         clus
vv                        DEL PEAK 19(11Q25) WILD-TYPE
  COMPLETED AS PLANNED                               7
  TREATMENT NOT COMPLETED                            1
[1] 2 2
[1] FALSE
                              vv
clus                           DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 19(11Q25) MUTATED                    1                2
  DEL PEAK 19(11Q25) WILD-TYPE                  1                0
                              vv
clus                           PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 19(11Q25) MUTATED                    20            19
  DEL PEAK 19(11Q25) WILD-TYPE                  16            14
D47V23, multiclass
                     clus
vv                    DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  DISTANT RECURRENCE                           1                            1
  LOCAL RECURRENCE                             2                            0
  PRIMARY TUMOR FIELD                         20                           16
  REGIONAL SITE                               19                           14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V24, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   32  4
  DEL PEAK 19(11Q25) WILD-TYPE 24  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     32    4
  DEL PEAK 19(11Q25) WILD-TYPE   24    1
     clus
vv    DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  CGY                         32                           24
  GY                           4                            1
[1] 2 2
[1] FALSE
D47V25, continuous
D47V26, continuous
D47V27, continuous
D47V28, continuous
D47V29, continuous
D47V30, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 19(11Q25) MUTATED                                     1
  DEL PEAK 19(11Q25) WILD-TYPE                                   1
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 19(11Q25) MUTATED                                     4
  DEL PEAK 19(11Q25) WILD-TYPE                                   3
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 19(11Q25) MUTATED                        22                       1
  DEL PEAK 19(11Q25) WILD-TYPE                      13                       0
                              vv
clus                           POSITIVE VAGINAL MARGIN
  DEL PEAK 19(11Q25) MUTATED                         5
  DEL PEAK 19(11Q25) WILD-TYPE                       3
D47V31, multiclass
                                     clus
vv                                    DEL PEAK 19(11Q25) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          4
  OTHER LOCATION, SPECIFY                                     22
  POSITIVE BLADDER MARGIN                                      1
  POSITIVE VAGINAL MARGIN                                      5
                                     clus
vv                                    DEL PEAK 19(11Q25) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                       13
  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)
  DEL PEAK 19(11Q25) MUTATED                                               2
  DEL PEAK 19(11Q25) WILD-TYPE                                             0
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 19(11Q25) MUTATED                                               17
  DEL PEAK 19(11Q25) WILD-TYPE                                              8
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 19(11Q25) MUTATED                                                                                  49
  DEL PEAK 19(11Q25) WILD-TYPE                                                                                32
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 19(11Q25) MUTATED                                                                                             58
  DEL PEAK 19(11Q25) WILD-TYPE                                                                                           62
D47V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 19(11Q25) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         58
                                                                                              clus
vv                                                                                             DEL PEAK 19(11Q25) 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)                                      32
  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"
D47V33, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   33 47
  DEL PEAK 19(11Q25) WILD-TYPE 37 26
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     33   47
  DEL PEAK 19(11Q25) WILD-TYPE   37   26
         clus
vv        DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  ABSENT                          33                           37
  PRESENT                         47                           26
[1] 2 2
[1] FALSE
D47V34, continuous
D47V35, continuous
D47V36, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   28 66
  DEL PEAK 19(11Q25) WILD-TYPE 20 50
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     28   66
  DEL PEAK 19(11Q25) WILD-TYPE   20   50
                                          clus
vv                                         DEL PEAK 19(11Q25) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         66
                                          clus
vv                                         DEL PEAK 19(11Q25) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               20
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           50
[1] 2 2
[1] FALSE
D47V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  DEL PEAK 19(11Q25) MUTATED              7          29         46
  DEL PEAK 19(11Q25) WILD-TYPE            8          24         38
D47V38, multiclass
              clus
vv             DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  CURRENT USER                          7                            8
  FORMER USER                          29                           24
  NEVER USED                           46                           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"
D47V39, continuous
D47V40, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   49 12
  DEL PEAK 19(11Q25) WILD-TYPE 43  5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     49   12
  DEL PEAK 19(11Q25) WILD-TYPE   43    5
         clus
vv        DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  ABSENT                          49                           43
  PRESENT                         12                            5
[1] 2 2
[1] FALSE
D47V41, continuous
                              vv
clus                           T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 19(11Q25) MUTATED      1  23   42    9  5   3    4    4  17  0   2
  DEL PEAK 19(11Q25) WILD-TYPE    0  11   27   21  1   7    3    5  19  2   0
                              vv
clus                           T3B T4 TIS TX
  DEL PEAK 19(11Q25) MUTATED    10  4   1  9
  DEL PEAK 19(11Q25) WILD-TYPE   7  4   0  7
D47V42, multiclass
      clus
vv     DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  T1A1                          1                            0
  T1B                          23                           11
  T1B1                         42                           27
  T1B2                          9                           21
  T2                            5                            1
  T2A                           3                            7
  T2A1                          4                            3
  T2A2                          4                            5
  T2B                          17                           19
  T3                            0                            2
  T3A                           2                            0
  T3B                          10                            7
  T4                            4                            4
  TIS                           1                            0
  TX                            9                            7
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 19(11Q25) MUTATED         4        0         1         1       26
  DEL PEAK 19(11Q25) WILD-TYPE       1        1         0         0        7
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 19(11Q25) MUTATED          44        13        3         2
  DEL PEAK 19(11Q25) WILD-TYPE        33        23        1         6
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 19(11Q25) MUTATED            4          4        23         0
  DEL PEAK 19(11Q25) WILD-TYPE          1          3        20         1
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 19(11Q25) MUTATED            2         21         3         5
  DEL PEAK 19(11Q25) WILD-TYPE          1         21         4         7
D47V44, multiclass
            clus
vv           DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  STAGE I                             4                            1
  STAGE IA                            0                            1
  STAGE IA1                           1                            0
  STAGE IA2                           1                            0
  STAGE IB                           26                            7
  STAGE IB1                          44                           33
  STAGE IB2                          13                           23
  STAGE II                            3                            1
  STAGE IIA                           2                            6
  STAGE IIA1                          4                            1
  STAGE IIA2                          4                            3
  STAGE IIB                          23                           20
  STAGE III                           0                            1
  STAGE IIIA                          2                            1
  STAGE IIIB                         21                           21
  STAGE IVA                           3                            4
  STAGE IVB                           5                            7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 20(13Q12.11) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(13Q12.11) MUTATED    71  21
  DEL PEAK 20(13Q12.11) WILD-TYPE 142  44
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                             92                             186 
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                             21                              44 
$`DEL PEAK 20(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       210.67       154.32       134.33 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XK 
      147.35       155.77       131.11        94.95         9.34        99.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT 
       11.87        58.88        87.75       117.99       118.65        12.36 
TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A5ZD TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       25.02        12.66        15.02         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27        19.27         0.43         0.59         0.59         1.45 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-EX-A69M 
       16.08         4.04         0.36         2.24        20.35         8.32 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC 
       23.84         1.45         1.58         1.97        25.41        10.82 
TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-AAVH 
       21.67         9.44       147.39        78.71        20.48        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MA-AA42 
       21.11        30.31        11.28         0.89        12.49         8.52 
TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PG 
        5.49        15.95         9.04        15.39        19.59        12.16 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q9 TCGA-VS-A8QM 
       10.03        40.50        26.43        18.05        46.03        31.27 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UD 
       39.78        15.68        48.07        43.40        25.74        19.69 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UU TCGA-WL-A834 TCGA-XS-A8TJ 
       40.96        14.53        27.25        14.53        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       67.59        19.13 

$`DEL PEAK 20(13Q12.11) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BQ 
       12.39        23.67        11.44        36.56       177.04        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF 
       44.22        78.35       100.14        33.24        52.01        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X5 
       20.42       101.82        15.48        20.35        17.19        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ 
        2.73        50.99        45.83         8.35       146.86        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       27.52        20.81        20.91         1.12        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ 
       40.04        58.88        36.76         2.66        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18        17.52         8.28        39.55        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.53        31.36        13.05        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       14.50        26.01        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2IP 
       13.91        14.99        14.96        13.58        13.48         6.64 
TCGA-EK-A2PG TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL 
        1.51         0.13         0.07         0.03         1.18        47.77 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
        0.10         0.07         0.10         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70        19.79        15.55         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        2.17        31.36        36.26         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.35         1.32         1.12         9.01        20.78        14.93 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81       117.40        96.95        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 
       28.37         8.28       195.85         7.99         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       13.35        22.52        20.28        17.82        19.56         9.17 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        13.87        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84         2.96        15.58        16.41        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       14.07        15.88         9.34        19.36         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       93.99        66.05        37.78        19.96        59.51        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94W TCGA-VS-A94X 
       36.13        11.51        57.93        39.78        36.26        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 
        4.73        24.39        50.86        50.63        50.14        45.34 
TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ 
       44.94        42.41        21.30        22.72        46.92         1.71 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY 
       41.42        43.27        35.97        20.09         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        14.04        14.89         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       16.24        15.42         0.69         1.41         0.16         3.91 

  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                           0.36                            0.03 
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                         210.67                          195.85 
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                          21.39                           19.10 
[1] "0.4 - 210.7 (21.4)" "0.0 - 195.8 (19.1)"
[1] "hr=" "1.4"
D48V2, continuous
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 20(13Q12.11) MUTATED   38 16 11  2
  DEL PEAK 20(13Q12.11) WILD-TYPE 96 52 10  6
D48V3, multiclass
    clus
vv   DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  T1                            38                              96
  T2                            16                              52
  T3                            11                              10
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   33 21
  DEL PEAK 20(13Q12.11) WILD-TYPE 94 34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     33   21
  DEL PEAK 20(13Q12.11) WILD-TYPE   94   34
   clus
vv  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  0                            33                              94
  1                            21                              34
[1] 2 2
[1] FALSE
D48V5, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   33  5
  DEL PEAK 20(13Q12.11) WILD-TYPE 74  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     33    5
  DEL PEAK 20(13Q12.11) WILD-TYPE   74    5
   clus
vv  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  0                            33                              74
  1                             5                               5
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 20(13Q12.11) MUTATED               2
  DEL PEAK 20(13Q12.11) WILD-TYPE             3
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(13Q12.11) MUTATED                                 92
  DEL PEAK 20(13Q12.11) WILD-TYPE                              149
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 20(13Q12.11) MUTATED                                               0
  DEL PEAK 20(13Q12.11) WILD-TYPE                                             6
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 20(13Q12.11) MUTATED                                     3
  DEL PEAK 20(13Q12.11) WILD-TYPE                                  19
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 20(13Q12.11) MUTATED                                           0
  DEL PEAK 20(13Q12.11) WILD-TYPE                                         3
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 20(13Q12.11) MUTATED                                              0
  DEL PEAK 20(13Q12.11) WILD-TYPE                                           15
D48V6, multiclass
                                               clus
vv                                              DEL PEAK 20(13Q12.11) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         92
  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(13Q12.11) WILD-TYPE
  ADENOSQUAMOUS                                                               3
  CERVICAL SQUAMOUS CELL CARCINOMA                                          149
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(13Q12.11) MUTATED    14  83
  DEL PEAK 20(13Q12.11) WILD-TYPE  16 179
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     14   83
  DEL PEAK 20(13Q12.11) WILD-TYPE   16  179
     clus
vv    DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  NO                             14                              16
  YES                            83                             179
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(13Q12.11) MUTATED                                  0     7
  DEL PEAK 20(13Q12.11) WILD-TYPE                                8    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(13Q12.11) MUTATED                          13
  DEL PEAK 20(13Q12.11) WILD-TYPE                        15
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 20(13Q12.11) MUTATED                                           1
  DEL PEAK 20(13Q12.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 20(13Q12.11) MUTATED      67
  DEL PEAK 20(13Q12.11) WILD-TYPE   134
D48V10, multiclass
                                           clus
vv                                          DEL PEAK 20(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                67
                                           clus
vv                                          DEL PEAK 20(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  11
  BLACK OR AFRICAN AMERICAN                                              15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                                 cls
clus                                0   1
  DEL PEAK 20(13Q12.11) MUTATED     5  53
  DEL PEAK 20(13Q12.11) WILD-TYPE  18 108
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED      5   53
  DEL PEAK 20(13Q12.11) WILD-TYPE   18  108
                        clus
vv                       DEL PEAK 20(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       DEL PEAK 20(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                  18
  NOT HISPANIC OR LATINO                             108
[1] 2 2
[1] FALSE
D48V12, continuous
D48V13, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   45 12
  DEL PEAK 20(13Q12.11) WILD-TYPE 89 29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     45   12
  DEL PEAK 20(13Q12.11) WILD-TYPE   89   29
            clus
vv           DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  TUMOR FREE                            45                              89
  WITH TUMOR                            12                              29
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 20(13Q12.11) MUTATED       17      1       0      2       2
  DEL PEAK 20(13Q12.11) WILD-TYPE     36      4       1      9       5
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 20(13Q12.11) MUTATED              70       5
  DEL PEAK 20(13Q12.11) WILD-TYPE           131       9
D48V14, multiclass
               clus
vv              DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  BRAZIL                                   17                              36
  CANADA                                    1                               4
  NIGERIA                                   0                               1
  RUSSIA                                    2                               9
  UKRAINE                                   2                               5
  UNITED STATES                            70                             131
  VIETNAM                                   5                               9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 20(13Q12.11) MUTATED    4 35 44  1 10
  DEL PEAK 20(13Q12.11) WILD-TYPE 14 94 69  0 14
D48V15, multiclass
    clus
vv   DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  G1                             4                              14
  G2                            35                              94
  G3                            44                              69
  G4                             1                               0
  GX                            10                              14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V16, continuous
D48V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 20(13Q12.11) MUTATED                                            10
  DEL PEAK 20(13Q12.11) WILD-TYPE                                          27
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 20(13Q12.11) MUTATED                                        4
  DEL PEAK 20(13Q12.11) WILD-TYPE                                      5
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 20(13Q12.11) MUTATED                                                 3
  DEL PEAK 20(13Q12.11) WILD-TYPE                                               0
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 20(13Q12.11) MUTATED               23                  39
  DEL PEAK 20(13Q12.11) WILD-TYPE             39                 103
D48V18, multiclass
                                                 clus
vv                                                DEL PEAK 20(13Q12.11) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             3
  CURRENT SMOKER                                                             23
  LIFELONG NON-SMOKER                                                        39
                                                 clus
vv                                                DEL PEAK 20(13Q12.11) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               0
  CURRENT SMOKER                                                               39
  LIFELONG NON-SMOKER                                                         103
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V19, continuous
D48V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 20(13Q12.11) MUTATED             9       32             4        6
  DEL PEAK 20(13Q12.11) WILD-TYPE          10       70             8       19
D48V21, multiclass
               clus
vv              DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  COMBINATION                               9                              10
  EXTERNAL                                 32                              70
  EXTERNAL BEAM                             4                               8
  INTERNAL                                  6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V22, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   12  1
  DEL PEAK 20(13Q12.11) WILD-TYPE 13  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     12    1
  DEL PEAK 20(13Q12.11) WILD-TYPE   13    2
                         clus
vv                        DEL PEAK 20(13Q12.11) MUTATED
  COMPLETED AS PLANNED                               12
  TREATMENT NOT COMPLETED                             1
                         clus
vv                        DEL PEAK 20(13Q12.11) WILD-TYPE
  COMPLETED AS PLANNED                                 13
  TREATMENT NOT COMPLETED                               2
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 20(13Q12.11) MUTATED                    1                1
  DEL PEAK 20(13Q12.11) WILD-TYPE                  1                1
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 20(13Q12.11) MUTATED                    14            12
  DEL PEAK 20(13Q12.11) WILD-TYPE                  22            21
D48V23, multiclass
                     clus
vv                    DEL PEAK 20(13Q12.11) MUTATED
  DISTANT RECURRENCE                              1
  LOCAL RECURRENCE                                1
  PRIMARY TUMOR FIELD                            14
  REGIONAL SITE                                  12
                     clus
vv                    DEL PEAK 20(13Q12.11) WILD-TYPE
  DISTANT RECURRENCE                                1
  LOCAL RECURRENCE                                  1
  PRIMARY TUMOR FIELD                              22
  REGIONAL SITE                                    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"
D48V24, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   19  2
  DEL PEAK 20(13Q12.11) WILD-TYPE 37  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     19    2
  DEL PEAK 20(13Q12.11) WILD-TYPE   37    3
     clus
vv    DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  CGY                            19                              37
  GY                              2                               3
[1] 2 2
[1] FALSE
D48V25, continuous
D48V26, continuous
D48V27, continuous
D48V28, continuous
D48V29, continuous
D48V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 20(13Q12.11) MUTATED                                     0
  DEL PEAK 20(13Q12.11) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 20(13Q12.11) MUTATED                                     2
  DEL PEAK 20(13Q12.11) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 20(13Q12.11) MUTATED                        10
  DEL PEAK 20(13Q12.11) WILD-TYPE                      25
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 20(13Q12.11) MUTATED                         0
  DEL PEAK 20(13Q12.11) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 20(13Q12.11) MUTATED                         3
  DEL PEAK 20(13Q12.11) WILD-TYPE                       5
D48V31, multiclass
                                     clus
vv                                    DEL PEAK 20(13Q12.11) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        10
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         3
                                     clus
vv                                    DEL PEAK 20(13Q12.11) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                          25
  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 20(13Q12.11) MUTATED                                               0
  DEL PEAK 20(13Q12.11) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 20(13Q12.11) MUTATED                                                6
  DEL PEAK 20(13Q12.11) WILD-TYPE                                             19
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 20(13Q12.11) MUTATED                                                                                  28
  DEL PEAK 20(13Q12.11) WILD-TYPE                                                                                53
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 20(13Q12.11) MUTATED                                                                                             41
  DEL PEAK 20(13Q12.11) WILD-TYPE                                                                                           79
D48V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 20(13Q12.11) 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)                                       28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            41
                                                                                              clus
vv                                                                                             DEL PEAK 20(13Q12.11) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V33, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   18 26
  DEL PEAK 20(13Q12.11) WILD-TYPE 52 47
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     18   26
  DEL PEAK 20(13Q12.11) WILD-TYPE   52   47
         clus
vv        DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  ABSENT                             18                              52
  PRESENT                            26                              47
[1] 2 2
[1] FALSE
D48V34, continuous
D48V35, continuous
D48V36, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   16 43
  DEL PEAK 20(13Q12.11) WILD-TYPE 32 73
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     16   43
  DEL PEAK 20(13Q12.11) WILD-TYPE   32   73
                                          clus
vv                                         DEL PEAK 20(13Q12.11) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            43
                                          clus
vv                                         DEL PEAK 20(13Q12.11) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              73
[1] 2 2
[1] FALSE
D48V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 20(13Q12.11) MUTATED              3          16         27
  DEL PEAK 20(13Q12.11) WILD-TYPE           12          37         57
D48V38, multiclass
              clus
vv             DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  CURRENT USER                             3                              12
  FORMER USER                             16                              37
  NEVER USED                              27                              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"
D48V39, continuous
D48V40, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   23  7
  DEL PEAK 20(13Q12.11) WILD-TYPE 69 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     23    7
  DEL PEAK 20(13Q12.11) WILD-TYPE   69   10
         clus
vv        DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  ABSENT                             23                              69
  PRESENT                             7                              10
[1] 2 2
[1] FALSE
D48V41, continuous
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 20(13Q12.11) MUTATED      0  11   17   10  3   1    2    3   7  1
  DEL PEAK 20(13Q12.11) WILD-TYPE    1  23   52   20  3   9    5    6  29  1
                                 vv
clus                              T3A T3B T4 TIS TX
  DEL PEAK 20(13Q12.11) MUTATED     2   8  2   1  7
  DEL PEAK 20(13Q12.11) WILD-TYPE   0   9  6   0  9
D48V42, multiclass
      clus
vv     DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  T1A1                             0                               1
  T1B                             11                              23
  T1B1                            17                              52
  T1B2                            10                              20
  T2                               3                               3
  T2A                              1                               9
  T2A1                             2                               5
  T2A2                             3                               6
  T2B                              7                              29
  T3                               1                               1
  T3A                              2                               0
  T3B                              8                               9
  T4                               2                               6
  TIS                              1                               0
  TX                               7                               9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 20(13Q12.11) MUTATED         3        1         0         1       17
  DEL PEAK 20(13Q12.11) WILD-TYPE       2        0         1         0       16
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 20(13Q12.11) MUTATED          16        12        0         2
  DEL PEAK 20(13Q12.11) WILD-TYPE        61        24        4         6
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 20(13Q12.11) MUTATED            2          1        12         0
  DEL PEAK 20(13Q12.11) WILD-TYPE          3          6        31         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 20(13Q12.11) MUTATED            3         18         2         4
  DEL PEAK 20(13Q12.11) WILD-TYPE          0         24         5         8
D48V44, multiclass
            clus
vv           DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                               1                               0
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                              17                              16
  STAGE IB1                             16                              61
  STAGE IB2                             12                              24
  STAGE II                               0                               4
  STAGE IIA                              2                               6
  STAGE IIA1                             2                               3
  STAGE IIA2                             1                               6
  STAGE IIB                             12                              31
  STAGE III                              0                               1
  STAGE IIIA                             3                               0
  STAGE IIIB                            18                              24
  STAGE IVA                              2                               5
  STAGE IVB                              4                               8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 21(13Q14.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(13Q14.2) MUTATED    85  24
  DEL PEAK 21(13Q14.2) WILD-TYPE 128  41
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           109                            169 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            24                             41 
$`DEL PEAK 21(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       210.67       154.32       134.33 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XI 
      147.35       155.77       131.11        94.95         9.34         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DR-A0ZL 
      146.86        99.91        20.91        11.87        58.88        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        25.02 
TCGA-EA-A439 TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.50        13.48         0.36        12.59        45.96        26.27 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA 
        1.51        19.27         0.43         0.59         1.45        16.08 
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         8.32        23.84 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC 
        1.45         1.58         1.48         1.97        25.41        10.82 
TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JW-A5VK 
       21.67        14.93         9.44       147.39        78.71        20.48 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
        8.28        18.15        21.11        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-MA-AA3W TCGA-MA-AA42 TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A6DT 
       12.49        22.52         8.52        35.05         5.49         9.04 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
        9.34        15.39        19.59        12.16        10.03        40.50 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QF TCGA-VS-A8QM 
       26.43        18.05        19.96        59.51        57.93        31.27 
TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A9U5 
        4.73        39.78        15.68        50.63        48.07        44.94 
TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP 
       25.74        19.69        40.96        14.53        27.25        43.27 
TCGA-VS-A9UU TCGA-VS-A9V1 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       14.53         5.16        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 
        0.69 

$`DEL PEAK 21(13Q14.2) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN 
       12.39        23.67        11.44        36.56       177.04         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
       19.86        67.46        46.32        30.21        35.01        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF 
       44.22        78.35       100.14        33.24        52.01        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X5 
       20.42       101.82        15.48        20.35        17.19        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        2.73        50.99        45.83        23.51        27.52        20.81 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        50.76        44.94        40.04        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
        2.66        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 
       37.35        30.90        31.53        31.36        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       24.56        26.01        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        13.91        15.02        14.99        14.96        13.58 
TCGA-EK-A2IP TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ 
        6.64         0.59         0.13         0.07         4.04         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
       47.77         2.24         0.10         0.07         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        7.92         6.94        14.70        19.79        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.92         2.17        31.36        36.26         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-IR-A3LA 
        1.35         1.32         1.12         9.01        20.78       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81       117.40        96.95        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        28.37 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3X 
      195.85         7.99         0.30         0.82        13.35        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       17.82        19.56         9.17        11.38        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        54.81        20.84         2.96        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73S 
       15.95        16.14        17.56        14.07        15.88        19.36 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8Q8 
        3.88        11.67        93.99        66.05        37.78        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94W TCGA-VS-A94X 
       46.03        36.13        11.51        39.78        36.26        16.64 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 
       24.39        50.86        50.14        45.34        43.40        42.41 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ 
       21.30        22.72        46.92         1.71        41.42        35.97 
TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V2 
       20.09         3.42        18.25        67.20        18.84        14.04 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       14.89         4.34        16.24        15.42         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                        210.67                         195.85 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                         21.11                          18.25 
[1] "0.0 - 210.7 (21.1)" "0.0 - 195.8 (18.2)"
[1] "hr=" "1.5"
D49V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 21(13Q14.2) MUTATED   48 23 15  1
  DEL PEAK 21(13Q14.2) WILD-TYPE 86 45  6  7
D49V3, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  T1                           48                             86
  T2                           23                             45
  T3                           15                              6
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   41 26
  DEL PEAK 21(13Q14.2) WILD-TYPE 86 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     41   26
  DEL PEAK 21(13Q14.2) WILD-TYPE   86   29
   clus
vv  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  0                           41                             86
  1                           26                             29
[1] 2 2
[1] FALSE
D49V5, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   42  5
  DEL PEAK 21(13Q14.2) WILD-TYPE 65  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     42    5
  DEL PEAK 21(13Q14.2) WILD-TYPE   65    5
   clus
vv  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  0                           42                             65
  1                            5                              5
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(13Q14.2) MUTATED               2                              108
  DEL PEAK 21(13Q14.2) WILD-TYPE             3                              133
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 21(13Q14.2) MUTATED                                               1
  DEL PEAK 21(13Q14.2) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 21(13Q14.2) MUTATED                                     4
  DEL PEAK 21(13Q14.2) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 21(13Q14.2) MUTATED                                           0
  DEL PEAK 21(13Q14.2) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 21(13Q14.2) MUTATED                                              2
  DEL PEAK 21(13Q14.2) WILD-TYPE                                           13
D49V6, multiclass
                                               clus
vv                                              DEL PEAK 21(13Q14.2) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       108
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              DEL PEAK 21(13Q14.2) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         133
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    14 103
  DEL PEAK 21(13Q14.2) WILD-TYPE  16 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     14  103
  DEL PEAK 21(13Q14.2) WILD-TYPE   16  159
     clus
vv    DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  NO                            14                             16
  YES                          103                            159
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(13Q14.2) MUTATED                                  1     8
  DEL PEAK 21(13Q14.2) WILD-TYPE                                7    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(13Q14.2) MUTATED                          17
  DEL PEAK 21(13Q14.2) WILD-TYPE                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 21(13Q14.2) MUTATED                                           2
  DEL PEAK 21(13Q14.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 21(13Q14.2) MUTATED      76
  DEL PEAK 21(13Q14.2) WILD-TYPE   125
D49V10, multiclass
                                           clus
vv                                          DEL PEAK 21(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                           17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               76
                                           clus
vv                                          DEL PEAK 21(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 10
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                125
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED     7  61
  DEL PEAK 21(13Q14.2) WILD-TYPE  16 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED      7   61
  DEL PEAK 21(13Q14.2) WILD-TYPE   16  100
                        clus
vv                       DEL PEAK 21(13Q14.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 21(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            100
[1] 2 2
[1] FALSE
D49V12, continuous
D49V13, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   55 13
  DEL PEAK 21(13Q14.2) WILD-TYPE 79 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     55   13
  DEL PEAK 21(13Q14.2) WILD-TYPE   79   28
            clus
vv           DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  TUMOR FREE                           55                             79
  WITH TUMOR                           13                             28
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 21(13Q14.2) MUTATED       23      1       0      2       1
  DEL PEAK 21(13Q14.2) WILD-TYPE     30      4       1      9       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 21(13Q14.2) MUTATED              84       6
  DEL PEAK 21(13Q14.2) WILD-TYPE           117       8
D49V14, multiclass
               clus
vv              DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  BRAZIL                                  23                             30
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   2                              9
  UKRAINE                                  1                              6
  UNITED STATES                           84                            117
  VIETNAM                                  6                              8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 21(13Q14.2) MUTATED    5 39 56  1 11
  DEL PEAK 21(13Q14.2) WILD-TYPE 13 90 57  0 13
D49V15, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  G1                            5                             13
  G2                           39                             90
  G3                           56                             57
  G4                            1                              0
  GX                           11                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V16, continuous
D49V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 21(13Q14.2) MUTATED                                            15
  DEL PEAK 21(13Q14.2) WILD-TYPE                                          22
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 21(13Q14.2) MUTATED                                        6
  DEL PEAK 21(13Q14.2) WILD-TYPE                                      3
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 21(13Q14.2) MUTATED                                                 3
  DEL PEAK 21(13Q14.2) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 21(13Q14.2) MUTATED               29                  45
  DEL PEAK 21(13Q14.2) WILD-TYPE             33                  97
D49V18, multiclass
                                                 clus
vv                                                DEL PEAK 21(13Q14.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            3
  CURRENT SMOKER                                                            29
  LIFELONG NON-SMOKER                                                       45
                                                 clus
vv                                                DEL PEAK 21(13Q14.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                              33
  LIFELONG NON-SMOKER                                                         97
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V19, continuous
D49V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 21(13Q14.2) MUTATED             8       42             5        7
  DEL PEAK 21(13Q14.2) WILD-TYPE          11       60             7       18
D49V21, multiclass
               clus
vv              DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  COMBINATION                              8                             11
  EXTERNAL                                42                             60
  EXTERNAL BEAM                            5                              7
  INTERNAL                                 7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V22, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   12  1
  DEL PEAK 21(13Q14.2) WILD-TYPE 13  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     12    1
  DEL PEAK 21(13Q14.2) WILD-TYPE   13    2
                         clus
vv                        DEL PEAK 21(13Q14.2) MUTATED
  COMPLETED AS PLANNED                              12
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 21(13Q14.2) WILD-TYPE
  COMPLETED AS PLANNED                                13
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 21(13Q14.2) MUTATED                    1                1
  DEL PEAK 21(13Q14.2) WILD-TYPE                  1                1
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 21(13Q14.2) MUTATED                    18            14
  DEL PEAK 21(13Q14.2) WILD-TYPE                  18            19
D49V23, multiclass
                     clus
vv                    DEL PEAK 21(13Q14.2) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                           18
  REGIONAL SITE                                 14
                     clus
vv                    DEL PEAK 21(13Q14.2) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             18
  REGIONAL SITE                                   19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V24, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   23  2
  DEL PEAK 21(13Q14.2) WILD-TYPE 33  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     23    2
  DEL PEAK 21(13Q14.2) WILD-TYPE   33    3
     clus
vv    DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  CGY                           23                             33
  GY                             2                              3
[1] 2 2
[1] FALSE
D49V25, continuous
D49V26, continuous
D49V27, continuous
D49V28, continuous
D49V29, continuous
D49V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 21(13Q14.2) MUTATED                                     0
  DEL PEAK 21(13Q14.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 21(13Q14.2) MUTATED                                     2
  DEL PEAK 21(13Q14.2) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 21(13Q14.2) MUTATED                        14
  DEL PEAK 21(13Q14.2) WILD-TYPE                      21
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 21(13Q14.2) MUTATED                         0
  DEL PEAK 21(13Q14.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 21(13Q14.2) MUTATED                         4
  DEL PEAK 21(13Q14.2) WILD-TYPE                       4
D49V31, multiclass
                                     clus
vv                                    DEL PEAK 21(13Q14.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       14
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        4
                                     clus
vv                                    DEL PEAK 21(13Q14.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         21
  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 21(13Q14.2) MUTATED                                               0
  DEL PEAK 21(13Q14.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 21(13Q14.2) MUTATED                                                9
  DEL PEAK 21(13Q14.2) WILD-TYPE                                             16
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 21(13Q14.2) MUTATED                                                                                  34
  DEL PEAK 21(13Q14.2) WILD-TYPE                                                                                47
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 21(13Q14.2) MUTATED                                                                                             48
  DEL PEAK 21(13Q14.2) WILD-TYPE                                                                                           72
D49V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 21(13Q14.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      34
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           48
                                                                                              clus
vv                                                                                             DEL PEAK 21(13Q14.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        47
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V33, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   21 29
  DEL PEAK 21(13Q14.2) WILD-TYPE 49 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     21   29
  DEL PEAK 21(13Q14.2) WILD-TYPE   49   44
         clus
vv        DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  ABSENT                            21                             49
  PRESENT                           29                             44
[1] 2 2
[1] FALSE
D49V34, continuous
D49V35, continuous
D49V36, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   19 50
  DEL PEAK 21(13Q14.2) WILD-TYPE 29 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     19   50
  DEL PEAK 21(13Q14.2) WILD-TYPE   29   66
                                          clus
vv                                         DEL PEAK 21(13Q14.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           50
                                          clus
vv                                         DEL PEAK 21(13Q14.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             66
[1] 2 2
[1] FALSE
D49V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 21(13Q14.2) MUTATED              4          20         29
  DEL PEAK 21(13Q14.2) WILD-TYPE           11          33         55
D49V38, multiclass
              clus
vv             DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  CURRENT USER                            4                             11
  FORMER USER                            20                             33
  NEVER USED                             29                             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"
D49V39, continuous
D49V40, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   25  9
  DEL PEAK 21(13Q14.2) WILD-TYPE 67  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     25    9
  DEL PEAK 21(13Q14.2) WILD-TYPE   67    8
         clus
vv        DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  ABSENT                            25                             67
  PRESENT                            9                              8
[1] 2 2
[1] FALSE
D49V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 21(13Q14.2) MUTATED      0  11   23   14  4   2    3    2  12  1   2
  DEL PEAK 21(13Q14.2) WILD-TYPE    1  23   46   16  2   8    4    7  24  1   0
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 21(13Q14.2) MUTATED    12  1   1  7
  DEL PEAK 21(13Q14.2) WILD-TYPE   5  7   0  9
D49V42, multiclass
      clus
vv     DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  T1A1                            0                              1
  T1B                            11                             23
  T1B1                           23                             46
  T1B2                           14                             16
  T2                              4                              2
  T2A                             2                              8
  T2A1                            3                              4
  T2A2                            2                              7
  T2B                            12                             24
  T3                              1                              1
  T3A                             2                              0
  T3B                            12                              5
  T4                              1                              7
  TIS                             1                              0
  TX                              7                              9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 21(13Q14.2) MUTATED         4        1         0         1       17
  DEL PEAK 21(13Q14.2) WILD-TYPE       1        0         1         0       16
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 21(13Q14.2) MUTATED          19        14        1         3
  DEL PEAK 21(13Q14.2) WILD-TYPE        58        22        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 21(13Q14.2) MUTATED            3          1        18         0
  DEL PEAK 21(13Q14.2) WILD-TYPE          2          6        25         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 21(13Q14.2) MUTATED            3         22         2         4
  DEL PEAK 21(13Q14.2) WILD-TYPE          0         20         5         8
D49V44, multiclass
            clus
vv           DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             17                             16
  STAGE IB1                            19                             58
  STAGE IB2                            14                             22
  STAGE II                              1                              3
  STAGE IIA                             3                              5
  STAGE IIA1                            3                              2
  STAGE IIA2                            1                              6
  STAGE IIB                            18                             25
  STAGE III                             0                              1
  STAGE IIIA                            3                              0
  STAGE IIIB                           22                             20
  STAGE IVA                             2                              5
  STAGE IVB                             4                              8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 22(14Q32.31) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 22(14Q32.31) MUTATED    35   8
  DEL PEAK 22(14Q32.31) WILD-TYPE 178  57
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                             43                             235 
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                              8                              57 
$`DEL PEAK 22(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-C5-A7CM TCGA-C5-A8XH TCGA-C5-A8YR TCGA-DG-A2KJ TCGA-EA-A3HQ 
       18.02        20.35        45.83        27.52        58.88        37.35 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A78R TCGA-EK-A2PG TCGA-EK-A2PM 
       14.50        24.56        26.01        13.48         1.51         0.59 
TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3TX 
        0.59         1.18         2.24        15.55        23.84         1.48 
TCGA-IR-A3LA TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A7HU 
      137.16        78.71        21.11        11.28         0.30        13.35 
TCGA-MA-AA42 TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A73R TCGA-UC-A7PG TCGA-VS-A8EL 
        8.52        54.81        16.41        15.39        12.16        59.51 
TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A959 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9V3 
       39.78         4.73        45.34        42.41        25.74        14.89 
TCGA-VS-A9V4 
        4.34 

$`DEL PEAK 22(14Q32.31) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        57.04        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       38.99        35.61         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 
       44.22        73.18        73.45        78.35       100.14        33.24 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       52.01        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI 
       94.95         9.34        13.61         2.73        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        23.51        20.81        20.91        11.87 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR 
       16.18        17.52         8.28        39.55        12.36        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 
       31.53        31.36        13.05        25.02        26.40        14.50 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         7.46        14.89        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ 
       15.02        14.99        14.96        13.58         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R8 
       45.96        26.27         6.64        19.27         0.43         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       47.77         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41        10.82        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       147.39        66.81       117.40        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
      195.85        30.31         7.99         0.89        12.49         0.82 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 
       22.52        20.28        17.82        19.56         9.17        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       13.87        34.62         5.42        35.05        20.84         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        15.58        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88         9.34        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        93.99        66.05        10.03        40.50        37.78 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       26.43        18.05        19.96        32.15        46.03        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z 
       11.51        57.93        31.27        36.26        16.64        24.39 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       39.78        50.86        15.68        50.63        48.07        50.14 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       44.94        43.40        21.30        22.72        19.69        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       40.96         1.71        14.53        27.25        41.42        43.27 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       35.97        20.09        14.53         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
       18.84         5.16        14.04        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                           0.30                            0.03 
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                         137.16                          210.67 
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                          20.35                           19.79 
[1] "0.3 - 137.2 (20.4)" "0.0 - 210.7 (19.8)"
[1] "hr=" "1.2"
D50V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 22(14Q32.31) MUTATED    21  14   3   2
  DEL PEAK 22(14Q32.31) WILD-TYPE 113  54  18   6
D50V3, multiclass
    clus
vv   DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  T1                            21                             113
  T2                            14                              54
  T3                             3                              18
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                                 cls
clus                                0   1
  DEL PEAK 22(14Q32.31) MUTATED    23  10
  DEL PEAK 22(14Q32.31) WILD-TYPE 104  45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     23   10
  DEL PEAK 22(14Q32.31) WILD-TYPE  104   45
   clus
vv  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  0                            23                             104
  1                            10                              45
[1] 2 2
[1] FALSE
D50V5, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED   25  0
  DEL PEAK 22(14Q32.31) WILD-TYPE 82 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     25    0
  DEL PEAK 22(14Q32.31) WILD-TYPE   82   10
   clus
vv  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  0                            25                              82
  1                             0                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 22(14Q32.31) MUTATED               0
  DEL PEAK 22(14Q32.31) WILD-TYPE             5
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(14Q32.31) MUTATED                                 38
  DEL PEAK 22(14Q32.31) WILD-TYPE                              203
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 22(14Q32.31) MUTATED                                               3
  DEL PEAK 22(14Q32.31) WILD-TYPE                                             3
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 22(14Q32.31) MUTATED                                     6
  DEL PEAK 22(14Q32.31) WILD-TYPE                                  16
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 22(14Q32.31) MUTATED                                           1
  DEL PEAK 22(14Q32.31) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 22(14Q32.31) MUTATED                                              2
  DEL PEAK 22(14Q32.31) WILD-TYPE                                           13
D50V6, multiclass
                                               clus
vv                                              DEL PEAK 22(14Q32.31) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              2
                                               clus
vv                                              DEL PEAK 22(14Q32.31) WILD-TYPE
  ADENOSQUAMOUS                                                               5
  CERVICAL SQUAMOUS CELL CARCINOMA                                          203
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                 cls
clus                                0   1
  DEL PEAK 22(14Q32.31) MUTATED     2  48
  DEL PEAK 22(14Q32.31) WILD-TYPE  28 214
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED      2   48
  DEL PEAK 22(14Q32.31) WILD-TYPE   28  214
     clus
vv    DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  NO                              2                              28
  YES                            48                             214
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(14Q32.31) MUTATED                                  0     4
  DEL PEAK 22(14Q32.31) WILD-TYPE                                8    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(14Q32.31) MUTATED                           3
  DEL PEAK 22(14Q32.31) WILD-TYPE                        25
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 22(14Q32.31) MUTATED                                           0
  DEL PEAK 22(14Q32.31) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  DEL PEAK 22(14Q32.31) MUTATED      38
  DEL PEAK 22(14Q32.31) WILD-TYPE   163
D50V10, multiclass
                                           clus
vv                                          DEL PEAK 22(14Q32.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 4
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                38
                                           clus
vv                                          DEL PEAK 22(14Q32.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  WHITE                                                                 163
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, binary
                                 cls
clus                                0   1
  DEL PEAK 22(14Q32.31) MUTATED     4  24
  DEL PEAK 22(14Q32.31) WILD-TYPE  19 137
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED      4   24
  DEL PEAK 22(14Q32.31) WILD-TYPE   19  137
                        clus
vv                       DEL PEAK 22(14Q32.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            24
                        clus
vv                       DEL PEAK 22(14Q32.31) WILD-TYPE
  HISPANIC OR LATINO                                  19
  NOT HISPANIC OR LATINO                             137
[1] 2 2
[1] FALSE
D50V12, continuous
D50V13, binary
                                 cls
clus                                0   1
  DEL PEAK 22(14Q32.31) MUTATED    26   2
  DEL PEAK 22(14Q32.31) WILD-TYPE 108  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     26    2
  DEL PEAK 22(14Q32.31) WILD-TYPE  108   39
            clus
vv           DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  TUMOR FREE                            26                             108
  WITH TUMOR                             2                              39
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 22(14Q32.31) MUTATED        8      1       0      2       2
  DEL PEAK 22(14Q32.31) WILD-TYPE     45      4       1      9       5
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 22(14Q32.31) MUTATED              33       4
  DEL PEAK 22(14Q32.31) WILD-TYPE           168      10
D50V14, multiclass
               clus
vv              DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  BRAZIL                                    8                              45
  CANADA                                    1                               4
  NIGERIA                                   0                               1
  RUSSIA                                    2                               9
  UKRAINE                                   2                               5
  UNITED STATES                            33                             168
  VIETNAM                                   4                              10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               G1  G2  G3  G4  GX
  DEL PEAK 22(14Q32.31) MUTATED     3  13  26   1   2
  DEL PEAK 22(14Q32.31) WILD-TYPE  15 116  87   0  22
D50V15, multiclass
    clus
vv   DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  G1                             3                              15
  G2                            13                             116
  G3                            26                              87
  G4                             1                               0
  GX                             2                              22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V16, continuous
D50V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 22(14Q32.31) MUTATED                                             8
  DEL PEAK 22(14Q32.31) WILD-TYPE                                          29
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 22(14Q32.31) MUTATED                                        0
  DEL PEAK 22(14Q32.31) WILD-TYPE                                      9
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 22(14Q32.31) MUTATED                                                 0
  DEL PEAK 22(14Q32.31) WILD-TYPE                                               3
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 22(14Q32.31) MUTATED                4                  28
  DEL PEAK 22(14Q32.31) WILD-TYPE             58                 114
D50V18, multiclass
                                                 clus
vv                                                DEL PEAK 22(14Q32.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                              4
  LIFELONG NON-SMOKER                                                        28
                                                 clus
vv                                                DEL PEAK 22(14Q32.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               3
  CURRENT SMOKER                                                               58
  LIFELONG NON-SMOKER                                                         114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V19, continuous
D50V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 22(14Q32.31) MUTATED             2       19             0        3
  DEL PEAK 22(14Q32.31) WILD-TYPE          17       83            12       22
D50V21, multiclass
               clus
vv              DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  COMBINATION                               2                              17
  EXTERNAL                                 19                              83
  EXTERNAL BEAM                             0                              12
  INTERNAL                                  3                              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"
D50V22, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED    2  0
  DEL PEAK 22(14Q32.31) WILD-TYPE 23  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED      2    0
  DEL PEAK 22(14Q32.31) WILD-TYPE   23    3
                         clus
vv                        DEL PEAK 22(14Q32.31) MUTATED
  COMPLETED AS PLANNED                                2
  TREATMENT NOT COMPLETED                             0
                         clus
vv                        DEL PEAK 22(14Q32.31) WILD-TYPE
  COMPLETED AS PLANNED                                 23
  TREATMENT NOT COMPLETED                               3
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 22(14Q32.31) MUTATED                    0                0
  DEL PEAK 22(14Q32.31) WILD-TYPE                  2                2
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 22(14Q32.31) MUTATED                     7             4
  DEL PEAK 22(14Q32.31) WILD-TYPE                  29            29
D50V23, multiclass
                     clus
vv                    DEL PEAK 22(14Q32.31) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                0
  PRIMARY TUMOR FIELD                             7
  REGIONAL SITE                                   4
                     clus
vv                    DEL PEAK 22(14Q32.31) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  2
  PRIMARY TUMOR FIELD                              29
  REGIONAL SITE                                    29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V24, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED   10  1
  DEL PEAK 22(14Q32.31) WILD-TYPE 46  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     10    1
  DEL PEAK 22(14Q32.31) WILD-TYPE   46    4
     clus
vv    DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  CGY                            10                              46
  GY                              1                               4
[1] 2 2
[1] FALSE
D50V25, continuous
D50V26, continuous
D50V27, continuous
D50V28, continuous
D50V29, continuous
D50V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 22(14Q32.31) MUTATED                                     0
  DEL PEAK 22(14Q32.31) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 22(14Q32.31) MUTATED                                     1
  DEL PEAK 22(14Q32.31) WILD-TYPE                                   6
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 22(14Q32.31) MUTATED                         6
  DEL PEAK 22(14Q32.31) WILD-TYPE                      29
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 22(14Q32.31) MUTATED                         0
  DEL PEAK 22(14Q32.31) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 22(14Q32.31) MUTATED                         2
  DEL PEAK 22(14Q32.31) WILD-TYPE                       6
D50V31, multiclass
                                     clus
vv                                    DEL PEAK 22(14Q32.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         6
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         2
                                     clus
vv                                    DEL PEAK 22(14Q32.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               6
  OTHER LOCATION, SPECIFY                                          29
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 22(14Q32.31) MUTATED                                               0
  DEL PEAK 22(14Q32.31) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 22(14Q32.31) MUTATED                                                1
  DEL PEAK 22(14Q32.31) WILD-TYPE                                             24
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 22(14Q32.31) MUTATED                                                                                  18
  DEL PEAK 22(14Q32.31) WILD-TYPE                                                                                63
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 22(14Q32.31) MUTATED                                                                                             16
  DEL PEAK 22(14Q32.31) WILD-TYPE                                                                                          104
D50V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 22(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)                                       18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            16
                                                                                              clus
vv                                                                                             DEL PEAK 22(14Q32.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         63
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V33, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED   10 14
  DEL PEAK 22(14Q32.31) WILD-TYPE 60 59
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     10   14
  DEL PEAK 22(14Q32.31) WILD-TYPE   60   59
         clus
vv        DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  ABSENT                             10                              60
  PRESENT                            14                              59
[1] 2 2
[1] FALSE
D50V34, continuous
D50V35, continuous
D50V36, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED    8 17
  DEL PEAK 22(14Q32.31) WILD-TYPE 40 99
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED      8   17
  DEL PEAK 22(14Q32.31) WILD-TYPE   40   99
                                          clus
vv                                         DEL PEAK 22(14Q32.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            17
                                          clus
vv                                         DEL PEAK 22(14Q32.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              99
[1] 2 2
[1] FALSE
D50V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 22(14Q32.31) MUTATED              3           9          9
  DEL PEAK 22(14Q32.31) WILD-TYPE           12          44         75
D50V38, multiclass
              clus
vv             DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  CURRENT USER                             3                              12
  FORMER USER                              9                              44
  NEVER USED                               9                              75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V39, continuous
D50V40, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED   16  3
  DEL PEAK 22(14Q32.31) WILD-TYPE 76 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     16    3
  DEL PEAK 22(14Q32.31) WILD-TYPE   76   14
         clus
vv        DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  ABSENT                             16                              76
  PRESENT                             3                              14
[1] 2 2
[1] FALSE
D50V41, continuous
[1] "Remove cluster labels:"        "DEL PEAK 22(14Q32.31) MUTATED"
clus
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                              1                              16 
                     TCGA-C5-A1BN                      TCGA-C5-A1MH 
"DEL PEAK 22(14Q32.31) WILD-TYPE" "DEL PEAK 22(14Q32.31) WILD-TYPE" 
                     TCGA-C5-A1ML                      TCGA-C5-A1MN 
"DEL PEAK 22(14Q32.31) WILD-TYPE" "DEL PEAK 22(14Q32.31) WILD-TYPE" 
                     TCGA-C5-A1MP                      TCGA-EK-A2RO 
"DEL PEAK 22(14Q32.31) WILD-TYPE" "DEL PEAK 22(14Q32.31) WILD-TYPE" 
                     TCGA-GH-A9DA                      TCGA-HM-A3JK 
"DEL PEAK 22(14Q32.31) WILD-TYPE" "DEL PEAK 22(14Q32.31) WILD-TYPE" 
                     TCGA-JW-A852                      TCGA-JX-A3Q8 
"DEL PEAK 22(14Q32.31) WILD-TYPE" "DEL PEAK 22(14Q32.31) WILD-TYPE" 
                     TCGA-MA-AA3W                      TCGA-MA-AA3Z 
"DEL PEAK 22(14Q32.31) WILD-TYPE" "DEL PEAK 22(14Q32.31) WILD-TYPE" 
                     TCGA-MU-A51Y                      TCGA-MU-A8JM 
"DEL PEAK 22(14Q32.31) WILD-TYPE" "DEL PEAK 22(14Q32.31) WILD-TYPE" 
                     TCGA-MY-A913                      TCGA-ZX-AA5X 
"DEL PEAK 22(14Q32.31) WILD-TYPE" "DEL PEAK 22(14Q32.31) WILD-TYPE" 
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 22(14Q32.31) MUTATED      0   5   10    6  3   2    3    0   6  1
  DEL PEAK 22(14Q32.31) WILD-TYPE    1  29   59   24  3   8    4    9  30  1
                                 vv
clus                              T3A T3B T4 TIS TX
  DEL PEAK 22(14Q32.31) MUTATED     0   2  2   0  3
  DEL PEAK 22(14Q32.31) WILD-TYPE   2  15  6   1 13
D50V42, multiclass
      clus
vv     DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  T1A1                             0                               1
  T1B                              5                              29
  T1B1                            10                              59
  T1B2                             6                              24
  T2                               3                               3
  T2A                              2                               8
  T2A1                             3                               4
  T2A2                             0                               9
  T2B                              6                              30
  T3                               1                               1
  T3A                              0                               2
  T3B                              2                              15
  T4                               2                               6
  TIS                              0                               1
  TX                               3                              13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 22(14Q32.31) MUTATED         1        0         0         0        5
  DEL PEAK 22(14Q32.31) WILD-TYPE       4        1         1         1       28
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 22(14Q32.31) MUTATED          14         7        2         1
  DEL PEAK 22(14Q32.31) WILD-TYPE        63        29        2         7
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 22(14Q32.31) MUTATED            2          0         7         0
  DEL PEAK 22(14Q32.31) WILD-TYPE          3          7        36         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 22(14Q32.31) MUTATED            1          5         1         1
  DEL PEAK 22(14Q32.31) WILD-TYPE          2         37         6        11
D50V44, multiclass
            clus
vv           DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               5                              28
  STAGE IB1                             14                              63
  STAGE IB2                              7                              29
  STAGE II                               2                               2
  STAGE IIA                              1                               7
  STAGE IIA1                             2                               3
  STAGE IIA2                             0                               7
  STAGE IIB                              7                              36
  STAGE III                              0                               1
  STAGE IIIA                             1                               2
  STAGE IIIB                             5                              37
  STAGE IVA                              1                               6
  STAGE IVB                              1                              11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 23(15Q21.1) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(15Q21.1) MUTATED    49  15
  DEL PEAK 23(15Q21.1) WILD-TYPE 164  50
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            64                            214 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            15                             50 
$`DEL PEAK 23(15Q21.1) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LV 
       57.04        35.01        38.99        20.91        40.93        73.45 
TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A8XK TCGA-C5-A8YQ 
       52.01       210.67       154.32        17.19        99.91        23.51 
TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A7WH TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 
       50.76        87.75        17.52        14.50        26.01        14.89 
TCGA-EK-A2GZ TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ 
       12.59         0.59         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         9.44       137.16        66.81 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-MA-AA3X 
       78.71        29.85        28.37        30.31        12.49        20.28 
TCGA-MA-AA42 TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
        8.52         5.42        54.81         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A8QH 
       16.41        15.95        18.05        19.96        57.93        39.78 
TCGA-VS-A94Z TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A9U5 TCGA-VS-A9UD 
       24.39        15.68        50.63        48.07        44.94        19.69 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV 
       46.92        40.96        41.42        35.97        20.09         3.42 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-ZJ-A8QR 
       67.20        18.84         4.34        19.13 

$`DEL PEAK 23(15Q21.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-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-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        33.24 
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 
       20.35       147.35       155.77       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       13.61         2.73        50.99        45.83         8.35       146.86 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52        20.81        20.91        11.87         1.12        58.88 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        40.04        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS 
      118.65        22.98        16.83        16.18         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       12.36        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA 
       25.02        14.50        26.40        24.56        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
        7.46        26.79        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48         0.36        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51        19.27         0.43         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       16.08         0.07         4.04         0.03         0.36        47.77 
TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
       14.70        19.79         8.32        15.55         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17        31.36        36.26         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC 
       25.41        10.82        20.78        14.93       147.39       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       96.95        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        20.48        15.58         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 
      195.85         7.99        11.28         0.89         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 
       13.35        22.52        17.82        19.56         9.17        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DT TCGA-Q1-A6DV 
       13.87        34.62        35.05        20.84         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59         3.88        11.67        93.99        12.16        66.05 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 
       10.03        40.50        37.78        26.43        59.51        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       46.03        36.13        11.51        31.27        36.26        16.64 
TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 
        4.73        39.78        50.86        50.14        45.34        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UL 
       42.41        25.74        21.30        22.72         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9V1 TCGA-VS-A9V2 
       27.25        43.27        14.53        18.25         5.16        14.04 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       14.89        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                        210.67                         195.85 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                        22.590                         19.005 
[1] "0.1 - 210.7 (22.6)" "0.0 - 195.8 (19.0)"
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 23(15Q21.1) MUTATED    26  15   6   4
  DEL PEAK 23(15Q21.1) WILD-TYPE 108  53  15   4
D51V3, multiclass
    clus
vv   DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  T1                           26                            108
  T2                           15                             53
  T3                            6                             15
  T4                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   29  7
  DEL PEAK 23(15Q21.1) WILD-TYPE 98 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     29    7
  DEL PEAK 23(15Q21.1) WILD-TYPE   98   48
   clus
vv  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  0                           29                             98
  1                            7                             48
[1] 2 2
[1] FALSE
D51V5, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   19  3
  DEL PEAK 23(15Q21.1) WILD-TYPE 88  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     19    3
  DEL PEAK 23(15Q21.1) WILD-TYPE   88    7
   clus
vv  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  0                           19                             88
  1                            3                              7
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(15Q21.1) MUTATED               1                               51
  DEL PEAK 23(15Q21.1) WILD-TYPE             4                              190
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 23(15Q21.1) MUTATED                                               0
  DEL PEAK 23(15Q21.1) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 23(15Q21.1) MUTATED                                     6
  DEL PEAK 23(15Q21.1) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 23(15Q21.1) MUTATED                                           2
  DEL PEAK 23(15Q21.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 23(15Q21.1) MUTATED                                              8
  DEL PEAK 23(15Q21.1) WILD-TYPE                                            7
D51V6, multiclass
                                               clus
vv                                              DEL PEAK 23(15Q21.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        51
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             8
                                               clus
vv                                              DEL PEAK 23(15Q21.1) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         190
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               7
[1] 6 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 23(15Q21.1) MUTATED     6  62
  DEL PEAK 23(15Q21.1) WILD-TYPE  24 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED      6   62
  DEL PEAK 23(15Q21.1) WILD-TYPE   24  200
     clus
vv    DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  NO                             6                             24
  YES                           62                            200
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(15Q21.1) MUTATED                                  0     4
  DEL PEAK 23(15Q21.1) WILD-TYPE                                8    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(15Q21.1) MUTATED                          10
  DEL PEAK 23(15Q21.1) WILD-TYPE                        18
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 23(15Q21.1) MUTATED                                           2
  DEL PEAK 23(15Q21.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 23(15Q21.1) MUTATED      44
  DEL PEAK 23(15Q21.1) WILD-TYPE   157
D51V10, multiclass
                                           clus
vv                                          DEL PEAK 23(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               44
                                           clus
vv                                          DEL PEAK 23(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                157
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q21.1) MUTATED     4  32
  DEL PEAK 23(15Q21.1) WILD-TYPE  19 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED      4   32
  DEL PEAK 23(15Q21.1) WILD-TYPE   19  129
                        clus
vv                       DEL PEAK 23(15Q21.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           32
                        clus
vv                       DEL PEAK 23(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            129
[1] 2 2
[1] FALSE
D51V12, continuous
D51V13, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   37  8
  DEL PEAK 23(15Q21.1) WILD-TYPE 97 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     37    8
  DEL PEAK 23(15Q21.1) WILD-TYPE   97   33
            clus
vv           DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  TUMOR FREE                           37                             97
  WITH TUMOR                            8                             33
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 23(15Q21.1) MUTATED       19      1       1      1       1
  DEL PEAK 23(15Q21.1) WILD-TYPE     34      4       0     10       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 23(15Q21.1) MUTATED              43       2
  DEL PEAK 23(15Q21.1) WILD-TYPE           158      12
D51V14, multiclass
               clus
vv              DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  BRAZIL                                  19                             34
  CANADA                                   1                              4
  NIGERIA                                  1                              0
  RUSSIA                                   1                             10
  UKRAINE                                  1                              6
  UNITED STATES                           43                            158
  VIETNAM                                  2                             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 23(15Q21.1) MUTATED     1  23  33   1   8
  DEL PEAK 23(15Q21.1) WILD-TYPE  17 106  80   0  16
D51V15, multiclass
    clus
vv   DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  G1                            1                             17
  G2                           23                            106
  G3                           33                             80
  G4                            1                              0
  GX                            8                             16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V16, continuous
D51V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 23(15Q21.1) MUTATED                                             8
  DEL PEAK 23(15Q21.1) WILD-TYPE                                          29
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 23(15Q21.1) MUTATED                                        2
  DEL PEAK 23(15Q21.1) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 23(15Q21.1) MUTATED                                                 1
  DEL PEAK 23(15Q21.1) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 23(15Q21.1) MUTATED               10                  34
  DEL PEAK 23(15Q21.1) WILD-TYPE             52                 108
D51V18, multiclass
                                                 clus
vv                                                DEL PEAK 23(15Q21.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            10
  LIFELONG NON-SMOKER                                                       34
                                                 clus
vv                                                DEL PEAK 23(15Q21.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              52
  LIFELONG NON-SMOKER                                                        108
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V19, continuous
D51V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 23(15Q21.1) MUTATED             4       31             2        4
  DEL PEAK 23(15Q21.1) WILD-TYPE          15       71            10       21
D51V21, multiclass
               clus
vv              DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                31                             71
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 4                             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"
D51V22, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED    6  0
  DEL PEAK 23(15Q21.1) WILD-TYPE 19  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED      6    0
  DEL PEAK 23(15Q21.1) WILD-TYPE   19    3
                         clus
vv                        DEL PEAK 23(15Q21.1) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 23(15Q21.1) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 23(15Q21.1) MUTATED                    0                1
  DEL PEAK 23(15Q21.1) WILD-TYPE                  2                1
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 23(15Q21.1) MUTATED                    12             8
  DEL PEAK 23(15Q21.1) WILD-TYPE                  24            25
D51V23, multiclass
                     clus
vv                    DEL PEAK 23(15Q21.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                           12
  REGIONAL SITE                                  8
                     clus
vv                    DEL PEAK 23(15Q21.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             24
  REGIONAL SITE                                   25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V24, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   18  2
  DEL PEAK 23(15Q21.1) WILD-TYPE 38  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     18    2
  DEL PEAK 23(15Q21.1) WILD-TYPE   38    3
     clus
vv    DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  CGY                           18                             38
  GY                             2                              3
[1] 2 2
[1] FALSE
D51V25, continuous
D51V26, continuous
D51V27, continuous
D51V28, continuous
D51V29, continuous
D51V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 23(15Q21.1) MUTATED                                     0
  DEL PEAK 23(15Q21.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 23(15Q21.1) MUTATED                                     2
  DEL PEAK 23(15Q21.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 23(15Q21.1) MUTATED                         6
  DEL PEAK 23(15Q21.1) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 23(15Q21.1) MUTATED                         0
  DEL PEAK 23(15Q21.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 23(15Q21.1) MUTATED                         1
  DEL PEAK 23(15Q21.1) WILD-TYPE                       7
D51V31, multiclass
                                     clus
vv                                    DEL PEAK 23(15Q21.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        6
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 23(15Q21.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 23(15Q21.1) MUTATED                                               0
  DEL PEAK 23(15Q21.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 23(15Q21.1) MUTATED                                                5
  DEL PEAK 23(15Q21.1) WILD-TYPE                                             20
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 23(15Q21.1) MUTATED                                                                                  27
  DEL PEAK 23(15Q21.1) WILD-TYPE                                                                                54
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 23(15Q21.1) MUTATED                                                                                             22
  DEL PEAK 23(15Q21.1) WILD-TYPE                                                                                           98
D51V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 23(15Q21.1) 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)                                      27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           22
                                                                                              clus
vv                                                                                             DEL PEAK 23(15Q21.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V33, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED    9 12
  DEL PEAK 23(15Q21.1) WILD-TYPE 61 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED      9   12
  DEL PEAK 23(15Q21.1) WILD-TYPE   61   61
         clus
vv        DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  ABSENT                             9                             61
  PRESENT                           12                             61
[1] 2 2
[1] FALSE
D51V34, continuous
D51V35, continuous
D51V36, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   10 20
  DEL PEAK 23(15Q21.1) WILD-TYPE 38 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     10   20
  DEL PEAK 23(15Q21.1) WILD-TYPE   38   96
                                          clus
vv                                         DEL PEAK 23(15Q21.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           20
                                          clus
vv                                         DEL PEAK 23(15Q21.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             96
[1] 2 2
[1] FALSE
D51V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 23(15Q21.1) MUTATED              2          11         23
  DEL PEAK 23(15Q21.1) WILD-TYPE           13          42         61
D51V38, multiclass
              clus
vv             DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                            11                             42
  NEVER USED                             23                             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"
D51V39, continuous
D51V40, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   13  3
  DEL PEAK 23(15Q21.1) WILD-TYPE 79 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     13    3
  DEL PEAK 23(15Q21.1) WILD-TYPE   79   14
         clus
vv        DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  ABSENT                            13                             79
  PRESENT                            3                             14
[1] 2 2
[1] FALSE
D51V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 23(15Q21.1) MUTATED      0   7   15    4  0   2    4    0   9  0   1
  DEL PEAK 23(15Q21.1) WILD-TYPE    1  27   54   26  6   8    3    9  27  2   1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 23(15Q21.1) MUTATED     5  4   1  5
  DEL PEAK 23(15Q21.1) WILD-TYPE  12  4   0 11
D51V42, multiclass
      clus
vv     DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  T1A1                            0                              1
  T1B                             7                             27
  T1B1                           15                             54
  T1B2                            4                             26
  T2                              0                              6
  T2A                             2                              8
  T2A1                            4                              3
  T2A2                            0                              9
  T2B                             9                             27
  T3                              0                              2
  T3A                             1                              1
  T3B                             5                             12
  T4                              4                              4
  TIS                             1                              0
  TX                              5                             11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 23(15Q21.1) MUTATED         1        0         0         1        8
  DEL PEAK 23(15Q21.1) WILD-TYPE       4        1         1         0       25
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 23(15Q21.1) MUTATED          17         5        0         2
  DEL PEAK 23(15Q21.1) WILD-TYPE        60        31        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 23(15Q21.1) MUTATED            3          0        13         0
  DEL PEAK 23(15Q21.1) WILD-TYPE          2          7        30         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 23(15Q21.1) MUTATED            1          8         4         1
  DEL PEAK 23(15Q21.1) WILD-TYPE          2         34         3        11
D51V44, multiclass
            clus
vv           DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              8                             25
  STAGE IB1                            17                             60
  STAGE IB2                             5                             31
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            3                              2
  STAGE IIA2                            0                              7
  STAGE IIB                            13                             30
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                            8                             34
  STAGE IVA                             4                              3
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 24(16Q11.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(16Q11.2) MUTATED    37  12
  DEL PEAK 24(16Q11.2) WILD-TYPE 176  53
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                            49                            229 
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                            12                             53 
$`DEL PEAK 24(16Q11.2) MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1ML 
       23.67       173.29        30.21        35.01        57.73        20.91 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG 
       44.22        73.18        83.05        38.43        18.02       210.67 
TCGA-C5-A7CO TCGA-C5-A8XH TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HR 
      147.35        45.83        16.83        17.52        12.36        30.90 
TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2RJ TCGA-EX-A1H6 TCGA-FU-A3TX 
       26.01         1.51        19.27         1.18         7.92         1.48 
TCGA-FU-A40J TCGA-FU-A770 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK 
        1.35         1.12       137.16        66.81        96.95        29.85 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA43 TCGA-MY-A5BF TCGA-MY-A913 
        7.99         0.30        13.35        11.38        20.84         5.49 
TCGA-Q1-A6DT TCGA-Q1-A73P TCGA-UC-A7PD TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8Q8 
        9.04        15.88        11.67        40.50        19.96        32.15 
TCGA-VS-A952 TCGA-VS-A9UD TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9UY TCGA-VS-A9V4 
       50.86        19.69        41.42        20.09        18.25         4.34 
TCGA-VS-A9V5 
       16.24 

$`DEL PEAK 24(16Q11.2) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        57.04        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       67.46        31.40        46.32        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        33.24        52.01        17.85        20.42       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48        20.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91        11.87         1.12        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
      118.65        22.98        16.18         8.28        39.55        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       24.56        14.50        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.48         0.36        12.59        45.96        26.27         6.64 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         4.04         0.03         0.36        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA 
        1.58         0.82         3.52         1.32         1.97         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        10.82        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      147.39       117.40        78.71        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
        8.28        18.15        21.11       195.85        30.31        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.89        12.49         0.82        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         9.17         8.52        13.87        34.62         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       54.81        35.05         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        17.56        14.07         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
       19.59         3.88        93.99        12.16        66.05        10.03 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA 
       37.78        26.43        18.05        59.51        46.03        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        57.93        39.78        31.27        36.26        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
        4.73        24.39        39.78        15.68        50.63        48.07 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        45.34        44.94        43.40        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       21.30        22.72        46.92        40.96         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ 
       27.25        43.27        35.97        14.53         3.42        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 
       18.84         5.16        14.04        14.89        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                          0.30                           0.03 
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                        210.67                         195.85 
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                         20.09                          19.59 
[1] "0.3 - 210.7 (20.1)" "0.0 - 195.8 (19.6)"
[1] "hr=" "1.1"
D52V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 24(16Q11.2) MUTATED    28  11   4   1
  DEL PEAK 24(16Q11.2) WILD-TYPE 106  57  17   7
D52V3, multiclass
    clus
vv   DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  T1                           28                            106
  T2                           11                             57
  T3                            4                             17
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED   32  5
  DEL PEAK 24(16Q11.2) WILD-TYPE 95 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     32    5
  DEL PEAK 24(16Q11.2) WILD-TYPE   95   50
   clus
vv  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  0                           32                             95
  1                            5                             50
[1] 2 2
[1] FALSE
D52V5, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED   20  2
  DEL PEAK 24(16Q11.2) WILD-TYPE 87  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     20    2
  DEL PEAK 24(16Q11.2) WILD-TYPE   87    8
   clus
vv  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  0                           20                             87
  1                            2                              8
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(16Q11.2) MUTATED               0                               32
  DEL PEAK 24(16Q11.2) WILD-TYPE             5                              209
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 24(16Q11.2) MUTATED                                               5
  DEL PEAK 24(16Q11.2) WILD-TYPE                                             1
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 24(16Q11.2) MUTATED                                    10
  DEL PEAK 24(16Q11.2) WILD-TYPE                                  12
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 24(16Q11.2) MUTATED                                           1
  DEL PEAK 24(16Q11.2) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 24(16Q11.2) MUTATED                                              5
  DEL PEAK 24(16Q11.2) WILD-TYPE                                           10
D52V6, multiclass
                                               clus
vv                                              DEL PEAK 24(16Q11.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        32
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             5
                                               clus
vv                                              DEL PEAK 24(16Q11.2) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         209
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              10
[1] 6 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 24(16Q11.2) MUTATED     6  47
  DEL PEAK 24(16Q11.2) WILD-TYPE  24 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED      6   47
  DEL PEAK 24(16Q11.2) WILD-TYPE   24  215
     clus
vv    DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  NO                             6                             24
  YES                           47                            215
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(16Q11.2) MUTATED                                  1     3
  DEL PEAK 24(16Q11.2) WILD-TYPE                                7    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(16Q11.2) MUTATED                           2
  DEL PEAK 24(16Q11.2) WILD-TYPE                        26
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 24(16Q11.2) MUTATED                                           0
  DEL PEAK 24(16Q11.2) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 24(16Q11.2) MUTATED      44
  DEL PEAK 24(16Q11.2) WILD-TYPE   157
D52V10, multiclass
                                           clus
vv                                          DEL PEAK 24(16Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               44
                                           clus
vv                                          DEL PEAK 24(16Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                157
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q11.2) MUTATED     3  30
  DEL PEAK 24(16Q11.2) WILD-TYPE  20 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED      3   30
  DEL PEAK 24(16Q11.2) WILD-TYPE   20  131
                        clus
vv                       DEL PEAK 24(16Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK 24(16Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            131
[1] 2 2
[1] FALSE
D52V12, continuous
D52V13, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q11.2) MUTATED    24   4
  DEL PEAK 24(16Q11.2) WILD-TYPE 110  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     24    4
  DEL PEAK 24(16Q11.2) WILD-TYPE  110   37
            clus
vv           DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  TUMOR FREE                           24                            110
  WITH TUMOR                            4                             37
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 24(16Q11.2) MUTATED       10      0       0      2       1
  DEL PEAK 24(16Q11.2) WILD-TYPE     43      5       1      9       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 24(16Q11.2) MUTATED              37       3
  DEL PEAK 24(16Q11.2) WILD-TYPE           164      11
D52V14, multiclass
               clus
vv              DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  BRAZIL                                  10                             43
  CANADA                                   0                              5
  NIGERIA                                  0                              1
  RUSSIA                                   2                              9
  UKRAINE                                  1                              6
  UNITED STATES                           37                            164
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 24(16Q11.2) MUTATED     5  25  19   0   2
  DEL PEAK 24(16Q11.2) WILD-TYPE  13 104  94   1  22
D52V15, multiclass
    clus
vv   DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  G1                            5                             13
  G2                           25                            104
  G3                           19                             94
  G4                            0                              1
  GX                            2                             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V16, continuous
D52V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 24(16Q11.2) MUTATED                                             6
  DEL PEAK 24(16Q11.2) WILD-TYPE                                          31
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 24(16Q11.2) MUTATED                                        2
  DEL PEAK 24(16Q11.2) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 24(16Q11.2) MUTATED                                                 1
  DEL PEAK 24(16Q11.2) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 24(16Q11.2) MUTATED                7                  31
  DEL PEAK 24(16Q11.2) WILD-TYPE             55                 111
D52V18, multiclass
                                                 clus
vv                                                DEL PEAK 24(16Q11.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             7
  LIFELONG NON-SMOKER                                                       31
                                                 clus
vv                                                DEL PEAK 24(16Q11.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              55
  LIFELONG NON-SMOKER                                                        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"
D52V19, continuous
D52V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 24(16Q11.2) MUTATED             3       17             3        6
  DEL PEAK 24(16Q11.2) WILD-TYPE          16       85             9       19
D52V21, multiclass
               clus
vv              DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  COMBINATION                              3                             16
  EXTERNAL                                17                             85
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V22, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED    6  0
  DEL PEAK 24(16Q11.2) WILD-TYPE 19  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED      6    0
  DEL PEAK 24(16Q11.2) WILD-TYPE   19    3
                         clus
vv                        DEL PEAK 24(16Q11.2) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 24(16Q11.2) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 24(16Q11.2) MUTATED                    0                0
  DEL PEAK 24(16Q11.2) WILD-TYPE                  2                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 24(16Q11.2) MUTATED                     5             6
  DEL PEAK 24(16Q11.2) WILD-TYPE                  31            27
D52V23, multiclass
                     clus
vv                    DEL PEAK 24(16Q11.2) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            5
  REGIONAL SITE                                  6
                     clus
vv                    DEL PEAK 24(16Q11.2) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             31
  REGIONAL SITE                                   27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V24, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED    9  2
  DEL PEAK 24(16Q11.2) WILD-TYPE 47  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED      9    2
  DEL PEAK 24(16Q11.2) WILD-TYPE   47    3
     clus
vv    DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  CGY                            9                             47
  GY                             2                              3
[1] 2 2
[1] FALSE
D52V25, continuous
D52V26, continuous
D52V27, continuous
D52V28, continuous
D52V29, continuous
D52V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 24(16Q11.2) MUTATED                                     0
  DEL PEAK 24(16Q11.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 24(16Q11.2) MUTATED                                     2
  DEL PEAK 24(16Q11.2) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 24(16Q11.2) MUTATED                        10
  DEL PEAK 24(16Q11.2) WILD-TYPE                      25
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 24(16Q11.2) MUTATED                         0
  DEL PEAK 24(16Q11.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 24(16Q11.2) MUTATED                         1
  DEL PEAK 24(16Q11.2) WILD-TYPE                       7
D52V31, multiclass
                                     clus
vv                                    DEL PEAK 24(16Q11.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       10
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 24(16Q11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         25
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 24(16Q11.2) MUTATED                                               1
  DEL PEAK 24(16Q11.2) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 24(16Q11.2) MUTATED                                                3
  DEL PEAK 24(16Q11.2) WILD-TYPE                                             22
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 24(16Q11.2) MUTATED                                                                                  20
  DEL PEAK 24(16Q11.2) WILD-TYPE                                                                                61
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 24(16Q11.2) MUTATED                                                                                             17
  DEL PEAK 24(16Q11.2) WILD-TYPE                                                                                          103
D52V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 24(16Q11.2) 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)                                      20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           17
                                                                                              clus
vv                                                                                             DEL PEAK 24(16Q11.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V33, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED   16 12
  DEL PEAK 24(16Q11.2) WILD-TYPE 54 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     16   12
  DEL PEAK 24(16Q11.2) WILD-TYPE   54   61
         clus
vv        DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  ABSENT                            16                             54
  PRESENT                           12                             61
[1] 2 2
[1] FALSE
D52V34, continuous
D52V35, continuous
D52V36, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q11.2) MUTATED    10  11
  DEL PEAK 24(16Q11.2) WILD-TYPE  38 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     10   11
  DEL PEAK 24(16Q11.2) WILD-TYPE   38  105
                                          clus
vv                                         DEL PEAK 24(16Q11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           11
                                          clus
vv                                         DEL PEAK 24(16Q11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            105
[1] 2 2
[1] FALSE
D52V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 24(16Q11.2) MUTATED              2          10         19
  DEL PEAK 24(16Q11.2) WILD-TYPE           13          43         65
D52V38, multiclass
              clus
vv             DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                            10                             43
  NEVER USED                             19                             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V39, continuous
D52V40, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED   22  1
  DEL PEAK 24(16Q11.2) WILD-TYPE 70 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     22    1
  DEL PEAK 24(16Q11.2) WILD-TYPE   70   16
         clus
vv        DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  ABSENT                            22                             70
  PRESENT                            1                             16
[1] 2 2
[1] FALSE
D52V41, continuous
[1] "Remove cluster labels:"       "DEL PEAK 24(16Q11.2) MUTATED"
clus
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 24(16Q11.2) WILD-TYPE" "DEL PEAK 24(16Q11.2) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-C5-A1MP 
"DEL PEAK 24(16Q11.2) WILD-TYPE" "DEL PEAK 24(16Q11.2) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-GH-A9DA 
"DEL PEAK 24(16Q11.2) WILD-TYPE" "DEL PEAK 24(16Q11.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 24(16Q11.2) WILD-TYPE" "DEL PEAK 24(16Q11.2) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MA-AA3W 
"DEL PEAK 24(16Q11.2) WILD-TYPE" "DEL PEAK 24(16Q11.2) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK 24(16Q11.2) WILD-TYPE" "DEL PEAK 24(16Q11.2) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 24(16Q11.2) WILD-TYPE" "DEL PEAK 24(16Q11.2) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"DEL PEAK 24(16Q11.2) WILD-TYPE" 
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 24(16Q11.2) MUTATED      0   9   12    7  2   3    1    2   3  0   1
  DEL PEAK 24(16Q11.2) WILD-TYPE    1  25   57   23  4   7    6    7  33  2   1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 24(16Q11.2) MUTATED     3  1   1  1
  DEL PEAK 24(16Q11.2) WILD-TYPE  14  7   0 15
D52V42, multiclass
      clus
vv     DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  T1A1                            0                              1
  T1B                             9                             25
  T1B1                           12                             57
  T1B2                            7                             23
  T2                              2                              4
  T2A                             3                              7
  T2A1                            1                              6
  T2A2                            2                              7
  T2B                             3                             33
  T3                              0                              2
  T3A                             1                              1
  T3B                             3                             14
  T4                              1                              7
  TIS                             1                              0
  TX                              1                             15
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 24(16Q11.2) MUTATED         1        0         0         0        7
  DEL PEAK 24(16Q11.2) WILD-TYPE       4        1         1         1       26
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 24(16Q11.2) MUTATED          17         8        2         3
  DEL PEAK 24(16Q11.2) WILD-TYPE        60        28        2         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 24(16Q11.2) MUTATED            0          1         3         0
  DEL PEAK 24(16Q11.2) WILD-TYPE          5          6        40         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 24(16Q11.2) MUTATED            1          6         1         1
  DEL PEAK 24(16Q11.2) WILD-TYPE          2         36         6        11
D52V44, multiclass
            clus
vv           DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              7                             26
  STAGE IB1                            17                             60
  STAGE IB2                             8                             28
  STAGE II                              2                              2
  STAGE IIA                             3                              5
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             3                             40
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                            6                             36
  STAGE IVA                             1                              6
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 25(16Q23.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(16Q23.1) MUTATED    40  11
  DEL PEAK 25(16Q23.1) WILD-TYPE 173  54
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            51                            227 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            11                             54 
$`DEL PEAK 25(16Q23.1) MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A2LS 
       23.67       173.29        35.01        57.73        20.91        44.22 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG 
       73.18        83.05        38.43        52.01        18.02       210.67 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A8XH TCGA-DG-A2KJ TCGA-DS-A3LQ TCGA-DS-A7WH 
      147.35       131.11        45.83        58.88        22.98        17.52 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2RJ 
       26.01        14.89        19.27         0.59         1.45         1.18 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A3EO TCGA-FU-A3TQ 
        0.03         7.92         8.32        15.55         2.17         1.58 
TCGA-FU-A3TX TCGA-FU-A40J TCGA-FU-A770 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
        1.48         1.35         1.12       137.16        66.81        96.95 
TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MA-AA43 TCGA-MY-A5BF TCGA-VS-A8EC TCGA-VS-A8EJ 
        7.99        13.35        11.38        20.84        40.50        19.96 
TCGA-VS-A8Q8 TCGA-VS-A94Y TCGA-VS-A9UD TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UY 
       32.15         4.73        19.69        41.42        43.27        18.25 
TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         4.34        16.24 

$`DEL PEAK 25(16Q23.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       12.39        49.48        57.04        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH 
       67.46        31.40        46.32        30.21        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV 
       35.61         0.46         2.43        40.93         3.58        73.45 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
       78.35       100.14        33.24        17.85        20.42       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48        20.35        17.19       155.77 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI 
       94.95         9.34        13.61         2.73        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
      146.86        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       11.87         1.12        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99       118.65        16.83 
TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18         8.28        39.55        12.36        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       24.56        14.50        12.66        12.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
        0.36        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.43         0.59         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.03         0.36        47.77         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.10        20.35         6.94        14.70        19.79 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84         0.92        31.36        36.26         1.45 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA 
        0.82         3.52         1.32         1.97         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       10.82        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
        8.28        18.15        21.11       195.85        30.31        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89        12.49         0.30         0.82        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI 
       17.82        19.56         9.17         8.52        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        54.81        35.05         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       11.67        93.99        12.16        66.05        10.03        37.78 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       26.43        18.05        59.51        46.03        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z 
       57.93        39.78        31.27        36.26        16.64        24.39 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       39.78        50.86        15.68        50.63        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       45.34        44.94        43.40        42.41        25.74        21.30 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       22.72        46.92        40.96         1.71        14.53        27.25 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V1 
       35.97        20.09        14.53         3.42        67.20         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       14.04        14.89        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         1.41         0.16         3.91 

  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                        210.67                         195.85 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                         19.96                          19.79 
[1] "0.0 - 210.7 (20.0)" "0.0 - 195.8 (19.8)"
[1] "hr=" "1.3"
D53V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 25(16Q23.1) MUTATED    26  13   5   1
  DEL PEAK 25(16Q23.1) WILD-TYPE 108  55  16   7
D53V3, multiclass
    clus
vv   DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  T1                           26                            108
  T2                           13                             55
  T3                            5                             16
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED    27   8
  DEL PEAK 25(16Q23.1) WILD-TYPE 100  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     27    8
  DEL PEAK 25(16Q23.1) WILD-TYPE  100   47
   clus
vv  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  0                           27                            100
  1                            8                             47
[1] 2 2
[1] FALSE
D53V5, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED   21  1
  DEL PEAK 25(16Q23.1) WILD-TYPE 86  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     21    1
  DEL PEAK 25(16Q23.1) WILD-TYPE   86    9
   clus
vv  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  0                           21                             86
  1                            1                              9
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(16Q23.1) MUTATED               0                               34
  DEL PEAK 25(16Q23.1) WILD-TYPE             5                              207
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 25(16Q23.1) MUTATED                                               4
  DEL PEAK 25(16Q23.1) WILD-TYPE                                             2
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 25(16Q23.1) MUTATED                                    10
  DEL PEAK 25(16Q23.1) WILD-TYPE                                  12
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 25(16Q23.1) MUTATED                                           2
  DEL PEAK 25(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 25(16Q23.1) MUTATED                                              5
  DEL PEAK 25(16Q23.1) WILD-TYPE                                           10
D53V6, multiclass
                                               clus
vv                                              DEL PEAK 25(16Q23.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        34
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             5
                                               clus
vv                                              DEL PEAK 25(16Q23.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         207
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              10
[1] 6 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 25(16Q23.1) MUTATED     7  48
  DEL PEAK 25(16Q23.1) WILD-TYPE  23 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      7   48
  DEL PEAK 25(16Q23.1) WILD-TYPE   23  214
     clus
vv    DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  NO                             7                             23
  YES                           48                            214
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(16Q23.1) MUTATED                                  0     2
  DEL PEAK 25(16Q23.1) WILD-TYPE                                8    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(16Q23.1) MUTATED                           0
  DEL PEAK 25(16Q23.1) WILD-TYPE                        28
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 25(16Q23.1) MUTATED                                           0
  DEL PEAK 25(16Q23.1) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 25(16Q23.1) MUTATED      46
  DEL PEAK 25(16Q23.1) WILD-TYPE   155
D53V10, multiclass
                                           clus
vv                                          DEL PEAK 25(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               46
                                           clus
vv                                          DEL PEAK 25(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                155
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED     2  30
  DEL PEAK 25(16Q23.1) WILD-TYPE  21 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      2   30
  DEL PEAK 25(16Q23.1) WILD-TYPE   21  131
                        clus
vv                       DEL PEAK 25(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK 25(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            131
[1] 2 2
[1] FALSE
D53V12, continuous
D53V13, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED    23   5
  DEL PEAK 25(16Q23.1) WILD-TYPE 111  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     23    5
  DEL PEAK 25(16Q23.1) WILD-TYPE  111   36
            clus
vv           DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  TUMOR FREE                           23                            111
  WITH TUMOR                            5                             36
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 25(16Q23.1) MUTATED       11      1       0      1       1
  DEL PEAK 25(16Q23.1) WILD-TYPE     42      4       1     10       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 25(16Q23.1) MUTATED              39       2
  DEL PEAK 25(16Q23.1) WILD-TYPE           162      12
D53V14, multiclass
               clus
vv              DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  BRAZIL                                  11                             42
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   1                             10
  UKRAINE                                  1                              6
  UNITED STATES                           39                            162
  VIETNAM                                  2                             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 25(16Q23.1) MUTATED     4  22  26   0   1
  DEL PEAK 25(16Q23.1) WILD-TYPE  14 107  87   1  23
D53V15, multiclass
    clus
vv   DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  G1                            4                             14
  G2                           22                            107
  G3                           26                             87
  G4                            0                              1
  GX                            1                             23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V16, continuous
D53V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 25(16Q23.1) MUTATED                                             9
  DEL PEAK 25(16Q23.1) WILD-TYPE                                          28
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 25(16Q23.1) MUTATED                                        3
  DEL PEAK 25(16Q23.1) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 25(16Q23.1) MUTATED                                                 0
  DEL PEAK 25(16Q23.1) WILD-TYPE                                               3
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 25(16Q23.1) MUTATED               10                  24
  DEL PEAK 25(16Q23.1) WILD-TYPE             52                 118
D53V18, multiclass
                                                 clus
vv                                                DEL PEAK 25(16Q23.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            10
  LIFELONG NON-SMOKER                                                       24
                                                 clus
vv                                                DEL PEAK 25(16Q23.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              3
  CURRENT SMOKER                                                              52
  LIFELONG NON-SMOKER                                                        118
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V19, continuous
D53V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 25(16Q23.1) MUTATED             4       19             3        5
  DEL PEAK 25(16Q23.1) WILD-TYPE          15       83             9       20
D53V21, multiclass
               clus
vv              DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                19                             83
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V22, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED    7  0
  DEL PEAK 25(16Q23.1) WILD-TYPE 18  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      7    0
  DEL PEAK 25(16Q23.1) WILD-TYPE   18    3
                         clus
vv                        DEL PEAK 25(16Q23.1) MUTATED
  COMPLETED AS PLANNED                               7
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 25(16Q23.1) WILD-TYPE
  COMPLETED AS PLANNED                                18
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 25(16Q23.1) MUTATED                    0                0
  DEL PEAK 25(16Q23.1) WILD-TYPE                  2                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 25(16Q23.1) MUTATED                     6             6
  DEL PEAK 25(16Q23.1) WILD-TYPE                  30            27
D53V23, multiclass
                     clus
vv                    DEL PEAK 25(16Q23.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            6
  REGIONAL SITE                                  6
                     clus
vv                    DEL PEAK 25(16Q23.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             30
  REGIONAL SITE                                   27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V24, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED   10  1
  DEL PEAK 25(16Q23.1) WILD-TYPE 46  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     10    1
  DEL PEAK 25(16Q23.1) WILD-TYPE   46    4
     clus
vv    DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  CGY                           10                             46
  GY                             1                              4
[1] 2 2
[1] FALSE
D53V25, continuous
D53V26, continuous
D53V27, continuous
D53V28, continuous
D53V29, continuous
D53V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 25(16Q23.1) MUTATED                                     0
  DEL PEAK 25(16Q23.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 25(16Q23.1) MUTATED                                     1
  DEL PEAK 25(16Q23.1) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 25(16Q23.1) MUTATED                         9
  DEL PEAK 25(16Q23.1) WILD-TYPE                      26
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 25(16Q23.1) MUTATED                         0
  DEL PEAK 25(16Q23.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 25(16Q23.1) MUTATED                         2
  DEL PEAK 25(16Q23.1) WILD-TYPE                       6
D53V31, multiclass
                                     clus
vv                                    DEL PEAK 25(16Q23.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        9
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 25(16Q23.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         26
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 25(16Q23.1) MUTATED                                               0
  DEL PEAK 25(16Q23.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 25(16Q23.1) MUTATED                                                4
  DEL PEAK 25(16Q23.1) WILD-TYPE                                             21
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 25(16Q23.1) MUTATED                                                                                  17
  DEL PEAK 25(16Q23.1) WILD-TYPE                                                                                64
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 25(16Q23.1) MUTATED                                                                                             19
  DEL PEAK 25(16Q23.1) WILD-TYPE                                                                                          101
D53V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 25(16Q23.1) 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)                                      17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           19
                                                                                              clus
vv                                                                                             DEL PEAK 25(16Q23.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V33, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED   14 12
  DEL PEAK 25(16Q23.1) WILD-TYPE 56 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     14   12
  DEL PEAK 25(16Q23.1) WILD-TYPE   56   61
         clus
vv        DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  ABSENT                            14                             56
  PRESENT                           12                             61
[1] 2 2
[1] FALSE
D53V34, continuous
D53V35, continuous
D53V36, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED    10  13
  DEL PEAK 25(16Q23.1) WILD-TYPE  38 103
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     10   13
  DEL PEAK 25(16Q23.1) WILD-TYPE   38  103
                                          clus
vv                                         DEL PEAK 25(16Q23.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           13
                                          clus
vv                                         DEL PEAK 25(16Q23.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            103
[1] 2 2
[1] FALSE
D53V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 25(16Q23.1) MUTATED              3          12         16
  DEL PEAK 25(16Q23.1) WILD-TYPE           12          41         68
D53V38, multiclass
              clus
vv             DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                            12                             41
  NEVER USED                             16                             68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V39, continuous
D53V40, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED   20  2
  DEL PEAK 25(16Q23.1) WILD-TYPE 72 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     20    2
  DEL PEAK 25(16Q23.1) WILD-TYPE   72   15
         clus
vv        DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  ABSENT                            20                             72
  PRESENT                            2                             15
[1] 2 2
[1] FALSE
D53V41, continuous
[1] "Remove cluster labels:"       "DEL PEAK 25(16Q23.1) MUTATED"
clus
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                             1                             16 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-C5-A1MP 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-GH-A9DA 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MA-AA3W 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                    TCGA-MY-A913                     TCGA-ZX-AA5X 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 25(16Q23.1) MUTATED      0   6   12    8  2   1    2    2   6  0   1
  DEL PEAK 25(16Q23.1) WILD-TYPE    1  28   57   22  4   9    5    7  30  2   1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 25(16Q23.1) MUTATED     4  1   0  1
  DEL PEAK 25(16Q23.1) WILD-TYPE  13  7   1 15
D53V42, multiclass
      clus
vv     DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  T1A1                            0                              1
  T1B                             6                             28
  T1B1                           12                             57
  T1B2                            8                             22
  T2                              2                              4
  T2A                             1                              9
  T2A1                            2                              5
  T2A2                            2                              7
  T2B                             6                             30
  T3                              0                              2
  T3A                             1                              1
  T3B                             4                             13
  T4                              1                              7
  TIS                             0                              1
  TX                              1                             15
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 25(16Q23.1) MUTATED         0        0         0         0        6
  DEL PEAK 25(16Q23.1) WILD-TYPE       5        1         1         1       27
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 25(16Q23.1) MUTATED          15         9        1         2
  DEL PEAK 25(16Q23.1) WILD-TYPE        62        27        3         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 25(16Q23.1) MUTATED            0          1         7         0
  DEL PEAK 25(16Q23.1) WILD-TYPE          5          6        36         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 25(16Q23.1) MUTATED            1         10         1         1
  DEL PEAK 25(16Q23.1) WILD-TYPE          2         32         6        11
D53V44, multiclass
            clus
vv           DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              6                             27
  STAGE IB1                            15                             62
  STAGE IB2                             9                             27
  STAGE II                              1                              3
  STAGE IIA                             2                              6
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             7                             36
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                           10                             32
  STAGE IVA                             1                              6
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 26(17P12) MUTATION ANALYSIS
D54V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(17P12) MUTATED    79  26
  DEL PEAK 26(17P12) WILD-TYPE 134  39
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                         105                          173 
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                          26                           39 
$`DEL PEAK 26(17P12) MUTATED`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BL 
       12.39        23.67        68.84        18.74       144.16       173.29 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT 
        5.46        19.86        67.46        38.99        40.93        73.18 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC 
       83.05        38.43        52.01        15.48       147.35        17.19 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ 
        9.34        13.61         2.73        50.99        45.83       146.86 
TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VN 
       23.51        20.91        58.88        87.75         2.66       118.65 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A5ZF 
       22.98        12.36        14.50        12.66        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PM 
       13.58        13.48         0.36        45.96         1.51         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM 
        1.45         0.13        16.08         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         8.32         2.17 
TCGA-FU-A3NI TCGA-GH-A9DA TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI 
        1.45         9.01        66.81        78.71        29.85        24.56 
TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
       28.37        11.28         0.89        20.28        17.82        19.56 
TCGA-MA-AA43 TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73Q 
       11.38        34.62         2.96        16.41         9.04         9.34 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.36         3.88        12.16        66.05        10.03        40.50 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y 
       18.05        19.96        11.51        57.93        39.78         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       24.39        39.78        50.63        48.07        50.14        45.34 
TCGA-VS-A9U6 TCGA-VS-A9UI TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UV 
       43.40        40.96        41.42        43.27        20.09         3.42 
TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       18.25        18.84        14.04        14.89        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZX-AA5X 
        0.69         1.41         3.91 

$`DEL PEAK 26(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-A1ML TCGA-C5-A1MP TCGA-C5-A2LS 
       35.61         0.46         2.43        20.91         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF 
       73.45        78.35       100.14        33.24        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM 
       20.42       210.67       154.32       101.82       134.33        20.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR 
      155.77       131.11        94.95         8.35        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.81        11.87         1.12        50.76        44.94        40.04 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       58.88        36.76       117.99        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        39.55        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05        25.02        14.50        26.40        24.56        26.01 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         7.46        14.89        26.79        13.91        15.02 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 
       12.59        26.27         6.64        19.27         0.43         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK 
        0.07         4.04         0.36        47.77         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        0.03         7.92        14.70        19.79        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
       23.84         0.92        31.36        36.26         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        10.82        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL 
      147.39       137.16       117.40        96.95        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
       27.42         3.29        21.44        20.48        15.58         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX 
       18.15        21.11       195.85        30.31         7.99        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA41 TCGA-MA-AA42 
        0.30         0.82        13.35        22.52         9.17         8.52 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       13.87         5.42        54.81        35.05        20.84         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EG TCGA-VS-A8EH 
       15.39        19.59        11.67        93.99        37.78        26.43 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QM TCGA-VS-A94W 
       59.51        32.15        46.03        36.13        31.27        36.26 
TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UA 
       16.64        50.86        15.68        44.94        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL 
       21.30        22.72        19.69        46.92         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V4 
       27.25        35.97        14.53        67.20         5.16         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXU 
       16.24        15.42        26.01        29.26         0.16 

  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                        0.03                         0.03 
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                      173.29                       210.67 
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                       18.74                        20.81 
[1] "0.0 - 173.3 (18.7)" "0.0 - 210.7 (20.8)"
[1] "hr=" "1.2"
D54V2, continuous
                              vv
clus                           T1 T2 T3 T4
  DEL PEAK 26(17P12) MUTATED   44 23  9  3
  DEL PEAK 26(17P12) WILD-TYPE 90 45 12  5
D54V3, multiclass
    clus
vv   DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  T1                         44                           90
  T2                         23                           45
  T3                          9                           12
  T4                          3                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   40 14
  DEL PEAK 26(17P12) WILD-TYPE 87 41
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     40   14
  DEL PEAK 26(17P12) WILD-TYPE   87   41
   clus
vv  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  0                         40                           87
  1                         14                           41
[1] 2 2
[1] FALSE
D54V5, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   35  3
  DEL PEAK 26(17P12) WILD-TYPE 72  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     35    3
  DEL PEAK 26(17P12) WILD-TYPE   72    7
   clus
vv  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  0                         35                           72
  1                          3                            7
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(17P12) MUTATED               1                               94
  DEL PEAK 26(17P12) WILD-TYPE             4                              147
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 26(17P12) MUTATED                                               1
  DEL PEAK 26(17P12) WILD-TYPE                                             5
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 26(17P12) MUTATED                                     5
  DEL PEAK 26(17P12) WILD-TYPE                                  17
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 26(17P12) MUTATED                                           1
  DEL PEAK 26(17P12) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 26(17P12) MUTATED                                              6
  DEL PEAK 26(17P12) WILD-TYPE                                            9
D54V6, multiclass
                                               clus
vv                                              DEL PEAK 26(17P12) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      94
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           6
                                               clus
vv                                              DEL PEAK 26(17P12) WILD-TYPE
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       147
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                              cls
clus                             0   1
  DEL PEAK 26(17P12) MUTATED    14  94
  DEL PEAK 26(17P12) WILD-TYPE  16 168
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     14   94
  DEL PEAK 26(17P12) WILD-TYPE   16  168
     clus
vv    DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  NO                          14                           16
  YES                         94                          168
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(17P12) MUTATED                                  2     8
  DEL PEAK 26(17P12) WILD-TYPE                                6    10
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(17P12) MUTATED                           7
  DEL PEAK 26(17P12) WILD-TYPE                        21
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 26(17P12) MUTATED                                           2    79
  DEL PEAK 26(17P12) WILD-TYPE                                         0   122
D54V10, multiclass
                                           clus
vv                                          DEL PEAK 26(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              8
  BLACK OR AFRICAN AMERICAN                                          7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             79
                                           clus
vv                                          DEL PEAK 26(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                           21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  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"
D54V11, binary
                              cls
clus                             0   1
  DEL PEAK 26(17P12) MUTATED     7  60
  DEL PEAK 26(17P12) WILD-TYPE  16 101
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED      7   60
  DEL PEAK 26(17P12) WILD-TYPE   16  101
                        clus
vv                       DEL PEAK 26(17P12) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         60
                        clus
vv                       DEL PEAK 26(17P12) WILD-TYPE
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          101
[1] 2 2
[1] FALSE
D54V12, continuous
D54V13, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   44 19
  DEL PEAK 26(17P12) WILD-TYPE 90 22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     44   19
  DEL PEAK 26(17P12) WILD-TYPE   90   22
            clus
vv           DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  TUMOR FREE                         44                           90
  WITH TUMOR                         19                           22
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 26(17P12) MUTATED       24      1       1      2       2
  DEL PEAK 26(17P12) WILD-TYPE     29      4       0      9       5
                              vv
clus                           UNITED STATES VIETNAM
  DEL PEAK 26(17P12) MUTATED              71       7
  DEL PEAK 26(17P12) WILD-TYPE           130       7
D54V14, multiclass
               clus
vv              DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  BRAZIL                                24                           29
  CANADA                                 1                            4
  NIGERIA                                1                            0
  RUSSIA                                 2                            9
  UKRAINE                                2                            5
  UNITED STATES                         71                          130
  VIETNAM                                7                            7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           G1 G2 G3 G4 GX
  DEL PEAK 26(17P12) MUTATED    4 43 44  1 14
  DEL PEAK 26(17P12) WILD-TYPE 14 86 69  0 10
D54V15, multiclass
    clus
vv   DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  G1                          4                           14
  G2                         43                           86
  G3                         44                           69
  G4                          1                            0
  GX                         14                           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"
D54V16, continuous
D54V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 26(17P12) MUTATED                                            15
  DEL PEAK 26(17P12) WILD-TYPE                                          22
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 26(17P12) MUTATED                                        7
  DEL PEAK 26(17P12) WILD-TYPE                                      2
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 26(17P12) MUTATED                                                 0
  DEL PEAK 26(17P12) WILD-TYPE                                               3
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 26(17P12) MUTATED               24                  45
  DEL PEAK 26(17P12) WILD-TYPE             38                  97
D54V18, multiclass
                                                 clus
vv                                                DEL PEAK 26(17P12) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          0
  CURRENT SMOKER                                                          24
  LIFELONG NON-SMOKER                                                     45
                                                 clus
vv                                                DEL PEAK 26(17P12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            3
  CURRENT SMOKER                                                            38
  LIFELONG NON-SMOKER                                                       97
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V19, continuous
D54V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 26(17P12) MUTATED            10       42             4        9
  DEL PEAK 26(17P12) WILD-TYPE           9       60             8       16
D54V21, multiclass
               clus
vv              DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  COMBINATION                           10                            9
  EXTERNAL                              42                           60
  EXTERNAL BEAM                          4                            8
  INTERNAL                               9                           16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V22, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   12  1
  DEL PEAK 26(17P12) WILD-TYPE 13  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     12    1
  DEL PEAK 26(17P12) WILD-TYPE   13    2
                         clus
vv                        DEL PEAK 26(17P12) MUTATED
  COMPLETED AS PLANNED                            12
  TREATMENT NOT COMPLETED                          1
                         clus
vv                        DEL PEAK 26(17P12) WILD-TYPE
  COMPLETED AS PLANNED                              13
  TREATMENT NOT COMPLETED                            2
[1] 2 2
[1] FALSE
                              vv
clus                           DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 26(17P12) MUTATED                    1                0
  DEL PEAK 26(17P12) WILD-TYPE                  1                2
                              vv
clus                           PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 26(17P12) MUTATED                    13            17
  DEL PEAK 26(17P12) WILD-TYPE                  23            16
D54V23, multiclass
                     clus
vv                    DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  DISTANT RECURRENCE                           1                            1
  LOCAL RECURRENCE                             0                            2
  PRIMARY TUMOR FIELD                         13                           23
  REGIONAL SITE                               17                           16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V24, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   24  1
  DEL PEAK 26(17P12) WILD-TYPE 32  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     24    1
  DEL PEAK 26(17P12) WILD-TYPE   32    4
     clus
vv    DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  CGY                         24                           32
  GY                           1                            4
[1] 2 2
[1] FALSE
D54V25, continuous
D54V26, continuous
D54V27, continuous
D54V28, continuous
D54V29, continuous
D54V30, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 26(17P12) MUTATED                                     0
  DEL PEAK 26(17P12) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 26(17P12) MUTATED                                     3
  DEL PEAK 26(17P12) WILD-TYPE                                   4
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 26(17P12) MUTATED                        13                       0
  DEL PEAK 26(17P12) WILD-TYPE                      22                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  DEL PEAK 26(17P12) MUTATED                         4
  DEL PEAK 26(17P12) WILD-TYPE                       4
D54V31, multiclass
                                     clus
vv                                    DEL PEAK 26(17P12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          3
  OTHER LOCATION, SPECIFY                                     13
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      4
                                     clus
vv                                    DEL PEAK 26(17P12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                       22
  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(17P12) MUTATED                                               1
  DEL PEAK 26(17P12) WILD-TYPE                                             1
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 26(17P12) MUTATED                                               11
  DEL PEAK 26(17P12) WILD-TYPE                                             14
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 26(17P12) MUTATED                                                                                  32
  DEL PEAK 26(17P12) WILD-TYPE                                                                                49
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 26(17P12) MUTATED                                                                                             40
  DEL PEAK 26(17P12) WILD-TYPE                                                                                           80
D54V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 26(17P12) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    32
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         40
                                                                                              clus
vv                                                                                             DEL PEAK 26(17P12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V33, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   22 24
  DEL PEAK 26(17P12) WILD-TYPE 48 49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     22   24
  DEL PEAK 26(17P12) WILD-TYPE   48   49
         clus
vv        DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  ABSENT                          22                           48
  PRESENT                         24                           49
[1] 2 2
[1] FALSE
D54V34, continuous
D54V35, continuous
D54V36, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   21 44
  DEL PEAK 26(17P12) WILD-TYPE 27 72
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     21   44
  DEL PEAK 26(17P12) WILD-TYPE   27   72
                                          clus
vv                                         DEL PEAK 26(17P12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         44
                                          clus
vv                                         DEL PEAK 26(17P12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           72
[1] 2 2
[1] FALSE
D54V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  DEL PEAK 26(17P12) MUTATED              3          18         34
  DEL PEAK 26(17P12) WILD-TYPE           12          35         50
D54V38, multiclass
              clus
vv             DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  CURRENT USER                          3                           12
  FORMER USER                          18                           35
  NEVER USED                           34                           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"
D54V39, continuous
D54V40, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   30  5
  DEL PEAK 26(17P12) WILD-TYPE 62 12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     30    5
  DEL PEAK 26(17P12) WILD-TYPE   62   12
         clus
vv        DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  ABSENT                          30                           62
  PRESENT                          5                           12
[1] 2 2
[1] FALSE
D54V41, continuous
                              vv
clus                           T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 26(17P12) MUTATED      1  12   19   12  3   3    3    2  12  0   1
  DEL PEAK 26(17P12) WILD-TYPE    0  22   50   18  3   7    4    7  24  2   1
                              vv
clus                           T3B T4 TIS TX
  DEL PEAK 26(17P12) MUTATED     8  3   0  9
  DEL PEAK 26(17P12) WILD-TYPE   9  5   1  7
D54V42, multiclass
      clus
vv     DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  T1A1                          1                            0
  T1B                          12                           22
  T1B1                         19                           50
  T1B2                         12                           18
  T2                            3                            3
  T2A                           3                            7
  T2A1                          3                            4
  T2A2                          2                            7
  T2B                          12                           24
  T3                            0                            2
  T3A                           1                            1
  T3B                           8                            9
  T4                            3                            5
  TIS                           0                            1
  TX                            9                            7
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 26(17P12) MUTATED         3        1         1         1       12
  DEL PEAK 26(17P12) WILD-TYPE       2        0         0         0       21
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 26(17P12) MUTATED          24        12        1         3
  DEL PEAK 26(17P12) WILD-TYPE        53        24        3         5
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 26(17P12) MUTATED            3          1        20         0
  DEL PEAK 26(17P12) WILD-TYPE          2          6        23         1
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 26(17P12) MUTATED            1         17         2         4
  DEL PEAK 26(17P12) WILD-TYPE          2         25         5         8
D54V44, multiclass
            clus
vv           DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                            1                            0
  STAGE IA1                           1                            0
  STAGE IA2                           1                            0
  STAGE IB                           12                           21
  STAGE IB1                          24                           53
  STAGE IB2                          12                           24
  STAGE II                            1                            3
  STAGE IIA                           3                            5
  STAGE IIA1                          3                            2
  STAGE IIA2                          1                            6
  STAGE IIB                          20                           23
  STAGE III                           0                            1
  STAGE IIIA                          1                            2
  STAGE IIIB                         17                           25
  STAGE IVA                           2                            5
  STAGE IVB                           4                            8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK 27(17Q25.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(17Q25.3) MUTATED    39   9
  DEL PEAK 27(17Q25.3) WILD-TYPE 174  56
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                            48                            230 
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                             9                             56 
$`DEL PEAK 27(17Q25.3) MUTATED`
TCGA-4J-AA1J TCGA-C5-A1BN TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A7UC 
       12.39         5.46        38.99        40.93        73.18        17.19 
TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-DS-A0VK TCGA-DS-A0VN 
      131.11        13.61         2.73       146.86        36.76       118.65 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       12.36        30.90         0.36         6.64         1.51         0.59 
TCGA-EK-A2R8 TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-FU-A3HY 
        1.45         0.03         1.18         0.10         0.10        31.36 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-GH-A9DA TCGA-HM-A4S6 TCGA-IR-A3LK TCGA-JW-A5VI 
        1.45         1.58         9.01        14.93        29.85        24.56 
TCGA-JW-A5VL TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MU-A51Y 
       15.58        12.49         0.82        20.28         9.17        13.87 
TCGA-Q1-A73O TCGA-VS-A8EB TCGA-VS-A8QC TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A9UI 
       14.07        10.03        11.51        39.78        50.63        40.96 
TCGA-VS-A9UP TCGA-VS-A9V3 TCGA-WL-A834 TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       43.27        14.89        26.01         0.69         1.41         0.16 

$`DEL PEAK 27(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-A1ML TCGA-C5-A1MP 
       53.16        35.61         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
      155.77        94.95         9.34        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52        20.81        20.91        11.87 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88         2.66       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       17.52         8.28        39.55        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM 
       12.59        45.96        26.27        19.27         0.43         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL 
        0.13        16.08         0.07         4.04         0.36        47.77 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        2.24         0.07         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB 
       23.84         0.92         2.17        36.26         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       10.82        21.67        20.78         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL 
       66.81       117.40        96.95        78.71        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 
       27.42         3.29        21.44        20.48        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       195.85        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.89         0.30        13.35        22.52        17.82        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.52        11.38        34.62         5.42        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       20.84         5.49         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
        9.04        16.14        17.56        15.88         9.34        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       19.36        19.59         3.88        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       66.05        40.50        37.78        26.43        18.05        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       59.51        32.15        46.03        36.13        57.93        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       31.27        36.26        16.64         4.73        24.39        50.86 
TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       15.68        48.07        50.14        45.34        44.94        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       42.41        25.74        21.30        22.72        19.69        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
        1.71        14.53        27.25        41.42        35.97        20.09 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       14.04         4.34        16.24        15.42        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       19.13         3.91 

  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                        146.86                         210.67 
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                         13.05                          20.63 
[1] "0.0 - 146.9 (13.1)" "0.0 - 210.7 (20.6)"
[1] "hr=" "1.1"
D55V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(17Q25.3) MUTATED    25  12   4   1
  DEL PEAK 27(17Q25.3) WILD-TYPE 109  56  17   7
D55V3, multiclass
    clus
vv   DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  T1                           25                            109
  T2                           12                             56
  T3                            4                             17
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(17Q25.3) MUTATED    21  12
  DEL PEAK 27(17Q25.3) WILD-TYPE 106  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     21   12
  DEL PEAK 27(17Q25.3) WILD-TYPE  106   43
   clus
vv  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  0                           21                            106
  1                           12                             43
[1] 2 2
[1] FALSE
D55V5, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED   16  2
  DEL PEAK 27(17Q25.3) WILD-TYPE 91  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     16    2
  DEL PEAK 27(17Q25.3) WILD-TYPE   91    8
   clus
vv  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  0                           16                             91
  1                            2                              8
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(17Q25.3) MUTATED               0                               49
  DEL PEAK 27(17Q25.3) WILD-TYPE             5                              192
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 27(17Q25.3) MUTATED                                               0
  DEL PEAK 27(17Q25.3) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 27(17Q25.3) MUTATED                                     0
  DEL PEAK 27(17Q25.3) WILD-TYPE                                  22
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 27(17Q25.3) MUTATED                                           0
  DEL PEAK 27(17Q25.3) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 27(17Q25.3) MUTATED                                              2
  DEL PEAK 27(17Q25.3) WILD-TYPE                                           13
D55V6, multiclass
                                               clus
vv                                              DEL PEAK 27(17Q25.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              DEL PEAK 27(17Q25.3) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(17Q25.3) MUTATED     5  46
  DEL PEAK 27(17Q25.3) WILD-TYPE  25 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED      5   46
  DEL PEAK 27(17Q25.3) WILD-TYPE   25  216
     clus
vv    DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  NO                             5                             25
  YES                           46                            216
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(17Q25.3) MUTATED                                  3     3
  DEL PEAK 27(17Q25.3) WILD-TYPE                                5    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(17Q25.3) MUTATED                           3
  DEL PEAK 27(17Q25.3) WILD-TYPE                        25
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(17Q25.3) MUTATED                                           1
  DEL PEAK 27(17Q25.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 27(17Q25.3) MUTATED      37
  DEL PEAK 27(17Q25.3) WILD-TYPE   164
D55V10, multiclass
                                           clus
vv                                          DEL PEAK 27(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               37
                                           clus
vv                                          DEL PEAK 27(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                164
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, binary
                                cls
clus                               0   1
  DEL PEAK 27(17Q25.3) MUTATED     4  33
  DEL PEAK 27(17Q25.3) WILD-TYPE  19 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED      4   33
  DEL PEAK 27(17Q25.3) WILD-TYPE   19  128
                        clus
vv                       DEL PEAK 27(17Q25.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           33
                        clus
vv                       DEL PEAK 27(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE
D55V12, continuous
D55V13, binary
                                cls
clus                               0   1
  DEL PEAK 27(17Q25.3) MUTATED    17   8
  DEL PEAK 27(17Q25.3) WILD-TYPE 117  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     17    8
  DEL PEAK 27(17Q25.3) WILD-TYPE  117   33
            clus
vv           DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  TUMOR FREE                           17                            117
  WITH TUMOR                            8                             33
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 27(17Q25.3) MUTATED        7      0       0      3       1
  DEL PEAK 27(17Q25.3) WILD-TYPE     46      5       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 27(17Q25.3) MUTATED              37       3
  DEL PEAK 27(17Q25.3) WILD-TYPE           164      11
D55V14, multiclass
               clus
vv              DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  BRAZIL                                   7                             46
  CANADA                                   0                              5
  NIGERIA                                  0                              1
  RUSSIA                                   3                              8
  UKRAINE                                  1                              6
  UNITED STATES                           37                            164
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 27(17Q25.3) MUTATED     1  19  26   0   3
  DEL PEAK 27(17Q25.3) WILD-TYPE  17 110  87   1  21
D55V15, multiclass
    clus
vv   DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  G1                            1                             17
  G2                           19                            110
  G3                           26                             87
  G4                            0                              1
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V16, continuous
D55V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 27(17Q25.3) MUTATED                                             4
  DEL PEAK 27(17Q25.3) WILD-TYPE                                          33
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 27(17Q25.3) MUTATED                                        3
  DEL PEAK 27(17Q25.3) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 27(17Q25.3) MUTATED                                                 0
  DEL PEAK 27(17Q25.3) WILD-TYPE                                               3
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 27(17Q25.3) MUTATED               15                  18
  DEL PEAK 27(17Q25.3) WILD-TYPE             47                 124
D55V18, multiclass
                                                 clus
vv                                                DEL PEAK 27(17Q25.3) 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                                                            15
  LIFELONG NON-SMOKER                                                       18
                                                 clus
vv                                                DEL PEAK 27(17Q25.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              3
  CURRENT SMOKER                                                              47
  LIFELONG NON-SMOKER                                                        124
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V19, continuous
D55V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 27(17Q25.3) MUTATED             3       16             3        4
  DEL PEAK 27(17Q25.3) WILD-TYPE          16       86             9       21
D55V21, multiclass
               clus
vv              DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  COMBINATION                              3                             16
  EXTERNAL                                16                             86
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 4                             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"
D55V22, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED    4  0
  DEL PEAK 27(17Q25.3) WILD-TYPE 21  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED      4    0
  DEL PEAK 27(17Q25.3) WILD-TYPE   21    3
                         clus
vv                        DEL PEAK 27(17Q25.3) MUTATED
  COMPLETED AS PLANNED                               4
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 27(17Q25.3) WILD-TYPE
  COMPLETED AS PLANNED                                21
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 27(17Q25.3) MUTATED                    0                0
  DEL PEAK 27(17Q25.3) WILD-TYPE                  2                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 27(17Q25.3) MUTATED                     6             6
  DEL PEAK 27(17Q25.3) WILD-TYPE                  30            27
D55V23, multiclass
                     clus
vv                    DEL PEAK 27(17Q25.3) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            6
  REGIONAL SITE                                  6
                     clus
vv                    DEL PEAK 27(17Q25.3) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             30
  REGIONAL SITE                                   27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V24, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED    8  0
  DEL PEAK 27(17Q25.3) WILD-TYPE 48  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED      8    0
  DEL PEAK 27(17Q25.3) WILD-TYPE   48    5
     clus
vv    DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  CGY                            8                             48
  GY                             0                              5
[1] 2 2
[1] FALSE
D55V25, continuous
D55V26, continuous
D55V27, continuous
D55V28, continuous
D55V29, continuous
D55V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 27(17Q25.3) MUTATED                                     0
  DEL PEAK 27(17Q25.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 27(17Q25.3) MUTATED                                     2
  DEL PEAK 27(17Q25.3) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 27(17Q25.3) MUTATED                         6
  DEL PEAK 27(17Q25.3) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 27(17Q25.3) MUTATED                         0
  DEL PEAK 27(17Q25.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 27(17Q25.3) MUTATED                         2
  DEL PEAK 27(17Q25.3) WILD-TYPE                       6
D55V31, multiclass
                                     clus
vv                                    DEL PEAK 27(17Q25.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        6
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 27(17Q25.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 27(17Q25.3) MUTATED                                               0
  DEL PEAK 27(17Q25.3) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 27(17Q25.3) MUTATED                                                3
  DEL PEAK 27(17Q25.3) WILD-TYPE                                             22
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 27(17Q25.3) MUTATED                                                                                  12
  DEL PEAK 27(17Q25.3) WILD-TYPE                                                                                69
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 27(17Q25.3) MUTATED                                                                                             21
  DEL PEAK 27(17Q25.3) WILD-TYPE                                                                                           99
D55V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 27(17Q25.3) 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)                           21
                                                                                              clus
vv                                                                                             DEL PEAK 27(17Q25.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        69
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V33, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED   12 13
  DEL PEAK 27(17Q25.3) WILD-TYPE 58 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     12   13
  DEL PEAK 27(17Q25.3) WILD-TYPE   58   60
         clus
vv        DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  ABSENT                            12                             58
  PRESENT                           13                             60
[1] 2 2
[1] FALSE
D55V34, continuous
D55V35, continuous
D55V36, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED   11 23
  DEL PEAK 27(17Q25.3) WILD-TYPE 37 93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     11   23
  DEL PEAK 27(17Q25.3) WILD-TYPE   37   93
                                          clus
vv                                         DEL PEAK 27(17Q25.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           23
                                          clus
vv                                         DEL PEAK 27(17Q25.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             93
[1] 2 2
[1] FALSE
D55V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 27(17Q25.3) MUTATED              2           9         15
  DEL PEAK 27(17Q25.3) WILD-TYPE           13          44         69
D55V38, multiclass
              clus
vv             DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                             9                             44
  NEVER USED                             15                             69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V39, continuous
D55V40, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED   14  1
  DEL PEAK 27(17Q25.3) WILD-TYPE 78 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     14    1
  DEL PEAK 27(17Q25.3) WILD-TYPE   78   16
         clus
vv        DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  ABSENT                            14                             78
  PRESENT                            1                             16
[1] 2 2
[1] FALSE
D55V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 27(17Q25.3) MUTATED      0   6   10    9  2   3    1    0   6  0   1
  DEL PEAK 27(17Q25.3) WILD-TYPE    1  28   59   21  4   7    6    9  30  2   1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 27(17Q25.3) MUTATED     3  1   0  2
  DEL PEAK 27(17Q25.3) WILD-TYPE  14  7   1 14
D55V42, multiclass
      clus
vv     DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  T1A1                            0                              1
  T1B                             6                             28
  T1B1                           10                             59
  T1B2                            9                             21
  T2                              2                              4
  T2A                             3                              7
  T2A1                            1                              6
  T2A2                            0                              9
  T2B                             6                             30
  T3                              0                              2
  T3A                             1                              1
  T3B                             3                             14
  T4                              1                              7
  TIS                             0                              1
  TX                              2                             14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 27(17Q25.3) MUTATED         0        0         0         1        8
  DEL PEAK 27(17Q25.3) WILD-TYPE       5        1         1         0       25
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 27(17Q25.3) MUTATED          10         9        2         1
  DEL PEAK 27(17Q25.3) WILD-TYPE        67        27        2         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 27(17Q25.3) MUTATED            1          0         5         0
  DEL PEAK 27(17Q25.3) WILD-TYPE          4          7        38         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 27(17Q25.3) MUTATED            1          8         1         2
  DEL PEAK 27(17Q25.3) WILD-TYPE          2         34         6        10
D55V44, multiclass
            clus
vv           DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              8                             25
  STAGE IB1                            10                             67
  STAGE IB2                             9                             27
  STAGE II                              2                              2
  STAGE IIA                             1                              7
  STAGE IIA1                            1                              4
  STAGE IIA2                            0                              7
  STAGE IIB                             5                             38
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                            8                             34
  STAGE IVA                             1                              6
  STAGE IVB                             2                             10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 28(18Q21.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(18Q21.2) MUTATED    57  21
  DEL PEAK 28(18Q21.2) WILD-TYPE 156  44
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            78                            200 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            21                             44 
$`DEL PEAK 28(18Q21.2) MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML 
       31.40        35.01        57.73        35.61         0.46        20.91 
TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 
       40.93        73.18        73.45        78.35        38.43        33.24 
TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH 
      154.32        17.19       131.11        13.61         2.73        45.83 
TCGA-C5-A8XK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A1QS TCGA-EA-A1QT 
       99.91        40.04        87.75       118.65        39.55        12.36 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       26.01        14.89        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EX-A1H6 TCGA-EX-A3L1 
        1.51         0.59        47.77         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-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX 
       81.96        24.56        28.37        21.11         0.89        12.49 
TCGA-LP-A7HU TCGA-MA-AA41 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73P 
       13.35         9.17        15.58        16.41         9.04        15.88 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
        3.88        11.67        10.03        18.05        19.96        59.51 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A959 
       46.03        36.13        39.78        39.78        50.86        45.34 
TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
       43.40        19.69        40.96        41.42        35.97        20.09 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 
       67.20         5.16        14.89         4.34        67.59         0.69 

$`DEL PEAK 28(18Q21.2) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF 
        5.46        19.86        67.46        46.32        30.21        53.16 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ 
       38.99         2.43         3.58        44.22        83.05       100.14 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       210.67       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI 
      134.33        15.48        20.35       147.35       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR 
        9.34        50.99         8.35       146.86        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.81        20.91        11.87         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       44.94        58.88        36.76         2.66       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.83        16.18        17.52         8.28        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       24.56        14.50        12.66        12.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.36        19.27         0.43         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-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-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92        31.36        36.26         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA 
        0.82         3.52         1.35         1.32         1.97         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        10.82        20.78        14.93         9.44       147.39 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        96.95        29.85        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       21.44        20.48        15.58         8.28        18.15       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W 
       30.31         7.99        11.28         0.30         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       20.28        17.82        19.56         8.52        11.38        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       34.62         5.42        54.81        35.05        20.84         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q 
        2.96        15.95        16.14        17.56        14.07         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       15.39        19.36        19.59        93.99        12.16        66.05 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF 
       40.50        37.78        26.43        32.15        11.51        57.93 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A953 
       31.27        36.26        16.64         4.73        24.39        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.63        48.07        50.14        44.94        42.41        25.74 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       21.30        22.72        46.92         1.71        14.53        27.25 
TCGA-VS-A9UP TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V2 
       43.27        14.53         3.42        18.25        18.84        14.04 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       16.24        15.42        26.01        29.26        19.13         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                          0.46                           0.03 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                        154.32                         210.67 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                         26.14                          18.79 
[1] "0.5 - 154.3 (26.1)" "0.0 - 210.7 (18.8)"
[1] "hr=" "1"  
D56V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 28(18Q21.2) MUTATED   35 16  7  3
  DEL PEAK 28(18Q21.2) WILD-TYPE 99 52 14  5
D56V3, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  T1                           35                             99
  T2                           16                             52
  T3                            7                             14
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   35 11
  DEL PEAK 28(18Q21.2) WILD-TYPE 92 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     35   11
  DEL PEAK 28(18Q21.2) WILD-TYPE   92   44
   clus
vv  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  0                           35                             92
  1                           11                             44
[1] 2 2
[1] FALSE
D56V5, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   29  5
  DEL PEAK 28(18Q21.2) WILD-TYPE 78  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     29    5
  DEL PEAK 28(18Q21.2) WILD-TYPE   78    5
   clus
vv  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  0                           29                             78
  1                            5                              5
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(18Q21.2) MUTATED               0                               55
  DEL PEAK 28(18Q21.2) WILD-TYPE             5                              186
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 28(18Q21.2) MUTATED                                               1
  DEL PEAK 28(18Q21.2) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 28(18Q21.2) MUTATED                                    14
  DEL PEAK 28(18Q21.2) WILD-TYPE                                   8
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 28(18Q21.2) MUTATED                                           2
  DEL PEAK 28(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 28(18Q21.2) MUTATED                                             10
  DEL PEAK 28(18Q21.2) WILD-TYPE                                            5
D56V6, multiclass
                                               clus
vv                                              DEL PEAK 28(18Q21.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        55
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            10
                                               clus
vv                                              DEL PEAK 28(18Q21.2) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         186
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    10  72
  DEL PEAK 28(18Q21.2) WILD-TYPE  20 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     10   72
  DEL PEAK 28(18Q21.2) WILD-TYPE   20  190
     clus
vv    DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  NO                            10                             20
  YES                           72                            190
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(18Q21.2) MUTATED                                  2     4
  DEL PEAK 28(18Q21.2) WILD-TYPE                                6    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(18Q21.2) MUTATED                           9
  DEL PEAK 28(18Q21.2) WILD-TYPE                        19
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 28(18Q21.2) MUTATED                                           0
  DEL PEAK 28(18Q21.2) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 28(18Q21.2) MUTATED      61
  DEL PEAK 28(18Q21.2) WILD-TYPE   140
D56V10, multiclass
                                           clus
vv                                          DEL PEAK 28(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               61
                                           clus
vv                                          DEL PEAK 28(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                140
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED     4  40
  DEL PEAK 28(18Q21.2) WILD-TYPE  19 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED      4   40
  DEL PEAK 28(18Q21.2) WILD-TYPE   19  121
                        clus
vv                       DEL PEAK 28(18Q21.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK 28(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            121
[1] 2 2
[1] FALSE
D56V12, continuous
D56V13, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   36 13
  DEL PEAK 28(18Q21.2) WILD-TYPE 98 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     36   13
  DEL PEAK 28(18Q21.2) WILD-TYPE   98   28
            clus
vv           DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  TUMOR FREE                           36                             98
  WITH TUMOR                           13                             28
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 28(18Q21.2) MUTATED       20      1       0      3       1
  DEL PEAK 28(18Q21.2) WILD-TYPE     33      4       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 28(18Q21.2) MUTATED              54       3
  DEL PEAK 28(18Q21.2) WILD-TYPE           147      11
D56V14, multiclass
               clus
vv              DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  BRAZIL                                  20                             33
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   3                              8
  UKRAINE                                  1                              6
  UNITED STATES                           54                            147
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 28(18Q21.2) MUTATED    4 33 32  1 10
  DEL PEAK 28(18Q21.2) WILD-TYPE 14 96 81  0 14
D56V15, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  G1                            4                             14
  G2                           33                             96
  G3                           32                             81
  G4                            1                              0
  GX                           10                             14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V16, continuous
D56V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 28(18Q21.2) MUTATED                                             7
  DEL PEAK 28(18Q21.2) WILD-TYPE                                          30
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 28(18Q21.2) MUTATED                                        1
  DEL PEAK 28(18Q21.2) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 28(18Q21.2) MUTATED                                                 0
  DEL PEAK 28(18Q21.2) WILD-TYPE                                               3
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 28(18Q21.2) MUTATED               16                  44
  DEL PEAK 28(18Q21.2) WILD-TYPE             46                  98
D56V18, multiclass
                                                 clus
vv                                                DEL PEAK 28(18Q21.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            16
  LIFELONG NON-SMOKER                                                       44
                                                 clus
vv                                                DEL PEAK 28(18Q21.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              3
  CURRENT SMOKER                                                              46
  LIFELONG NON-SMOKER                                                         98
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V19, continuous
D56V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 28(18Q21.2) MUTATED             5       30             5        7
  DEL PEAK 28(18Q21.2) WILD-TYPE          14       72             7       18
D56V21, multiclass
               clus
vv              DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  COMBINATION                              5                             14
  EXTERNAL                                30                             72
  EXTERNAL BEAM                            5                              7
  INTERNAL                                 7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V22, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED    8  1
  DEL PEAK 28(18Q21.2) WILD-TYPE 17  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED      8    1
  DEL PEAK 28(18Q21.2) WILD-TYPE   17    2
                         clus
vv                        DEL PEAK 28(18Q21.2) MUTATED
  COMPLETED AS PLANNED                               8
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 28(18Q21.2) WILD-TYPE
  COMPLETED AS PLANNED                                17
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 28(18Q21.2) MUTATED                    0                1
  DEL PEAK 28(18Q21.2) WILD-TYPE                  2                1
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 28(18Q21.2) MUTATED                    10             9
  DEL PEAK 28(18Q21.2) WILD-TYPE                  26            24
D56V23, multiclass
                     clus
vv                    DEL PEAK 28(18Q21.2) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                           10
  REGIONAL SITE                                  9
                     clus
vv                    DEL PEAK 28(18Q21.2) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             26
  REGIONAL SITE                                   24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V24, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   16  1
  DEL PEAK 28(18Q21.2) WILD-TYPE 40  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     16    1
  DEL PEAK 28(18Q21.2) WILD-TYPE   40    4
     clus
vv    DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  CGY                           16                             40
  GY                             1                              4
[1] 2 2
[1] FALSE
D56V25, continuous
D56V26, continuous
D56V27, continuous
D56V28, continuous
D56V29, continuous
D56V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 28(18Q21.2) MUTATED                                     0
  DEL PEAK 28(18Q21.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 28(18Q21.2) MUTATED                                     1
  DEL PEAK 28(18Q21.2) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 28(18Q21.2) MUTATED                        12
  DEL PEAK 28(18Q21.2) WILD-TYPE                      23
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 28(18Q21.2) MUTATED                         0
  DEL PEAK 28(18Q21.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 28(18Q21.2) MUTATED                         4
  DEL PEAK 28(18Q21.2) WILD-TYPE                       4
D56V31, multiclass
                                     clus
vv                                    DEL PEAK 28(18Q21.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                       12
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        4
                                     clus
vv                                    DEL PEAK 28(18Q21.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         23
  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 28(18Q21.2) MUTATED                                               0
  DEL PEAK 28(18Q21.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 28(18Q21.2) MUTATED                                                8
  DEL PEAK 28(18Q21.2) WILD-TYPE                                             17
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 28(18Q21.2) MUTATED                                                                                  26
  DEL PEAK 28(18Q21.2) WILD-TYPE                                                                                55
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 28(18Q21.2) MUTATED                                                                                             31
  DEL PEAK 28(18Q21.2) WILD-TYPE                                                                                           89
D56V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 28(18Q21.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           31
                                                                                              clus
vv                                                                                             DEL PEAK 28(18Q21.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V33, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   22 12
  DEL PEAK 28(18Q21.2) WILD-TYPE 48 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     22   12
  DEL PEAK 28(18Q21.2) WILD-TYPE   48   61
         clus
vv        DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  ABSENT                            22                             48
  PRESENT                           12                             61
[1] 2 2
[1] FALSE
D56V34, continuous
D56V35, continuous
D56V36, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   12 24
  DEL PEAK 28(18Q21.2) WILD-TYPE 36 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     12   24
  DEL PEAK 28(18Q21.2) WILD-TYPE   36   92
                                          clus
vv                                         DEL PEAK 28(18Q21.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           24
                                          clus
vv                                         DEL PEAK 28(18Q21.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             92
[1] 2 2
[1] FALSE
D56V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 28(18Q21.2) MUTATED              5          21         26
  DEL PEAK 28(18Q21.2) WILD-TYPE           10          32         58
D56V38, multiclass
              clus
vv             DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  CURRENT USER                            5                             10
  FORMER USER                            21                             32
  NEVER USED                             26                             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"
D56V39, continuous
D56V40, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   27  1
  DEL PEAK 28(18Q21.2) WILD-TYPE 65 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     27    1
  DEL PEAK 28(18Q21.2) WILD-TYPE   65   16
         clus
vv        DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  ABSENT                            27                             65
  PRESENT                            1                             16
[1] 2 2
[1] FALSE
D56V41, continuous
[1] "Remove cluster labels:"       "DEL PEAK 28(18Q21.2) MUTATED"
clus
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 28(18Q21.2) WILD-TYPE" "DEL PEAK 28(18Q21.2) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK 28(18Q21.2) WILD-TYPE" "DEL PEAK 28(18Q21.2) WILD-TYPE" 
                    TCGA-GH-A9DA                     TCGA-HM-A3JK 
"DEL PEAK 28(18Q21.2) WILD-TYPE" "DEL PEAK 28(18Q21.2) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-JX-A3Q8 
"DEL PEAK 28(18Q21.2) WILD-TYPE" "DEL PEAK 28(18Q21.2) WILD-TYPE" 
                    TCGA-MA-AA3W                     TCGA-MA-AA3Z 
"DEL PEAK 28(18Q21.2) WILD-TYPE" "DEL PEAK 28(18Q21.2) WILD-TYPE" 
                    TCGA-MA-AA42                     TCGA-MU-A51Y 
"DEL PEAK 28(18Q21.2) WILD-TYPE" "DEL PEAK 28(18Q21.2) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-MY-A913 
"DEL PEAK 28(18Q21.2) WILD-TYPE" "DEL PEAK 28(18Q21.2) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"DEL PEAK 28(18Q21.2) WILD-TYPE" 
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 28(18Q21.2) MUTATED      0  11   20    4  3   2    2    1   8  0   2
  DEL PEAK 28(18Q21.2) WILD-TYPE    1  23   49   26  3   8    5    8  28  2   0
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 28(18Q21.2) MUTATED     5  3   0  4
  DEL PEAK 28(18Q21.2) WILD-TYPE  12  5   1 12
D56V42, multiclass
      clus
vv     DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  T1A1                            0                              1
  T1B                            11                             23
  T1B1                           20                             49
  T1B2                            4                             26
  T2                              3                              3
  T2A                             2                              8
  T2A1                            2                              5
  T2A2                            1                              8
  T2B                             8                             28
  T3                              0                              2
  T3A                             2                              0
  T3B                             5                             12
  T4                              3                              5
  TIS                             0                              1
  TX                              4                             12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 28(18Q21.2) MUTATED         1        1         0         0       11
  DEL PEAK 28(18Q21.2) WILD-TYPE       4        0         1         1       22
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 28(18Q21.2) MUTATED          26         5        2         2
  DEL PEAK 28(18Q21.2) WILD-TYPE        51        31        2         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 28(18Q21.2) MUTATED            2          0        15         0
  DEL PEAK 28(18Q21.2) WILD-TYPE          3          7        28         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 28(18Q21.2) MUTATED            2          6         1         5
  DEL PEAK 28(18Q21.2) WILD-TYPE          1         36         6         7
D56V44, multiclass
            clus
vv           DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             11                             22
  STAGE IB1                            26                             51
  STAGE IB2                             5                             31
  STAGE II                              2                              2
  STAGE IIA                             2                              6
  STAGE IIA1                            2                              3
  STAGE IIA2                            0                              7
  STAGE IIB                            15                             28
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                            6                             36
  STAGE IVA                             1                              6
  STAGE IVB                             5                              7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 29(19P13.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(19P13.3) MUTATED    67  30
  DEL PEAK 29(19P13.3) WILD-TYPE 146  35
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            97                            181 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            30                             35 
$`DEL PEAK 29(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-A1ML 
       35.01        57.73        53.16        35.61         0.46        20.91 
TCGA-C5-A1MN TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7X3 
       40.93        52.01        18.02        15.48       147.35         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ 
       13.61         2.73        50.99        45.83        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A907 TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH 
       27.52        11.87       117.99       118.65        16.83        17.52 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        8.28        12.36        14.50        24.56        14.50        26.01 
TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2IP 
       13.91        14.99        14.96        13.58         0.36         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RJ 
       19.27         0.43         0.59         1.45        16.08         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        19.79        23.84 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-JW-A5VI 
        1.97         9.01        10.82        14.93       117.40        24.56 
TCGA-JW-A5VK TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX TCGA-MY-A913 TCGA-PN-A8MA 
       20.48        21.11         7.99        12.49         5.49         2.96 
TCGA-Q1-A5R3 TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EJ 
       15.95        19.36         3.88        12.16        10.03        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y 
       32.15        46.03        36.13        57.93        16.64         4.73 
TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UD 
       39.78        48.07        45.34        43.40        42.41        19.69 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9V0 TCGA-VS-A9V1 
       40.96        14.53        27.25        43.27        18.84         5.16 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       14.89         4.34        16.24        15.42        67.59        19.13 
TCGA-ZJ-AAX4 
        0.69 

$`DEL PEAK 29(19P13.3) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
       12.39        49.48        57.04        68.84        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-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       38.99         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        33.24        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM 
       20.42       210.67       154.32       101.82       134.33        20.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8XI TCGA-C5-A8XJ 
       17.19       155.77       131.11        94.95         8.35       146.86 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.81        20.91         1.12        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ 
       40.04        87.75        58.88        36.76         2.66        22.98 
TCGA-DS-A7WF TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       16.18        39.55        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       13.05        25.02        26.40        12.66        12.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.89        26.79        15.02        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC 
       26.27         1.51         0.59         0.13         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EX-A1H5 
        0.03         0.36        47.77         0.07         0.10        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        7.92         6.94        14.70         8.32        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
        1.48         0.82         3.52         1.35         1.32         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       25.41        21.67        20.78         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       27.42         3.29        21.44        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
       18.15       195.85        30.31        11.28         0.89         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        20.28        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        9.17         8.52        11.38        13.87        34.62         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       54.81        35.05        20.84        15.58        16.41         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        15.39 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
       19.59        11.67        93.99        66.05        40.50        37.78 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       26.43        18.05        59.51        11.51        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 
       36.26        24.39        50.86        15.68        50.63        50.14 
TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ 
       44.94        25.74        21.30        22.72        46.92         1.71 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       41.42        35.97        20.09        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V2 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       67.20        14.04        26.01        29.26         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                        147.35                         210.67 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                         16.83                          20.91 
[1] "0.0 - 147.3 (16.8)" "0.0 - 210.7 (20.9)"
[1] "hr=" "2.1"
D57V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 29(19P13.3) MUTATED   47 19  9  3
  DEL PEAK 29(19P13.3) WILD-TYPE 87 49 12  5
D57V3, multiclass
    clus
vv   DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  T1                           47                             87
  T2                           19                             49
  T3                            9                             12
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   40 18
  DEL PEAK 29(19P13.3) WILD-TYPE 87 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     40   18
  DEL PEAK 29(19P13.3) WILD-TYPE   87   37
   clus
vv  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  0                           40                             87
  1                           18                             37
[1] 2 2
[1] FALSE
D57V5, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   33  4
  DEL PEAK 29(19P13.3) WILD-TYPE 74  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     33    4
  DEL PEAK 29(19P13.3) WILD-TYPE   74    6
   clus
vv  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  0                           33                             74
  1                            4                              6
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(19P13.3) MUTATED               2                               89
  DEL PEAK 29(19P13.3) WILD-TYPE             3                              152
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 29(19P13.3) MUTATED                                               1
  DEL PEAK 29(19P13.3) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 29(19P13.3) MUTATED                                     5
  DEL PEAK 29(19P13.3) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 29(19P13.3) MUTATED                                           0
  DEL PEAK 29(19P13.3) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 29(19P13.3) MUTATED                                              6
  DEL PEAK 29(19P13.3) WILD-TYPE                                            9
D57V6, multiclass
                                               clus
vv                                              DEL PEAK 29(19P13.3) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        89
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             6
                                               clus
vv                                              DEL PEAK 29(19P13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         152
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    12  91
  DEL PEAK 29(19P13.3) WILD-TYPE  18 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     12   91
  DEL PEAK 29(19P13.3) WILD-TYPE   18  171
     clus
vv    DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  NO                            12                             18
  YES                           91                            171
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(19P13.3) MUTATED                                  1     6
  DEL PEAK 29(19P13.3) WILD-TYPE                                7    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(19P13.3) MUTATED                           8
  DEL PEAK 29(19P13.3) WILD-TYPE                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(19P13.3) MUTATED                                           2
  DEL PEAK 29(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 29(19P13.3) MUTATED      80
  DEL PEAK 29(19P13.3) WILD-TYPE   121
D57V10, multiclass
                                           clus
vv                                          DEL PEAK 29(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               80
                                           clus
vv                                          DEL PEAK 29(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D57V11, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED     4  60
  DEL PEAK 29(19P13.3) WILD-TYPE  19 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED      4   60
  DEL PEAK 29(19P13.3) WILD-TYPE   19  101
                        clus
vv                       DEL PEAK 29(19P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 29(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            101
[1] 2 2
[1] FALSE
D57V12, continuous
D57V13, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   37 17
  DEL PEAK 29(19P13.3) WILD-TYPE 97 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     37   17
  DEL PEAK 29(19P13.3) WILD-TYPE   97   24
            clus
vv           DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  TUMOR FREE                           37                             97
  WITH TUMOR                           17                             24
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 29(19P13.3) MUTATED       24      0       1      2       4
  DEL PEAK 29(19P13.3) WILD-TYPE     29      5       0      9       3
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 29(19P13.3) MUTATED              67       5
  DEL PEAK 29(19P13.3) WILD-TYPE           134       9
D57V14, multiclass
               clus
vv              DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  BRAZIL                                  24                             29
  CANADA                                   0                              5
  NIGERIA                                  1                              0
  RUSSIA                                   2                              9
  UKRAINE                                  4                              3
  UNITED STATES                           67                            134
  VIETNAM                                  5                              9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 29(19P13.3) MUTATED    3 40 48  0  8
  DEL PEAK 29(19P13.3) WILD-TYPE 15 89 65  1 16
D57V15, multiclass
    clus
vv   DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  G1                            3                             15
  G2                           40                             89
  G3                           48                             65
  G4                            0                              1
  GX                            8                             16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V16, continuous
D57V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 29(19P13.3) MUTATED                                            14
  DEL PEAK 29(19P13.3) WILD-TYPE                                          23
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 29(19P13.3) MUTATED                                        3
  DEL PEAK 29(19P13.3) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 29(19P13.3) MUTATED                                                 1
  DEL PEAK 29(19P13.3) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 29(19P13.3) MUTATED               21                  49
  DEL PEAK 29(19P13.3) WILD-TYPE             41                  93
D57V18, multiclass
                                                 clus
vv                                                DEL PEAK 29(19P13.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            21
  LIFELONG NON-SMOKER                                                       49
                                                 clus
vv                                                DEL PEAK 29(19P13.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              41
  LIFELONG NON-SMOKER                                                         93
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V19, continuous
D57V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 29(19P13.3) MUTATED             8       43             4        9
  DEL PEAK 29(19P13.3) WILD-TYPE          11       59             8       16
D57V21, multiclass
               clus
vv              DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  COMBINATION                              8                             11
  EXTERNAL                                43                             59
  EXTERNAL BEAM                            4                              8
  INTERNAL                                 9                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V22, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   10  1
  DEL PEAK 29(19P13.3) WILD-TYPE 15  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     10    1
  DEL PEAK 29(19P13.3) WILD-TYPE   15    2
                         clus
vv                        DEL PEAK 29(19P13.3) MUTATED
  COMPLETED AS PLANNED                              10
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 29(19P13.3) WILD-TYPE
  COMPLETED AS PLANNED                                15
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 29(19P13.3) MUTATED                    1                1
  DEL PEAK 29(19P13.3) WILD-TYPE                  1                1
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 29(19P13.3) MUTATED                    15            15
  DEL PEAK 29(19P13.3) WILD-TYPE                  21            18
D57V23, multiclass
                     clus
vv                    DEL PEAK 29(19P13.3) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                           15
  REGIONAL SITE                                 15
                     clus
vv                    DEL PEAK 29(19P13.3) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             21
  REGIONAL SITE                                   18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V24, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   25  3
  DEL PEAK 29(19P13.3) WILD-TYPE 31  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     25    3
  DEL PEAK 29(19P13.3) WILD-TYPE   31    2
     clus
vv    DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  CGY                           25                             31
  GY                             3                              2
[1] 2 2
[1] FALSE
D57V25, continuous
D57V26, continuous
D57V27, continuous
D57V28, continuous
D57V29, continuous
D57V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 29(19P13.3) MUTATED                                     0
  DEL PEAK 29(19P13.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 29(19P13.3) MUTATED                                     2
  DEL PEAK 29(19P13.3) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 29(19P13.3) MUTATED                        13
  DEL PEAK 29(19P13.3) WILD-TYPE                      22
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 29(19P13.3) MUTATED                         0
  DEL PEAK 29(19P13.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 29(19P13.3) MUTATED                         2
  DEL PEAK 29(19P13.3) WILD-TYPE                       6
D57V31, multiclass
                                     clus
vv                                    DEL PEAK 29(19P13.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       13
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 29(19P13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         22
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 29(19P13.3) MUTATED                                               1
  DEL PEAK 29(19P13.3) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 29(19P13.3) MUTATED                                                9
  DEL PEAK 29(19P13.3) WILD-TYPE                                             16
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 29(19P13.3) MUTATED                                                                                  22
  DEL PEAK 29(19P13.3) WILD-TYPE                                                                                59
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 29(19P13.3) MUTATED                                                                                             41
  DEL PEAK 29(19P13.3) WILD-TYPE                                                                                           79
D57V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 29(19P13.3) MUTATED
  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)                                      22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           41
                                                                                              clus
vv                                                                                             DEL PEAK 29(19P13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        59
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V33, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   19 25
  DEL PEAK 29(19P13.3) WILD-TYPE 51 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     19   25
  DEL PEAK 29(19P13.3) WILD-TYPE   51   48
         clus
vv        DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  ABSENT                            19                             51
  PRESENT                           25                             48
[1] 2 2
[1] FALSE
D57V34, continuous
D57V35, continuous
D57V36, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   18 36
  DEL PEAK 29(19P13.3) WILD-TYPE 30 80
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     18   36
  DEL PEAK 29(19P13.3) WILD-TYPE   30   80
                                          clus
vv                                         DEL PEAK 29(19P13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           36
                                          clus
vv                                         DEL PEAK 29(19P13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             80
[1] 2 2
[1] FALSE
D57V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 29(19P13.3) MUTATED              5          20         28
  DEL PEAK 29(19P13.3) WILD-TYPE           10          33         56
D57V38, multiclass
              clus
vv             DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  CURRENT USER                            5                             10
  FORMER USER                            20                             33
  NEVER USED                             28                             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V39, continuous
D57V40, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   27  5
  DEL PEAK 29(19P13.3) WILD-TYPE 65 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     27    5
  DEL PEAK 29(19P13.3) WILD-TYPE   65   12
         clus
vv        DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  ABSENT                            27                             65
  PRESENT                            5                             12
[1] 2 2
[1] FALSE
D57V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 29(19P13.3) MUTATED      0  11   23   13  1   2    2    2  12  0   2
  DEL PEAK 29(19P13.3) WILD-TYPE    1  23   46   17  5   8    5    7  24  2   0
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 29(19P13.3) MUTATED     7  3   1  6
  DEL PEAK 29(19P13.3) WILD-TYPE  10  5   0 10
D57V42, multiclass
      clus
vv     DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  T1A1                            0                              1
  T1B                            11                             23
  T1B1                           23                             46
  T1B2                           13                             17
  T2                              1                              5
  T2A                             2                              8
  T2A1                            2                              5
  T2A2                            2                              7
  T2B                            12                             24
  T3                              0                              2
  T3A                             2                              0
  T3B                             7                             10
  T4                              3                              5
  TIS                             1                              0
  TX                              6                             10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 29(19P13.3) MUTATED         1        0         0         0       11
  DEL PEAK 29(19P13.3) WILD-TYPE       4        1         1         1       22
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 29(19P13.3) MUTATED          30        14        1         3
  DEL PEAK 29(19P13.3) WILD-TYPE        47        22        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 29(19P13.3) MUTATED            2          2        16         0
  DEL PEAK 29(19P13.3) WILD-TYPE          3          5        27         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 29(19P13.3) MUTATED            2         13         1         5
  DEL PEAK 29(19P13.3) WILD-TYPE          1         29         6         7
D57V44, multiclass
            clus
vv           DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             11                             22
  STAGE IB1                            30                             47
  STAGE IB2                            14                             22
  STAGE II                              1                              3
  STAGE IIA                             3                              5
  STAGE IIA1                            2                              3
  STAGE IIA2                            2                              5
  STAGE IIB                            16                             27
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                           13                             29
  STAGE IVA                             1                              6
  STAGE IVB                             5                              7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 30(19Q13.33) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 30(19Q13.33) MUTATED    26  11
  DEL PEAK 30(19Q13.33) WILD-TYPE 187  54
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                             37                             241 
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                             11                              54 
$`DEL PEAK 30(19Q13.33) MUTATED`
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A7CM TCGA-C5-A7UI 
       30.21        35.01         0.46        20.91        20.35        94.95 
TCGA-C5-A7X8 TCGA-C5-A8YQ TCGA-DG-A2KJ TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR 
        2.73        23.51        58.88       118.65        12.36        30.90 
TCGA-EA-A556 TCGA-EK-A2IP TCGA-EK-A2PM TCGA-EK-A3GJ TCGA-FU-A3NI TCGA-GH-A9DA 
       14.89         6.64         0.59         0.10         1.45         9.01 
TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JX-A3Q8 
      117.40        78.71        81.96        24.56        20.48        30.31 
TCGA-MY-A5BD TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QH 
       54.81         9.04        26.43        19.96        46.03        39.78 
TCGA-VS-A957 TCGA-VS-A9U7 TCGA-VS-A9UM TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-VS-A9V5 
       48.07        42.41        27.25        18.84         4.34        16.24 
TCGA-ZJ-AAX4 
        0.69 

$`DEL PEAK 30(19Q13.33) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.39        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME 
        5.46        19.86        67.46        31.40        46.32        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99        35.61         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
      210.67       154.32       101.82       134.33        15.48       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
       17.19       155.77       131.11         9.34        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35       146.86        99.91        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91        11.87         1.12        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       87.75        58.88        36.76         2.66       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18        17.52         8.28        39.55        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        14.50        26.01        12.66        12.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG 
       13.48         0.36        12.59        45.96        26.27         1.51 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
       19.27         0.43         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.10         0.07         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        7.92         6.94        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17        31.36        36.26 
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-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.97         1.12        25.41        10.82        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       14.93         9.44       147.39       137.16        66.81        96.95 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VL 
       29.85        36.36        27.42         3.29        21.44        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       28.37         8.28        18.15        21.11       195.85         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        20.28        17.82        19.56         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF 
       11.38        13.87        34.62         5.42        35.05        20.84 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        5.49         2.96        15.58        16.41        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59         3.88        11.67        93.99        12.16        66.05 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 
       10.03        40.50        37.78        18.05        59.51        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        11.51        57.93        31.27        36.26        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
        4.73        24.39        39.78        50.86        15.68        50.63 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        45.34        44.94        43.40        25.74        21.30 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       22.72        19.69        46.92        40.96         1.71        14.53 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV 
       41.42        43.27        35.97        20.09        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 
       18.25        67.20         5.16        14.04        14.89        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       26.01        29.26        67.59        19.13         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                         118.65                          210.67 
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                          23.51                           19.36 
[1] "0.1 - 118.7 (23.5)" "0.0 - 210.7 (19.4)"
[1] "hr=" "1.3"
D58V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 30(19Q13.33) MUTATED    17   9   3   1
  DEL PEAK 30(19Q13.33) WILD-TYPE 117  59  18   7
D58V3, multiclass
    clus
vv   DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  T1                            17                             117
  T2                             9                              59
  T3                             3                              18
  T4                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                                 cls
clus                                0   1
  DEL PEAK 30(19Q13.33) MUTATED    15   6
  DEL PEAK 30(19Q13.33) WILD-TYPE 112  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED     15    6
  DEL PEAK 30(19Q13.33) WILD-TYPE  112   49
   clus
vv  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  0                            15                             112
  1                             6                              49
[1] 2 2
[1] FALSE
D58V5, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED   13  2
  DEL PEAK 30(19Q13.33) WILD-TYPE 94  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED     13    2
  DEL PEAK 30(19Q13.33) WILD-TYPE   94    8
   clus
vv  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  0                            13                              94
  1                             2                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 30(19Q13.33) MUTATED               0
  DEL PEAK 30(19Q13.33) WILD-TYPE             5
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(19Q13.33) MUTATED                                 26
  DEL PEAK 30(19Q13.33) WILD-TYPE                              215
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 30(19Q13.33) MUTATED                                               1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                             5
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 30(19Q13.33) MUTATED                                     4
  DEL PEAK 30(19Q13.33) WILD-TYPE                                  18
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 30(19Q13.33) MUTATED                                           1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 30(19Q13.33) MUTATED                                              5
  DEL PEAK 30(19Q13.33) WILD-TYPE                                           10
D58V6, multiclass
                                               clus
vv                                              DEL PEAK 30(19Q13.33) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         26
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
                                               clus
vv                                              DEL PEAK 30(19Q13.33) WILD-TYPE
  ADENOSQUAMOUS                                                               5
  CERVICAL SQUAMOUS CELL CARCINOMA                                          215
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 30(19Q13.33) MUTATED     4  33
  DEL PEAK 30(19Q13.33) WILD-TYPE  26 229
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      4   33
  DEL PEAK 30(19Q13.33) WILD-TYPE   26  229
     clus
vv    DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  NO                              4                              26
  YES                            33                             229
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(19Q13.33) MUTATED                                  1     1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                7    17
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(19Q13.33) MUTATED                           4
  DEL PEAK 30(19Q13.33) WILD-TYPE                        24
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(19Q13.33) MUTATED                                           1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 30(19Q13.33) MUTATED      27
  DEL PEAK 30(19Q13.33) WILD-TYPE   174
D58V10, multiclass
                                           clus
vv                                          DEL PEAK 30(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 1
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                27
                                           clus
vv                                          DEL PEAK 30(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  17
  BLACK OR AFRICAN AMERICAN                                              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 174
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                                 cls
clus                                0   1
  DEL PEAK 30(19Q13.33) MUTATED     3  15
  DEL PEAK 30(19Q13.33) WILD-TYPE  20 146
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      3   15
  DEL PEAK 30(19Q13.33) WILD-TYPE   20  146
                        clus
vv                       DEL PEAK 30(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            15
                        clus
vv                       DEL PEAK 30(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             146
[1] 2 2
[1] FALSE
D58V12, continuous
D58V13, binary
                                 cls
clus                                0   1
  DEL PEAK 30(19Q13.33) MUTATED    16   5
  DEL PEAK 30(19Q13.33) WILD-TYPE 118  36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED     16    5
  DEL PEAK 30(19Q13.33) WILD-TYPE  118   36
            clus
vv           DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  TUMOR FREE                            16                             118
  WITH TUMOR                             5                              36
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 30(19Q13.33) MUTATED       10      1       0      3       0
  DEL PEAK 30(19Q13.33) WILD-TYPE     43      4       1      8       7
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 30(19Q13.33) MUTATED              23       0
  DEL PEAK 30(19Q13.33) WILD-TYPE           178      14
D58V14, multiclass
               clus
vv              DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  BRAZIL                                   10                              43
  CANADA                                    1                               4
  NIGERIA                                   0                               1
  RUSSIA                                    3                               8
  UKRAINE                                   0                               7
  UNITED STATES                            23                             178
  VIETNAM                                   0                              14
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               G1  G2  G3  G4  GX
  DEL PEAK 30(19Q13.33) MUTATED     1  16  18   1   1
  DEL PEAK 30(19Q13.33) WILD-TYPE  17 113  95   0  23
D58V15, multiclass
    clus
vv   DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  G1                             1                              17
  G2                            16                             113
  G3                            18                              95
  G4                             1                               0
  GX                             1                              23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V16, continuous
D58V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 30(19Q13.33) MUTATED                                             5
  DEL PEAK 30(19Q13.33) WILD-TYPE                                          32
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 30(19Q13.33) MUTATED                                        1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                      8
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 30(19Q13.33) MUTATED                                                 0
  DEL PEAK 30(19Q13.33) WILD-TYPE                                               3
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 30(19Q13.33) MUTATED                9                  18
  DEL PEAK 30(19Q13.33) WILD-TYPE             53                 124
D58V18, multiclass
                                                 clus
vv                                                DEL PEAK 30(19Q13.33) 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                                                              9
  LIFELONG NON-SMOKER                                                        18
                                                 clus
vv                                                DEL PEAK 30(19Q13.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               3
  CURRENT SMOKER                                                               53
  LIFELONG NON-SMOKER                                                         124
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V19, continuous
D58V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 30(19Q13.33) MUTATED             1       18             3        1
  DEL PEAK 30(19Q13.33) WILD-TYPE          18       84             9       24
D58V21, multiclass
               clus
vv              DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  COMBINATION                               1                              18
  EXTERNAL                                 18                              84
  EXTERNAL BEAM                             3                               9
  INTERNAL                                  1                              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V22, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED    3  0
  DEL PEAK 30(19Q13.33) WILD-TYPE 22  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      3    0
  DEL PEAK 30(19Q13.33) WILD-TYPE   22    3
                         clus
vv                        DEL PEAK 30(19Q13.33) MUTATED
  COMPLETED AS PLANNED                                3
  TREATMENT NOT COMPLETED                             0
                         clus
vv                        DEL PEAK 30(19Q13.33) WILD-TYPE
  COMPLETED AS PLANNED                                 22
  TREATMENT NOT COMPLETED                               3
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 30(19Q13.33) MUTATED                    0                0
  DEL PEAK 30(19Q13.33) WILD-TYPE                  2                2
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 30(19Q13.33) MUTATED                     6             4
  DEL PEAK 30(19Q13.33) WILD-TYPE                  30            29
D58V23, multiclass
                     clus
vv                    DEL PEAK 30(19Q13.33) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                0
  PRIMARY TUMOR FIELD                             6
  REGIONAL SITE                                   4
                     clus
vv                    DEL PEAK 30(19Q13.33) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  2
  PRIMARY TUMOR FIELD                              30
  REGIONAL SITE                                    29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V24, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED   10  0
  DEL PEAK 30(19Q13.33) WILD-TYPE 46  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED     10    0
  DEL PEAK 30(19Q13.33) WILD-TYPE   46    5
     clus
vv    DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  CGY                            10                              46
  GY                              0                               5
[1] 2 2
[1] FALSE
D58V25, continuous
D58V26, continuous
D58V27, continuous
D58V28, continuous
D58V29, continuous
D58V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 30(19Q13.33) MUTATED                                     0
  DEL PEAK 30(19Q13.33) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 30(19Q13.33) MUTATED                                     1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                   6
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 30(19Q13.33) MUTATED                         6
  DEL PEAK 30(19Q13.33) WILD-TYPE                      29
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 30(19Q13.33) MUTATED                         0
  DEL PEAK 30(19Q13.33) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 30(19Q13.33) MUTATED                         2
  DEL PEAK 30(19Q13.33) WILD-TYPE                       6
D58V31, multiclass
                                     clus
vv                                    DEL PEAK 30(19Q13.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         6
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         2
                                     clus
vv                                    DEL PEAK 30(19Q13.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               6
  OTHER LOCATION, SPECIFY                                          29
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 30(19Q13.33) MUTATED                                               1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                             1
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 30(19Q13.33) MUTATED                                                3
  DEL PEAK 30(19Q13.33) WILD-TYPE                                             22
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 30(19Q13.33) MUTATED                                                                                  13
  DEL PEAK 30(19Q13.33) WILD-TYPE                                                                                68
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 30(19Q13.33) MUTATED                                                                                             12
  DEL PEAK 30(19Q13.33) WILD-TYPE                                                                                          108
D58V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 30(19Q13.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            12
                                                                                              clus
vv                                                                                             DEL PEAK 30(19Q13.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V33, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED    8  8
  DEL PEAK 30(19Q13.33) WILD-TYPE 62 65
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      8    8
  DEL PEAK 30(19Q13.33) WILD-TYPE   62   65
         clus
vv        DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  ABSENT                              8                              62
  PRESENT                             8                              65
[1] 2 2
[1] FALSE
D58V34, continuous
D58V35, continuous
D58V36, binary
                                 cls
clus                                0   1
  DEL PEAK 30(19Q13.33) MUTATED     4  10
  DEL PEAK 30(19Q13.33) WILD-TYPE  44 106
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      4   10
  DEL PEAK 30(19Q13.33) WILD-TYPE   44  106
                                          clus
vv                                         DEL PEAK 30(19Q13.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            10
                                          clus
vv                                         DEL PEAK 30(19Q13.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             106
[1] 2 2
[1] FALSE
D58V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 30(19Q13.33) MUTATED              2           5         12
  DEL PEAK 30(19Q13.33) WILD-TYPE           13          48         72
D58V38, multiclass
              clus
vv             DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  CURRENT USER                             2                              13
  FORMER USER                              5                              48
  NEVER USED                              12                              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V39, continuous
D58V40, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED   14  1
  DEL PEAK 30(19Q13.33) WILD-TYPE 78 16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED     14    1
  DEL PEAK 30(19Q13.33) WILD-TYPE   78   16
         clus
vv        DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  ABSENT                             14                              78
  PRESENT                             1                              16
[1] 2 2
[1] FALSE
D58V41, continuous
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 30(19Q13.33) MUTATED      0   6    9    2  1   2    1    0   5  0
  DEL PEAK 30(19Q13.33) WILD-TYPE    1  28   60   28  5   8    6    9  31  2
                                 vv
clus                              T3A T3B T4 TIS TX
  DEL PEAK 30(19Q13.33) MUTATED     0   3  1   0  3
  DEL PEAK 30(19Q13.33) WILD-TYPE   2  14  7   1 13
D58V42, multiclass
      clus
vv     DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  T1A1                             0                               1
  T1B                              6                              28
  T1B1                             9                              60
  T1B2                             2                              28
  T2                               1                               5
  T2A                              2                               8
  T2A1                             1                               6
  T2A2                             0                               9
  T2B                              5                              31
  T3                               0                               2
  T3A                              0                               2
  T3B                              3                              14
  T4                               1                               7
  TIS                              0                               1
  TX                               3                              13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 30(19Q13.33) MUTATED         1        0         0         0        3
  DEL PEAK 30(19Q13.33) WILD-TYPE       4        1         1         1       30
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 30(19Q13.33) MUTATED          17         3        2         0
  DEL PEAK 30(19Q13.33) WILD-TYPE        60        33        2         8
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 30(19Q13.33) MUTATED            1          0         5         0
  DEL PEAK 30(19Q13.33) WILD-TYPE          4          7        38         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 30(19Q13.33) MUTATED            0          2         1         2
  DEL PEAK 30(19Q13.33) WILD-TYPE          3         40         6        10
D58V44, multiclass
            clus
vv           DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               3                              30
  STAGE IB1                             17                              60
  STAGE IB2                              3                              33
  STAGE II                               2                               2
  STAGE IIA                              0                               8
  STAGE IIA1                             1                               4
  STAGE IIA2                             0                               7
  STAGE IIB                              5                              38
  STAGE III                              0                               1
  STAGE IIIA                             0                               3
  STAGE IIIB                             2                              40
  STAGE IVA                              1                               6
  STAGE IVB                              2                              10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK 31(20P12.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(20P12.1) MUTATED    22  12
  DEL PEAK 31(20P12.1) WILD-TYPE 191  53
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            34                            244 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            12                             53 
$`DEL PEAK 31(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-C5-A8XH TCGA-DG-A2KK TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A50E TCGA-EK-A2H0 
       45.83        50.76        12.36        24.56         7.46        45.96 
TCGA-EK-A2PI TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A770 TCGA-GH-A9DA 
       19.27         7.92         2.17        31.36         1.12         9.01 
TCGA-IR-A3LB TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX 
       66.81        29.85        24.56        21.11         7.99        12.49 
TCGA-MU-A5YI TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8Q9 TCGA-VS-A94Y 
       34.62         5.49         3.88        11.67        46.03         4.73 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       18.84         5.16        15.42        67.59 

$`DEL PEAK 31(20P12.1) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI 
       12.39        57.04        23.67        11.44        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-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       46.32        30.21        35.01        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
       17.19       155.77       131.11        94.95         9.34         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL 
       20.81        20.91        11.87         1.12        58.88        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       25.02        14.50        26.40        14.50        26.01        12.66 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82        14.89        26.79        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 
       14.96        13.58        13.48         0.36        12.59        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64         1.51         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        47.77         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.03        20.35         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HZ 
        8.32        15.55         1.22        23.84         0.92        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97        25.41        10.82        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       147.39       137.16       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ 
       78.71        81.96        36.36        27.42         3.29        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       20.48        15.58        28.37         8.28        18.15       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       30.31        11.28         0.89         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        20.28        17.82        19.56         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       11.38        13.87         5.42        54.81        35.05        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59        93.99        12.16        66.05        10.03        40.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       37.78        26.43        18.05        19.96        59.51        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       36.13        11.51        57.93        39.78        31.27        36.26 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       16.64        24.39        39.78        50.86        15.68        50.63 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       48.07        50.14        45.34        44.94        43.40        42.41 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       25.74        21.30        22.72        19.69        46.92        40.96 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        41.42        43.27        35.97 
TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V2 
       20.09        14.53         3.42        18.25        67.20        14.04 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
       14.89         4.34        16.24        26.01        29.26        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                          1.12                           0.03 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                        177.04                         210.67 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                        20.190                         19.825 
[1] "1.1 - 177.0 (20.2)" "0.0 - 210.7 (19.8)"
[1] "hr=" "1.7"
D59V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 31(20P12.1) MUTATED    20   6   1   1
  DEL PEAK 31(20P12.1) WILD-TYPE 114  62  20   7
D59V3, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  T1                           20                            114
  T2                            6                             62
  T3                            1                             20
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED    17   6
  DEL PEAK 31(20P12.1) WILD-TYPE 110  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     17    6
  DEL PEAK 31(20P12.1) WILD-TYPE  110   49
   clus
vv  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  0                           17                            110
  1                            6                             49
[1] 2 2
[1] FALSE
D59V5, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED   14  1
  DEL PEAK 31(20P12.1) WILD-TYPE 93  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     14    1
  DEL PEAK 31(20P12.1) WILD-TYPE   93    9
   clus
vv  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  0                           14                             93
  1                            1                              9
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(20P12.1) MUTATED               0                               28
  DEL PEAK 31(20P12.1) WILD-TYPE             5                              213
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 31(20P12.1) MUTATED                                               1
  DEL PEAK 31(20P12.1) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 31(20P12.1) MUTATED                                     4
  DEL PEAK 31(20P12.1) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 31(20P12.1) MUTATED                                           0
  DEL PEAK 31(20P12.1) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 31(20P12.1) MUTATED                                              2
  DEL PEAK 31(20P12.1) WILD-TYPE                                           13
D59V6, multiclass
                                               clus
vv                                              DEL PEAK 31(20P12.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              DEL PEAK 31(20P12.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         213
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED     3  32
  DEL PEAK 31(20P12.1) WILD-TYPE  27 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      3   32
  DEL PEAK 31(20P12.1) WILD-TYPE   27  230
     clus
vv    DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  NO                             3                             27
  YES                           32                            230
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(20P12.1) MUTATED                                  2     3
  DEL PEAK 31(20P12.1) WILD-TYPE                                6    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(20P12.1) MUTATED                           4
  DEL PEAK 31(20P12.1) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(20P12.1) MUTATED                                           0
  DEL PEAK 31(20P12.1) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 31(20P12.1) MUTATED      24
  DEL PEAK 31(20P12.1) WILD-TYPE   177
D59V10, multiclass
                                           clus
vv                                          DEL PEAK 31(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               24
                                           clus
vv                                          DEL PEAK 31(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED     2  19
  DEL PEAK 31(20P12.1) WILD-TYPE  21 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      2   19
  DEL PEAK 31(20P12.1) WILD-TYPE   21  142
                        clus
vv                       DEL PEAK 31(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       DEL PEAK 31(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            142
[1] 2 2
[1] FALSE
D59V12, continuous
D59V13, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED     9   7
  DEL PEAK 31(20P12.1) WILD-TYPE 125  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      9    7
  DEL PEAK 31(20P12.1) WILD-TYPE  125   34
            clus
vv           DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  TUMOR FREE                            9                            125
  WITH TUMOR                            7                             34
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 31(20P12.1) MUTATED        5      1       0      2       0
  DEL PEAK 31(20P12.1) WILD-TYPE     48      4       1      9       7
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 31(20P12.1) MUTATED              24       3
  DEL PEAK 31(20P12.1) WILD-TYPE           177      11
D59V14, multiclass
               clus
vv              DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  BRAZIL                                   5                             48
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   2                              9
  UKRAINE                                  0                              7
  UNITED STATES                           24                            177
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 31(20P12.1) MUTATED     2  16  13   0   3
  DEL PEAK 31(20P12.1) WILD-TYPE  16 113 100   1  21
D59V15, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  G1                            2                             16
  G2                           16                            113
  G3                           13                            100
  G4                            0                              1
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V16, continuous
D59V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 31(20P12.1) MUTATED                                             6
  DEL PEAK 31(20P12.1) WILD-TYPE                                          31
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 31(20P12.1) MUTATED                                        3
  DEL PEAK 31(20P12.1) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 31(20P12.1) MUTATED                                                 1
  DEL PEAK 31(20P12.1) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 31(20P12.1) MUTATED                9                  13
  DEL PEAK 31(20P12.1) WILD-TYPE             53                 129
D59V18, multiclass
                                                 clus
vv                                                DEL PEAK 31(20P12.1) 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                                                             9
  LIFELONG NON-SMOKER                                                       13
                                                 clus
vv                                                DEL PEAK 31(20P12.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              53
  LIFELONG NON-SMOKER                                                        129
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V19, continuous
D59V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 31(20P12.1) MUTATED             2       14             1        4
  DEL PEAK 31(20P12.1) WILD-TYPE          17       88            11       21
D59V21, multiclass
               clus
vv              DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  COMBINATION                              2                             17
  EXTERNAL                                14                             88
  EXTERNAL BEAM                            1                             11
  INTERNAL                                 4                             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"
D59V22, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED    2  1
  DEL PEAK 31(20P12.1) WILD-TYPE 23  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      2    1
  DEL PEAK 31(20P12.1) WILD-TYPE   23    2
                         clus
vv                        DEL PEAK 31(20P12.1) MUTATED
  COMPLETED AS PLANNED                               2
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 31(20P12.1) WILD-TYPE
  COMPLETED AS PLANNED                                23
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 31(20P12.1) MUTATED                    0                0
  DEL PEAK 31(20P12.1) WILD-TYPE                  2                2
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 31(20P12.1) MUTATED                     6             1
  DEL PEAK 31(20P12.1) WILD-TYPE                  30            32
D59V23, multiclass
                     clus
vv                    DEL PEAK 31(20P12.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            6
  REGIONAL SITE                                  1
                     clus
vv                    DEL PEAK 31(20P12.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             30
  REGIONAL SITE                                   32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V24, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED    5  1
  DEL PEAK 31(20P12.1) WILD-TYPE 51  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      5    1
  DEL PEAK 31(20P12.1) WILD-TYPE   51    4
     clus
vv    DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  CGY                            5                             51
  GY                             1                              4
[1] 2 2
[1] FALSE
D59V25, continuous
D59V26, continuous
D59V27, continuous
D59V28, continuous
D59V29, continuous
D59V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 31(20P12.1) MUTATED                                     0
  DEL PEAK 31(20P12.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 31(20P12.1) MUTATED                                     1
  DEL PEAK 31(20P12.1) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 31(20P12.1) MUTATED                         5
  DEL PEAK 31(20P12.1) WILD-TYPE                      30
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 31(20P12.1) MUTATED                         1
  DEL PEAK 31(20P12.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 31(20P12.1) MUTATED                         1
  DEL PEAK 31(20P12.1) WILD-TYPE                       7
D59V31, multiclass
                                     clus
vv                                    DEL PEAK 31(20P12.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        5
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 31(20P12.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         30
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 31(20P12.1) MUTATED                                               0
  DEL PEAK 31(20P12.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 31(20P12.1) MUTATED                                                2
  DEL PEAK 31(20P12.1) WILD-TYPE                                             23
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 31(20P12.1) MUTATED                                                                                  12
  DEL PEAK 31(20P12.1) WILD-TYPE                                                                                69
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 31(20P12.1) MUTATED                                                                                             16
  DEL PEAK 31(20P12.1) WILD-TYPE                                                                                          104
D59V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 31(20P12.1) 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)                                      12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           16
                                                                                              clus
vv                                                                                             DEL PEAK 31(20P12.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        69
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V33, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED    9  9
  DEL PEAK 31(20P12.1) WILD-TYPE 61 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      9    9
  DEL PEAK 31(20P12.1) WILD-TYPE   61   64
         clus
vv        DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  ABSENT                             9                             61
  PRESENT                            9                             64
[1] 2 2
[1] FALSE
D59V34, continuous
D59V35, continuous
D59V36, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED     6  12
  DEL PEAK 31(20P12.1) WILD-TYPE  42 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      6   12
  DEL PEAK 31(20P12.1) WILD-TYPE   42  104
                                          clus
vv                                         DEL PEAK 31(20P12.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           12
                                          clus
vv                                         DEL PEAK 31(20P12.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            104
[1] 2 2
[1] FALSE
D59V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 31(20P12.1) MUTATED              3           9          8
  DEL PEAK 31(20P12.1) WILD-TYPE           12          44         76
D59V38, multiclass
              clus
vv             DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                             9                             44
  NEVER USED                              8                             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V39, continuous
D59V40, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED   13  3
  DEL PEAK 31(20P12.1) WILD-TYPE 79 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     13    3
  DEL PEAK 31(20P12.1) WILD-TYPE   79   14
         clus
vv        DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  ABSENT                            13                             79
  PRESENT                            3                             14
[1] 2 2
[1] FALSE
D59V41, continuous
[1] "Remove cluster labels:"       "DEL PEAK 31(20P12.1) MUTATED"
clus
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 31(20P12.1) WILD-TYPE" "DEL PEAK 31(20P12.1) WILD-TYPE" 
                    TCGA-C5-A1ML                     TCGA-C5-A1MN 
"DEL PEAK 31(20P12.1) WILD-TYPE" "DEL PEAK 31(20P12.1) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK 31(20P12.1) WILD-TYPE" "DEL PEAK 31(20P12.1) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 31(20P12.1) WILD-TYPE" "DEL PEAK 31(20P12.1) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MA-AA3W 
"DEL PEAK 31(20P12.1) WILD-TYPE" "DEL PEAK 31(20P12.1) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK 31(20P12.1) WILD-TYPE" "DEL PEAK 31(20P12.1) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 31(20P12.1) WILD-TYPE" "DEL PEAK 31(20P12.1) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"DEL PEAK 31(20P12.1) WILD-TYPE" 
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 31(20P12.1) MUTATED      1   8    8    3  0   0    0    1   5  0   0
  DEL PEAK 31(20P12.1) WILD-TYPE    0  26   61   27  6  10    7    8  31  2   2
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 31(20P12.1) MUTATED     1  1   1  1
  DEL PEAK 31(20P12.1) WILD-TYPE  16  7   0 15
D59V42, multiclass
      clus
vv     DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  T1A1                            1                              0
  T1B                             8                             26
  T1B1                            8                             61
  T1B2                            3                             27
  T2                              0                              6
  T2A                             0                             10
  T2A1                            0                              7
  T2A2                            1                              8
  T2B                             5                             31
  T3                              0                              2
  T3A                             0                              2
  T3B                             1                             16
  T4                              1                              7
  TIS                             1                              0
  TX                              1                             15
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 31(20P12.1) MUTATED         0        0         1         0        6
  DEL PEAK 31(20P12.1) WILD-TYPE       5        1         0         1       27
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 31(20P12.1) MUTATED           9         3        0         1
  DEL PEAK 31(20P12.1) WILD-TYPE        68        33        4         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 31(20P12.1) MUTATED            0          0         8         0
  DEL PEAK 31(20P12.1) WILD-TYPE          5          7        35         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 31(20P12.1) MUTATED            0          4         1         2
  DEL PEAK 31(20P12.1) WILD-TYPE          3         38         6        10
D59V44, multiclass
            clus
vv           DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                              6                             27
  STAGE IB1                             9                             68
  STAGE IB2                             3                             33
  STAGE II                              0                              4
  STAGE IIA                             1                              7
  STAGE IIA1                            0                              5
  STAGE IIA2                            0                              7
  STAGE IIB                             8                             35
  STAGE III                             0                              1
  STAGE IIIA                            0                              3
  STAGE IIIB                            4                             38
  STAGE IVA                             1                              6
  STAGE IVB                             2                             10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 32(21Q11.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(21Q11.2) MUTATED    37  18
  DEL PEAK 32(21Q11.2) WILD-TYPE 176  47
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                            55                            223 
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                            18                             47 
$`DEL PEAK 32(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-C5-A8YQ TCGA-C5-A8YR 
       73.18        73.45       101.82         9.34        23.51        27.52 
TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 
       58.88        87.75         2.66        30.90        24.56        14.50 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R8 
        7.46        14.89         0.36        12.59         1.51         1.45 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3HY 
        1.18        47.77         0.03         6.94        23.84        31.36 
TCGA-FU-A3NI TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3LB TCGA-JW-A5VG TCGA-LP-A4AW 
        1.45        21.67         9.44        66.81        27.42         0.89 
TCGA-LP-A7HU TCGA-PN-A8MA TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI 
       13.35         2.96        12.16        10.03        26.43        18.05 
TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 
       19.96        46.03         4.73        39.78        15.68        48.07 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UP 
       45.34        44.94        19.69        46.92        14.53        43.27 
TCGA-WL-A834 
       26.01 

$`DEL PEAK 32(21Q11.2) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       12.39        49.48        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-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-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX 
       35.61         2.43        20.91         3.58        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       154.32       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19       155.77       131.11        94.95 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       13.61         2.73        50.99        45.83         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       99.91        20.81        20.91        11.87         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       44.94        40.04        58.88        36.76       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A5FO 
       14.50        26.40        26.01        12.66        12.82        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM 
       45.96        26.27         6.64        19.27         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.36         2.24         0.10         0.07         0.10         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
       20.35         7.92        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        1.22         0.92         2.17        36.26         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 
        9.01        25.41        10.82        20.78        14.93       147.39 
TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16       117.40        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W 
        7.99        11.28        12.49         0.30         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       20.28        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87        34.62         5.42        54.81        35.05        20.84 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        5.49        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC 
       19.59         3.88        11.67        93.99        66.05        40.50 
TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       37.78        59.51        32.15        36.13        11.51        57.93 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        36.26        16.64        24.39        50.86 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.63        50.14        43.40        42.41        25.74        21.30 
TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ 
       22.72        40.96         1.71        27.25        41.42        35.97 
TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       20.09        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
        5.16        14.04        14.89         4.34        16.24        15.42 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                        101.82                         210.67 
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                         21.67                          19.59 
[1] "0.0 - 101.8 (21.7)" "0.0 - 210.7 (19.6)"
[1] "hr=" "1.8"
D60V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 32(21Q11.2) MUTATED    24  14   9   3
  DEL PEAK 32(21Q11.2) WILD-TYPE 110  54  12   5
D60V3, multiclass
    clus
vv   DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  T1                           24                            110
  T2                           14                             54
  T3                            9                             12
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                                cls
clus                               0   1
  DEL PEAK 32(21Q11.2) MUTATED    21  14
  DEL PEAK 32(21Q11.2) WILD-TYPE 106  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     21   14
  DEL PEAK 32(21Q11.2) WILD-TYPE  106   41
   clus
vv  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  0                           21                            106
  1                           14                             41
[1] 2 2
[1] FALSE
D60V5, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   23  3
  DEL PEAK 32(21Q11.2) WILD-TYPE 84  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     23    3
  DEL PEAK 32(21Q11.2) WILD-TYPE   84    7
   clus
vv  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  0                           23                             84
  1                            3                              7
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(21Q11.2) MUTATED               1                               49
  DEL PEAK 32(21Q11.2) WILD-TYPE             4                              192
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 32(21Q11.2) MUTATED                                               1
  DEL PEAK 32(21Q11.2) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 32(21Q11.2) MUTATED                                     5
  DEL PEAK 32(21Q11.2) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 32(21Q11.2) MUTATED                                           1
  DEL PEAK 32(21Q11.2) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 32(21Q11.2) MUTATED                                              1
  DEL PEAK 32(21Q11.2) WILD-TYPE                                           14
D60V6, multiclass
                                               clus
vv                                              DEL PEAK 32(21Q11.2) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK 32(21Q11.2) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(21Q11.2) MUTATED     5  53
  DEL PEAK 32(21Q11.2) WILD-TYPE  25 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED      5   53
  DEL PEAK 32(21Q11.2) WILD-TYPE   25  209
     clus
vv    DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  NO                             5                             25
  YES                           53                            209
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(21Q11.2) MUTATED                                  1     5
  DEL PEAK 32(21Q11.2) WILD-TYPE                                7    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(21Q11.2) MUTATED                           9
  DEL PEAK 32(21Q11.2) WILD-TYPE                        19
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 32(21Q11.2) MUTATED                                           0
  DEL PEAK 32(21Q11.2) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 32(21Q11.2) MUTATED      36
  DEL PEAK 32(21Q11.2) WILD-TYPE   165
D60V10, multiclass
                                           clus
vv                                          DEL PEAK 32(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               36
                                           clus
vv                                          DEL PEAK 32(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                165
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                                cls
clus                               0   1
  DEL PEAK 32(21Q11.2) MUTATED     1  35
  DEL PEAK 32(21Q11.2) WILD-TYPE  22 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED      1   35
  DEL PEAK 32(21Q11.2) WILD-TYPE   22  126
                        clus
vv                       DEL PEAK 32(21Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       DEL PEAK 32(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            126
[1] 2 2
[1] FALSE
D60V12, continuous
D60V13, binary
                                cls
clus                               0   1
  DEL PEAK 32(21Q11.2) MUTATED    25   9
  DEL PEAK 32(21Q11.2) WILD-TYPE 109  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     25    9
  DEL PEAK 32(21Q11.2) WILD-TYPE  109   32
            clus
vv           DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  TUMOR FREE                           25                            109
  WITH TUMOR                            9                             32
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 32(21Q11.2) MUTATED       15      1       1      3       1
  DEL PEAK 32(21Q11.2) WILD-TYPE     38      4       0      8       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 32(21Q11.2) MUTATED              33       4
  DEL PEAK 32(21Q11.2) WILD-TYPE           168      10
D60V14, multiclass
               clus
vv              DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  BRAZIL                                  15                             38
  CANADA                                   1                              4
  NIGERIA                                  1                              0
  RUSSIA                                   3                              8
  UKRAINE                                  1                              6
  UNITED STATES                           33                            168
  VIETNAM                                  4                             10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 32(21Q11.2) MUTATED     2  18  33   0   5
  DEL PEAK 32(21Q11.2) WILD-TYPE  16 111  80   1  19
D60V15, multiclass
    clus
vv   DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  G1                            2                             16
  G2                           18                            111
  G3                           33                             80
  G4                            0                              1
  GX                            5                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V16, continuous
[1] "Remove cluster labels:"       "DEL PEAK 32(21Q11.2) MUTATED"
clus
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                             2                             40 
                    TCGA-BI-A0VR                     TCGA-C5-A1BJ 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1BL                     TCGA-C5-A1BQ 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1ME                     TCGA-C5-A1MF 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1MH                     TCGA-C5-A2M2 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A3HD                     TCGA-C5-A7CM 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A7CO                     TCGA-C5-A8XH 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A907                     TCGA-DG-A2KK 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-DS-A3LQ                     TCGA-EK-A2RA 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-EX-A69M                     TCGA-FU-A2QG 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-FU-A3TX                     TCGA-FU-A3WB 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-HM-A4S6 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-IR-A3L7                     TCGA-IR-A3LH 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-JX-A3Q0                     TCGA-MA-AA43 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-MU-A5YI                     TCGA-MU-A8JM 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-Q1-A6DW                     TCGA-Q1-A73S 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-RA-A741                     TCGA-VS-A8QF 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-VS-A94Z                     TCGA-VS-A9V0 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-VS-A9V4                     TCGA-ZJ-A8QR 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-ZJ-AAX4                     TCGA-ZJ-AAXA 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-ZJ-AAXT                     TCGA-ZJ-AB0I 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
D60V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 32(21Q11.2) MUTATED                                             1
  DEL PEAK 32(21Q11.2) WILD-TYPE                                          36
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 32(21Q11.2) MUTATED                                        1
  DEL PEAK 32(21Q11.2) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 32(21Q11.2) MUTATED                                                 0
  DEL PEAK 32(21Q11.2) WILD-TYPE                                               3
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 32(21Q11.2) MUTATED               15                  29
  DEL PEAK 32(21Q11.2) WILD-TYPE             47                 113
D60V18, multiclass
                                                 clus
vv                                                DEL PEAK 32(21Q11.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            15
  LIFELONG NON-SMOKER                                                       29
                                                 clus
vv                                                DEL PEAK 32(21Q11.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              3
  CURRENT SMOKER                                                              47
  LIFELONG NON-SMOKER                                                        113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V19, continuous
D60V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 32(21Q11.2) MUTATED             1       26             4        1
  DEL PEAK 32(21Q11.2) WILD-TYPE          18       76             8       24
D60V21, multiclass
               clus
vv              DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  COMBINATION                              1                             18
  EXTERNAL                                26                             76
  EXTERNAL BEAM                            4                              8
  INTERNAL                                 1                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V22, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED    4  1
  DEL PEAK 32(21Q11.2) WILD-TYPE 21  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED      4    1
  DEL PEAK 32(21Q11.2) WILD-TYPE   21    2
                         clus
vv                        DEL PEAK 32(21Q11.2) MUTATED
  COMPLETED AS PLANNED                               4
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 32(21Q11.2) WILD-TYPE
  COMPLETED AS PLANNED                                21
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 32(21Q11.2) MUTATED                    0                2
  DEL PEAK 32(21Q11.2) WILD-TYPE                  2                0
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 32(21Q11.2) MUTATED                    13             6
  DEL PEAK 32(21Q11.2) WILD-TYPE                  23            27
D60V23, multiclass
                     clus
vv                    DEL PEAK 32(21Q11.2) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                           13
  REGIONAL SITE                                  6
                     clus
vv                    DEL PEAK 32(21Q11.2) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             23
  REGIONAL SITE                                   27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V24, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   19  0
  DEL PEAK 32(21Q11.2) WILD-TYPE 37  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     19    0
  DEL PEAK 32(21Q11.2) WILD-TYPE   37    5
     clus
vv    DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  CGY                           19                             37
  GY                             0                              5
[1] 2 2
[1] FALSE
D60V25, continuous
D60V26, continuous
D60V27, continuous
D60V28, continuous
D60V29, continuous
D60V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 32(21Q11.2) MUTATED                                     0
  DEL PEAK 32(21Q11.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 32(21Q11.2) MUTATED                                     3
  DEL PEAK 32(21Q11.2) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 32(21Q11.2) MUTATED                         6
  DEL PEAK 32(21Q11.2) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 32(21Q11.2) MUTATED                         1
  DEL PEAK 32(21Q11.2) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 32(21Q11.2) MUTATED                         0
  DEL PEAK 32(21Q11.2) WILD-TYPE                       8
D60V31, multiclass
                                     clus
vv                                    DEL PEAK 32(21Q11.2) 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 32(21Q11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 32(21Q11.2) MUTATED                                               0
  DEL PEAK 32(21Q11.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 32(21Q11.2) MUTATED                                                4
  DEL PEAK 32(21Q11.2) WILD-TYPE                                             21
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 32(21Q11.2) MUTATED                                                                                  17
  DEL PEAK 32(21Q11.2) WILD-TYPE                                                                                64
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 32(21Q11.2) MUTATED                                                                                             25
  DEL PEAK 32(21Q11.2) WILD-TYPE                                                                                           95
D60V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 32(21Q11.2) 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)                                      17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           25
                                                                                              clus
vv                                                                                             DEL PEAK 32(21Q11.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V33, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   13 15
  DEL PEAK 32(21Q11.2) WILD-TYPE 57 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     13   15
  DEL PEAK 32(21Q11.2) WILD-TYPE   57   58
         clus
vv        DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  ABSENT                            13                             57
  PRESENT                           15                             58
[1] 2 2
[1] FALSE
D60V34, continuous
D60V35, continuous
D60V36, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED    8 24
  DEL PEAK 32(21Q11.2) WILD-TYPE 40 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED      8   24
  DEL PEAK 32(21Q11.2) WILD-TYPE   40   92
                                          clus
vv                                         DEL PEAK 32(21Q11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           24
                                          clus
vv                                         DEL PEAK 32(21Q11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             92
[1] 2 2
[1] FALSE
D60V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 32(21Q11.2) MUTATED              3           9         22
  DEL PEAK 32(21Q11.2) WILD-TYPE           12          44         62
D60V38, multiclass
              clus
vv             DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                             9                             44
  NEVER USED                             22                             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V39, continuous
D60V40, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   17  5
  DEL PEAK 32(21Q11.2) WILD-TYPE 75 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     17    5
  DEL PEAK 32(21Q11.2) WILD-TYPE   75   12
         clus
vv        DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  ABSENT                            17                             75
  PRESENT                            5                             12
[1] 2 2
[1] FALSE
D60V41, continuous
[1] "Remove cluster labels:"       "DEL PEAK 32(21Q11.2) MUTATED"
clus
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                             1                             16 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1ML                     TCGA-C5-A1MP 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-GH-A9DA 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MA-AA3W 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-MY-A913                     TCGA-ZX-AA5X 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 32(21Q11.2) MUTATED      0   6   13    5  1   5    3    0   5  0   2
  DEL PEAK 32(21Q11.2) WILD-TYPE    1  28   56   25  5   5    4    9  31  2   0
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 32(21Q11.2) MUTATED     7  3   0  2
  DEL PEAK 32(21Q11.2) WILD-TYPE  10  5   1 14
D60V42, multiclass
      clus
vv     DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  T1A1                            0                              1
  T1B                             6                             28
  T1B1                           13                             56
  T1B2                            5                             25
  T2                              1                              5
  T2A                             5                              5
  T2A1                            3                              4
  T2A2                            0                              9
  T2B                             5                             31
  T3                              0                              2
  T3A                             2                              0
  T3B                             7                             10
  T4                              3                              5
  TIS                             0                              1
  TX                              2                             14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 32(21Q11.2) MUTATED         0        1         0         0        7
  DEL PEAK 32(21Q11.2) WILD-TYPE       5        0         1         1       26
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 32(21Q11.2) MUTATED          12         6        2         3
  DEL PEAK 32(21Q11.2) WILD-TYPE        65        30        2         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 32(21Q11.2) MUTATED            3          0         6         0
  DEL PEAK 32(21Q11.2) WILD-TYPE          2          7        37         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 32(21Q11.2) MUTATED            2         10         3         1
  DEL PEAK 32(21Q11.2) WILD-TYPE          1         32         4        11
D60V44, multiclass
            clus
vv           DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              7                             26
  STAGE IB1                            12                             65
  STAGE IB2                             6                             30
  STAGE II                              2                              2
  STAGE IIA                             3                              5
  STAGE IIA1                            3                              2
  STAGE IIA2                            0                              7
  STAGE IIB                             6                             37
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                           10                             32
  STAGE IVA                             3                              4
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 33(22Q13.32) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(22Q13.32) MUTATED    60  21
  DEL PEAK 33(22Q13.32) WILD-TYPE 153  44
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             81                             197 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             21                              44 
$`DEL PEAK 33(22Q13.32) MUTATED`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 
       12.39        23.67        18.74       173.29         5.46        31.40 
TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX 
       30.21        57.73         0.46        40.93        73.18        83.05 
TCGA-C5-A3HD TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ 
       52.01         9.34         2.73        27.52         1.12        58.88 
TCGA-DG-A2KL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 
       44.94       118.65        12.36        30.90        24.56        14.50 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG 
       12.66        14.89        13.58         0.36        12.59         1.51 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H5 
        0.59         1.45         1.18         0.10         0.10        20.35 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3HY TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-HM-A4S6 
       15.55         1.22        31.36         9.01        21.67        14.93 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A852 
      137.16        66.81       117.40        27.42        24.56         8.28 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MY-A913 
        7.99         0.89        13.35        22.52        20.28         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG 
       15.58        16.41         9.04        19.59        11.67        12.16 
TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QH 
       40.50        18.05        19.96        59.51        46.03        39.78 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A9UB 
       16.64         4.73        50.86        15.68        48.07        21.30 
TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9V0 TCGA-VS-A9V4 
       19.69        40.96        14.53        27.25        18.84         4.34 
TCGA-XS-A8TJ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       29.26         0.69         1.41 

$`DEL PEAK 33(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-A1ML TCGA-C5-A1MP 
       53.16        38.99        35.61         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        73.45        78.35       100.14        38.43        33.24 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
      131.11        94.95        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        23.51        20.81        20.91        11.87 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       50.76        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       39.55        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       14.50        26.40        26.01        12.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 
       13.91        15.02        14.99        14.96        13.48        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R9 
       26.27         6.64        19.27         0.43         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       16.08         0.07         4.04         0.03         0.36        47.77 
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        19.79         8.32        23.84         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
        1.35         1.32         1.97         1.12        25.41        10.82 
TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
       20.78         9.44       147.39        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       29.85        36.36         3.29        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
       28.37        18.15        21.11       195.85        30.31        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       12.49         0.30         0.82        17.82        19.56         9.17 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        13.87        34.62         5.42        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       35.05        20.84         2.96        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       14.07        15.88         9.34        15.39        19.36         3.88 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 
       93.99        66.05        10.03        37.78        26.43        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z 
       36.13        11.51        57.93        31.27        36.26        24.39 
TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       39.78        50.63        50.14        45.34        44.94        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UO 
       42.41        25.74        22.72        46.92         1.71        41.42 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       43.27        35.97        20.09        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       67.20         5.16        14.04        14.89        16.24        15.42 
TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       26.01        67.59        19.13         0.16         3.91 

  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                         173.29                          210.67 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                          18.05                           20.48 
[1] "0.1 - 173.3 (18.1)" "0.0 - 210.7 (20.5)"
[1] "hr=" "1.4"
D61V2, continuous
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 33(22Q13.32) MUTATED   38 21 10  2
  DEL PEAK 33(22Q13.32) WILD-TYPE 96 47 11  6
D61V3, multiclass
    clus
vv   DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  T1                            38                              96
  T2                            21                              47
  T3                            10                              11
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   36 20
  DEL PEAK 33(22Q13.32) WILD-TYPE 91 35
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     36   20
  DEL PEAK 33(22Q13.32) WILD-TYPE   91   35
   clus
vv  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  0                            36                              91
  1                            20                              35
[1] 2 2
[1] FALSE
D61V5, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   37  2
  DEL PEAK 33(22Q13.32) WILD-TYPE 70  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     37    2
  DEL PEAK 33(22Q13.32) WILD-TYPE   70    8
   clus
vv  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  0                            37                              70
  1                             2                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 33(22Q13.32) MUTATED               1
  DEL PEAK 33(22Q13.32) WILD-TYPE             4
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(22Q13.32) MUTATED                                 73
  DEL PEAK 33(22Q13.32) WILD-TYPE                              168
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 33(22Q13.32) MUTATED                                               0
  DEL PEAK 33(22Q13.32) WILD-TYPE                                             6
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 33(22Q13.32) MUTATED                                     5
  DEL PEAK 33(22Q13.32) WILD-TYPE                                  17
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 33(22Q13.32) MUTATED                                           2
  DEL PEAK 33(22Q13.32) WILD-TYPE                                         1
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 33(22Q13.32) MUTATED                                              6
  DEL PEAK 33(22Q13.32) WILD-TYPE                                            9
D61V6, multiclass
                                               clus
vv                                              DEL PEAK 33(22Q13.32) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         73
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              6
                                               clus
vv                                              DEL PEAK 33(22Q13.32) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          168
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED    12  75
  DEL PEAK 33(22Q13.32) WILD-TYPE  18 187
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     12   75
  DEL PEAK 33(22Q13.32) WILD-TYPE   18  187
     clus
vv    DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  NO                             12                              18
  YES                            75                             187
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(22Q13.32) MUTATED                                  3     4
  DEL PEAK 33(22Q13.32) WILD-TYPE                                5    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(22Q13.32) MUTATED                          10
  DEL PEAK 33(22Q13.32) WILD-TYPE                        18
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 33(22Q13.32) MUTATED                                           1
  DEL PEAK 33(22Q13.32) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 33(22Q13.32) MUTATED      60
  DEL PEAK 33(22Q13.32) WILD-TYPE   141
D61V10, multiclass
                                           clus
vv                                          DEL PEAK 33(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 4
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                60
                                           clus
vv                                          DEL PEAK 33(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        5
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 141
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED     7  44
  DEL PEAK 33(22Q13.32) WILD-TYPE  16 117
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED      7   44
  DEL PEAK 33(22Q13.32) WILD-TYPE   16  117
                        clus
vv                       DEL PEAK 33(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            44
                        clus
vv                       DEL PEAK 33(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                  16
  NOT HISPANIC OR LATINO                             117
[1] 2 2
[1] FALSE
D61V12, continuous
D61V13, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   39 10
  DEL PEAK 33(22Q13.32) WILD-TYPE 95 31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     39   10
  DEL PEAK 33(22Q13.32) WILD-TYPE   95   31
            clus
vv           DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  TUMOR FREE                            39                              95
  WITH TUMOR                            10                              31
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 33(22Q13.32) MUTATED       19      3       0      5       2
  DEL PEAK 33(22Q13.32) WILD-TYPE     34      2       1      6       5
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 33(22Q13.32) MUTATED              54       4
  DEL PEAK 33(22Q13.32) WILD-TYPE           147      10
D61V14, multiclass
               clus
vv              DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  BRAZIL                                   19                              34
  CANADA                                    3                               2
  NIGERIA                                   0                               1
  RUSSIA                                    5                               6
  UKRAINE                                   2                               5
  UNITED STATES                            54                             147
  VIETNAM                                   4                              10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 33(22Q13.32) MUTATED    5 34 40  0  6
  DEL PEAK 33(22Q13.32) WILD-TYPE 13 95 73  1 18
D61V15, multiclass
    clus
vv   DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  G1                             5                              13
  G2                            34                              95
  G3                            40                              73
  G4                             0                               1
  GX                             6                              18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V16, continuous
D61V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 33(22Q13.32) MUTATED                                             8
  DEL PEAK 33(22Q13.32) WILD-TYPE                                          29
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 33(22Q13.32) MUTATED                                        3
  DEL PEAK 33(22Q13.32) WILD-TYPE                                      6
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 33(22Q13.32) MUTATED                                                 2
  DEL PEAK 33(22Q13.32) WILD-TYPE                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 33(22Q13.32) MUTATED               17                  42
  DEL PEAK 33(22Q13.32) WILD-TYPE             45                 100
D61V18, multiclass
                                                 clus
vv                                                DEL PEAK 33(22Q13.32) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             17
  LIFELONG NON-SMOKER                                                        42
                                                 clus
vv                                                DEL PEAK 33(22Q13.32) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               45
  LIFELONG NON-SMOKER                                                         100
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V19, continuous
D61V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 33(22Q13.32) MUTATED             7       34             4        6
  DEL PEAK 33(22Q13.32) WILD-TYPE          12       68             8       19
D61V21, multiclass
               clus
vv              DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  COMBINATION                               7                              12
  EXTERNAL                                 34                              68
  EXTERNAL BEAM                             4                               8
  INTERNAL                                  6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V22, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   11  0
  DEL PEAK 33(22Q13.32) WILD-TYPE 14  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     11    0
  DEL PEAK 33(22Q13.32) WILD-TYPE   14    3
                         clus
vv                        DEL PEAK 33(22Q13.32) MUTATED
  COMPLETED AS PLANNED                               11
  TREATMENT NOT COMPLETED                             0
                         clus
vv                        DEL PEAK 33(22Q13.32) WILD-TYPE
  COMPLETED AS PLANNED                                 14
  TREATMENT NOT COMPLETED                               3
[1] 2 2
[1] FALSE
                                 vv
clus                              DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 33(22Q13.32) MUTATED                    1                1
  DEL PEAK 33(22Q13.32) WILD-TYPE                  1                1
                                 vv
clus                              PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 33(22Q13.32) MUTATED                    15             7
  DEL PEAK 33(22Q13.32) WILD-TYPE                  21            26
D61V23, multiclass
                     clus
vv                    DEL PEAK 33(22Q13.32) MUTATED
  DISTANT RECURRENCE                              1
  LOCAL RECURRENCE                                1
  PRIMARY TUMOR FIELD                            15
  REGIONAL SITE                                   7
                     clus
vv                    DEL PEAK 33(22Q13.32) WILD-TYPE
  DISTANT RECURRENCE                                1
  LOCAL RECURRENCE                                  1
  PRIMARY TUMOR FIELD                              21
  REGIONAL SITE                                    26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V24, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   20  2
  DEL PEAK 33(22Q13.32) WILD-TYPE 36  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     20    2
  DEL PEAK 33(22Q13.32) WILD-TYPE   36    3
     clus
vv    DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  CGY                            20                              36
  GY                              2                               3
[1] 2 2
[1] FALSE
D61V25, continuous
D61V26, continuous
D61V27, continuous
D61V28, continuous
D61V29, continuous
D61V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 33(22Q13.32) MUTATED                                     0
  DEL PEAK 33(22Q13.32) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 33(22Q13.32) MUTATED                                     2
  DEL PEAK 33(22Q13.32) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 33(22Q13.32) MUTATED                        10
  DEL PEAK 33(22Q13.32) WILD-TYPE                      25
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 33(22Q13.32) MUTATED                         0
  DEL PEAK 33(22Q13.32) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 33(22Q13.32) MUTATED                         3
  DEL PEAK 33(22Q13.32) WILD-TYPE                       5
D61V31, multiclass
                                     clus
vv                                    DEL PEAK 33(22Q13.32) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        10
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         3
                                     clus
vv                                    DEL PEAK 33(22Q13.32) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                          25
  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(22Q13.32) MUTATED                                               1
  DEL PEAK 33(22Q13.32) WILD-TYPE                                             1
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 33(22Q13.32) MUTATED                                                5
  DEL PEAK 33(22Q13.32) WILD-TYPE                                             20
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 33(22Q13.32) MUTATED                                                                                  30
  DEL PEAK 33(22Q13.32) WILD-TYPE                                                                                51
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 33(22Q13.32) MUTATED                                                                                             33
  DEL PEAK 33(22Q13.32) WILD-TYPE                                                                                           87
D61V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 33(22Q13.32) 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)                                       30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            33
                                                                                              clus
vv                                                                                             DEL PEAK 33(22Q13.32) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V33, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   18 27
  DEL PEAK 33(22Q13.32) WILD-TYPE 52 46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     18   27
  DEL PEAK 33(22Q13.32) WILD-TYPE   52   46
         clus
vv        DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  ABSENT                             18                              52
  PRESENT                            27                              46
[1] 2 2
[1] FALSE
D61V34, continuous
D61V35, continuous
D61V36, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   14 38
  DEL PEAK 33(22Q13.32) WILD-TYPE 34 78
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     14   38
  DEL PEAK 33(22Q13.32) WILD-TYPE   34   78
                                          clus
vv                                         DEL PEAK 33(22Q13.32) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            38
                                          clus
vv                                         DEL PEAK 33(22Q13.32) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              78
[1] 2 2
[1] FALSE
D61V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 33(22Q13.32) MUTATED              5          16         28
  DEL PEAK 33(22Q13.32) WILD-TYPE           10          37         56
D61V38, multiclass
              clus
vv             DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  CURRENT USER                             5                              10
  FORMER USER                             16                              37
  NEVER USED                              28                              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V39, continuous
D61V40, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   32  3
  DEL PEAK 33(22Q13.32) WILD-TYPE 60 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     32    3
  DEL PEAK 33(22Q13.32) WILD-TYPE   60   14
         clus
vv        DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  ABSENT                             32                              60
  PRESENT                             3                              14
[1] 2 2
[1] FALSE
D61V41, continuous
                                 vv
clus                              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 33(22Q13.32) MUTATED      0  12   19    7  3   4    2    1  11  0
  DEL PEAK 33(22Q13.32) WILD-TYPE    1  22   50   23  3   6    5    8  25  2
                                 vv
clus                              T3A T3B T4 TIS TX
  DEL PEAK 33(22Q13.32) MUTATED     1   9  2   1  5
  DEL PEAK 33(22Q13.32) WILD-TYPE   1   8  6   0 11
D61V42, multiclass
      clus
vv     DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  T1A1                             0                               1
  T1B                             12                              22
  T1B1                            19                              50
  T1B2                             7                              23
  T2                               3                               3
  T2A                              4                               6
  T2A1                             2                               5
  T2A2                             1                               8
  T2B                             11                              25
  T3                               0                               2
  T3A                              1                               1
  T3B                              9                               8
  T4                               2                               6
  TIS                              1                               0
  TX                               5                              11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 33(22Q13.32) MUTATED         1        1         0         0       10
  DEL PEAK 33(22Q13.32) WILD-TYPE       4        0         1         1       23
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 33(22Q13.32) MUTATED          27         6        3         4
  DEL PEAK 33(22Q13.32) WILD-TYPE        50        30        1         4
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 33(22Q13.32) MUTATED            1          0        13         0
  DEL PEAK 33(22Q13.32) WILD-TYPE          4          7        30         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 33(22Q13.32) MUTATED            1         15         2         1
  DEL PEAK 33(22Q13.32) WILD-TYPE          2         27         5        11
D61V44, multiclass
            clus
vv           DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               1                               0
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                              10                              23
  STAGE IB1                             27                              50
  STAGE IB2                              6                              30
  STAGE II                               3                               1
  STAGE IIA                              4                               4
  STAGE IIA1                             1                               4
  STAGE IIA2                             0                               7
  STAGE IIB                             13                              30
  STAGE III                              0                               1
  STAGE IIIA                             1                               2
  STAGE IIIB                            15                              27
  STAGE IVA                              2                               5
  STAGE IVB                              1                              11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = DEL PEAK 34(XP11.3) MUTATION ANALYSIS
D62V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 34(XP11.3) MUTATED    50  18
  DEL PEAK 34(XP11.3) WILD-TYPE 163  47
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           68                           210 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           18                            47 
$`DEL PEAK 34(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-A1ML TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A3HD 
       30.21        53.16        20.91        40.93        73.45        52.01 
TCGA-C5-A7UH TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WF 
      131.11        99.91        23.51       118.65        22.98        16.18 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QE TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 
       12.36        30.90        25.02        26.01        12.66        14.89 
TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RB 
       14.96        45.96         1.51         0.43         0.59         0.07 
TCGA-EK-A2RE TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A3HY 
        0.36         0.10         0.10        20.35         0.92        31.36 
TCGA-FU-A3NI TCGA-FU-A5XV TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LK TCGA-JX-A3PZ 
        1.45         1.97       137.16        66.81        29.85        21.11 
TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MA-AA42 TCGA-MY-A5BF TCGA-Q1-A6DT 
       30.31         0.89         0.82         8.52        20.84         9.04 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QF 
       66.05        10.03        26.43        18.05        11.51        57.93 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A9U5 TCGA-VS-A9U7 
       16.64         4.73        39.78        15.68        44.94        42.41 
TCGA-VS-A9UC TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9V5 TCGA-ZJ-A8QQ 
       22.72        27.25        41.42        20.09        16.24        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       19.13         0.69 

$`DEL PEAK 34(XP11.3) WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       12.39        49.48        68.84        18.74        36.56       144.16 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 
      173.29        82.85        19.86        67.46        31.40        35.01 
TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP 
       57.73        38.99        35.61         0.46         2.43         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.18        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       33.24        18.02        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      155.77        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       45.83         8.35       146.86        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       11.87         1.12        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A5RQ 
       87.75        58.88        36.76         2.66       117.99        16.83 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       17.52         8.28        39.55        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA 
       13.05        14.50        26.40        24.56        14.50        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
        7.46        26.79        13.91        15.02        14.99        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       13.48         0.36        12.59        26.27         6.64        19.27 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         1.45         0.13        16.08         4.04         0.03 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        1.18        47.77         2.24         0.10         0.07         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        7.92         6.94        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        1.22        23.84         2.17        36.26         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.35         1.32         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        10.82        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL 
      147.39       117.40        96.95        78.71        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU 
       28.37         8.28        18.15       195.85         7.99        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
       12.49         0.30        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         9.17        11.38        13.87        34.62         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       54.81        35.05         5.49         2.96        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       12.16        40.50        37.78        19.96        59.51        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z 
       46.03        36.13        39.78        31.27        36.26        24.39 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 
       50.86        50.63        48.07        50.14        45.34        43.40 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       25.74        21.30        19.69        46.92        40.96         1.71 
TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       14.53        43.27        35.97        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        14.04        14.89         4.34 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        26.01        29.26         1.41         0.16         3.91 

  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                       177.04                        210.67 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                        21.01                         19.46 
[1] "0.1 - 177.0 (21.0)" "0.0 - 210.7 (19.5)"
[1] "hr=" "1.2"
D62V2, continuous
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 34(XP11.3) MUTATED    33  15   6   1
  DEL PEAK 34(XP11.3) WILD-TYPE 101  53  15   7
D62V3, multiclass
    clus
vv   DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  T1                          33                           101
  T2                          15                            53
  T3                           6                            15
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   32 10
  DEL PEAK 34(XP11.3) WILD-TYPE 95 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     32   10
  DEL PEAK 34(XP11.3) WILD-TYPE   95   45
   clus
vv  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  0                          32                            95
  1                          10                            45
[1] 2 2
[1] FALSE
D62V5, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   24  1
  DEL PEAK 34(XP11.3) WILD-TYPE 83  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     24    1
  DEL PEAK 34(XP11.3) WILD-TYPE   83    9
   clus
vv  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  0                          24                            83
  1                           1                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(XP11.3) MUTATED               1                               60
  DEL PEAK 34(XP11.3) WILD-TYPE             4                              181
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 34(XP11.3) MUTATED                                               1
  DEL PEAK 34(XP11.3) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 34(XP11.3) MUTATED                                     3
  DEL PEAK 34(XP11.3) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 34(XP11.3) MUTATED                                           3
  DEL PEAK 34(XP11.3) WILD-TYPE                                         0
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 34(XP11.3) MUTATED                                              3
  DEL PEAK 34(XP11.3) WILD-TYPE                                           12
D62V6, multiclass
                                               clus
vv                                              DEL PEAK 34(XP11.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       60
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              DEL PEAK 34(XP11.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        181
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP11.3) MUTATED    11  60
  DEL PEAK 34(XP11.3) WILD-TYPE  19 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     11   60
  DEL PEAK 34(XP11.3) WILD-TYPE   19  202
     clus
vv    DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  NO                           11                            19
  YES                          60                           202
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(XP11.3) MUTATED                                  0     4
  DEL PEAK 34(XP11.3) WILD-TYPE                                8    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(XP11.3) MUTATED                           8
  DEL PEAK 34(XP11.3) WILD-TYPE                        20
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 34(XP11.3) MUTATED                                           2    51
  DEL PEAK 34(XP11.3) WILD-TYPE                                         0   150
D62V10, multiclass
                                           clus
vv                                          DEL PEAK 34(XP11.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              51
                                           clus
vv                                          DEL PEAK 34(XP11.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               150
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP11.3) MUTATED     2  42
  DEL PEAK 34(XP11.3) WILD-TYPE  21 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED      2   42
  DEL PEAK 34(XP11.3) WILD-TYPE   21  119
                        clus
vv                       DEL PEAK 34(XP11.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       DEL PEAK 34(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           119
[1] 2 2
[1] FALSE
D62V12, continuous
D62V13, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP11.3) MUTATED    30   9
  DEL PEAK 34(XP11.3) WILD-TYPE 104  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     30    9
  DEL PEAK 34(XP11.3) WILD-TYPE  104   32
            clus
vv           DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  TUMOR FREE                          30                           104
  WITH TUMOR                           9                            32
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 34(XP11.3) MUTATED       16      0       0      4       2
  DEL PEAK 34(XP11.3) WILD-TYPE     37      5       1      7       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 34(XP11.3) MUTATED              46       3
  DEL PEAK 34(XP11.3) WILD-TYPE           155      11
D62V14, multiclass
               clus
vv              DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  BRAZIL                                 16                            37
  CANADA                                  0                             5
  NIGERIA                                 0                             1
  RUSSIA                                  4                             7
  UKRAINE                                 2                             5
  UNITED STATES                          46                           155
  VIETNAM                                 3                            11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK 34(XP11.3) MUTATED     3  27  31   0   8
  DEL PEAK 34(XP11.3) WILD-TYPE  15 102  82   1  16
D62V15, multiclass
    clus
vv   DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  G1                           3                            15
  G2                          27                           102
  G3                          31                            82
  G4                           0                             1
  GX                           8                            16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V16, continuous
D62V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 34(XP11.3) MUTATED                                             6
  DEL PEAK 34(XP11.3) WILD-TYPE                                          31
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 34(XP11.3) MUTATED                                        2
  DEL PEAK 34(XP11.3) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 34(XP11.3) MUTATED                                                 0
  DEL PEAK 34(XP11.3) WILD-TYPE                                               3
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 34(XP11.3) MUTATED               20                  33
  DEL PEAK 34(XP11.3) WILD-TYPE             42                 109
D62V18, multiclass
                                                 clus
vv                                                DEL PEAK 34(XP11.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           20
  LIFELONG NON-SMOKER                                                      33
                                                 clus
vv                                                DEL PEAK 34(XP11.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             3
  CURRENT SMOKER                                                             42
  LIFELONG NON-SMOKER                                                       109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V19, continuous
D62V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 34(XP11.3) MUTATED             5       22             5        5
  DEL PEAK 34(XP11.3) WILD-TYPE          14       80             7       20
D62V21, multiclass
               clus
vv              DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  COMBINATION                             5                            14
  EXTERNAL                               22                            80
  EXTERNAL BEAM                           5                             7
  INTERNAL                                5                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V22, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED    8  2
  DEL PEAK 34(XP11.3) WILD-TYPE 17  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED      8    2
  DEL PEAK 34(XP11.3) WILD-TYPE   17    1
                         clus
vv                        DEL PEAK 34(XP11.3) MUTATED
  COMPLETED AS PLANNED                              8
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK 34(XP11.3) WILD-TYPE
  COMPLETED AS PLANNED                               17
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
                               vv
clus                            DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 34(XP11.3) MUTATED                    1                1
  DEL PEAK 34(XP11.3) WILD-TYPE                  1                1
                               vv
clus                            PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 34(XP11.3) MUTATED                     6            10
  DEL PEAK 34(XP11.3) WILD-TYPE                  30            23
D62V23, multiclass
                     clus
vv                    DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  DISTANT RECURRENCE                            1                             1
  LOCAL RECURRENCE                              1                             1
  PRIMARY TUMOR FIELD                           6                            30
  REGIONAL SITE                                10                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V24, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   15  1
  DEL PEAK 34(XP11.3) WILD-TYPE 41  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     15    1
  DEL PEAK 34(XP11.3) WILD-TYPE   41    4
     clus
vv    DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  CGY                          15                            41
  GY                            1                             4
[1] 2 2
[1] FALSE
D62V25, continuous
D62V26, continuous
D62V27, continuous
D62V28, continuous
D62V29, continuous
D62V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 34(XP11.3) MUTATED                                     0
  DEL PEAK 34(XP11.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 34(XP11.3) MUTATED                                     4
  DEL PEAK 34(XP11.3) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 34(XP11.3) MUTATED                         7                       0
  DEL PEAK 34(XP11.3) WILD-TYPE                      28                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 34(XP11.3) MUTATED                         1
  DEL PEAK 34(XP11.3) WILD-TYPE                       7
D62V31, multiclass
                                     clus
vv                                    DEL PEAK 34(XP11.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                       7
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK 34(XP11.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        28
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 34(XP11.3) MUTATED                                               1
  DEL PEAK 34(XP11.3) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 34(XP11.3) MUTATED                                                9
  DEL PEAK 34(XP11.3) WILD-TYPE                                             16
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 34(XP11.3) MUTATED                                                                                  16
  DEL PEAK 34(XP11.3) WILD-TYPE                                                                                65
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 34(XP11.3) MUTATED                                                                                             32
  DEL PEAK 34(XP11.3) WILD-TYPE                                                                                           88
D62V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 34(XP11.3) MUTATED
  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)                                     16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          32
                                                                                              clus
vv                                                                                             DEL PEAK 34(XP11.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V33, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   17 17
  DEL PEAK 34(XP11.3) WILD-TYPE 53 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     17   17
  DEL PEAK 34(XP11.3) WILD-TYPE   53   56
         clus
vv        DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  ABSENT                           17                            53
  PRESENT                          17                            56
[1] 2 2
[1] FALSE
D62V34, continuous
D62V35, continuous
D62V36, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   15 22
  DEL PEAK 34(XP11.3) WILD-TYPE 33 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     15   22
  DEL PEAK 34(XP11.3) WILD-TYPE   33   94
                                          clus
vv                                         DEL PEAK 34(XP11.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          22
                                          clus
vv                                         DEL PEAK 34(XP11.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            94
[1] 2 2
[1] FALSE
D62V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 34(XP11.3) MUTATED              3          11         31
  DEL PEAK 34(XP11.3) WILD-TYPE           12          42         53
D62V38, multiclass
              clus
vv             DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           11                            42
  NEVER USED                            31                            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"
D62V39, continuous
D62V40, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   24  1
  DEL PEAK 34(XP11.3) WILD-TYPE 68 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     24    1
  DEL PEAK 34(XP11.3) WILD-TYPE   68   16
         clus
vv        DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  ABSENT                           24                            68
  PRESENT                           1                            16
[1] 2 2
[1] FALSE
D62V41, continuous
                               vv
clus                            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 34(XP11.3) MUTATED      0  10   15    8  1   2    0    3   9  0   1
  DEL PEAK 34(XP11.3) WILD-TYPE    1  24   54   22  5   8    7    6  27  2   1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 34(XP11.3) MUTATED     5  1   0  4
  DEL PEAK 34(XP11.3) WILD-TYPE  12  7   1 12
D62V42, multiclass
      clus
vv     DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  T1A1                           0                             1
  T1B                           10                            24
  T1B1                          15                            54
  T1B2                           8                            22
  T2                             1                             5
  T2A                            2                             8
  T2A1                           0                             7
  T2A2                           3                             6
  T2B                            9                            27
  T3                             0                             2
  T3A                            1                             1
  T3B                            5                            12
  T4                             1                             7
  TIS                            0                             1
  TX                             4                            12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 34(XP11.3) MUTATED         2        1         0         1        8
  DEL PEAK 34(XP11.3) WILD-TYPE       3        0         1         0       25
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 34(XP11.3) MUTATED          16         8        2         2
  DEL PEAK 34(XP11.3) WILD-TYPE        61        28        2         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 34(XP11.3) MUTATED            0          1        15         0
  DEL PEAK 34(XP11.3) WILD-TYPE          5          6        28         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 34(XP11.3) MUTATED            1          8         2         2
  DEL PEAK 34(XP11.3) WILD-TYPE          2         34         5        10
D62V44, multiclass
            clus
vv           DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             8                            25
  STAGE IB1                           16                            61
  STAGE IB2                            8                            28
  STAGE II                             2                             2
  STAGE IIA                            2                             6
  STAGE IIA1                           0                             5
  STAGE IIA2                           1                             6
  STAGE IIB                           15                            28
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                           8                            34
  STAGE IVA                            2                             5
  STAGE IVB                            2                            10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 35(XQ21.33) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(XQ21.33) MUTATED    38  19
  DEL PEAK 35(XQ21.33) WILD-TYPE 175  46
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            57                            221 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            19                             46 
$`DEL PEAK 35(XQ21.33) MUTATED`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 
       12.39        23.67        11.44        19.86        67.46        30.21 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CJ 
        2.43        20.91        40.93        83.05        52.01       101.82 
TCGA-C5-A7CO TCGA-C5-A7X5 TCGA-C5-A8XK TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WF 
      147.35        13.61        99.91        36.76       118.65        16.18 
TCGA-EA-A1QT TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EK-A2IP TCGA-EK-A2PL 
       12.36        12.66        14.89        14.99         6.64         0.43 
TCGA-EK-A2PM TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A69M 
        0.59         0.10         0.10        20.35         7.92         8.32 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A5XV TCGA-IR-A3LK TCGA-JW-A5VL TCGA-JW-A852 
        0.92        31.36         1.97        29.85        15.58         8.28 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A5U3 TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MY-A5BF 
       21.11        30.31         0.82         9.17         8.52        20.84 
TCGA-Q1-A73Q TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8QA TCGA-VS-A94Y TCGA-VS-A9U6 
        9.34        66.05        10.03        36.13         4.73        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UC TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9V0 TCGA-VS-A9V1 
       42.41        22.72        41.42        20.09        18.84         5.16 
TCGA-VS-A9V5 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
       16.24        29.26        19.13 

$`DEL PEAK 35(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        33.24        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      154.32       134.33        15.48        20.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      131.11        94.95         9.34         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35       146.86        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       11.87         1.12        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       87.75        58.88         2.66       117.99        22.98        16.83 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50        26.01        12.82         7.46        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       15.02        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2R7 TCGA-EK-A2R8 
       45.96        26.27         1.51        19.27         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        1.18        47.77         2.24         0.10         0.07         0.03 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70        19.79        15.55         1.22        23.84 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17        36.26         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        3.52         1.35         1.32         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       10.82        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       28.37        18.15       195.85         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
       12.49         0.30        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
       19.56        11.38        13.87        34.62         5.42        54.81 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       35.05         5.49         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R 
        9.04        16.14        17.56        14.07        15.88        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       19.36        19.59         3.88        11.67        93.99        12.16 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       40.50        37.78        26.43        18.05        19.96        59.51 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        46.03        11.51        57.93        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       36.26        16.64        24.39        39.78        50.86        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA 
       50.63        48.07        50.14        45.34        44.94        25.74 
TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       21.30        19.69        46.92        40.96         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       27.25        43.27        35.97        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-WL-A834 
       67.20        14.04        14.89         4.34        15.42        26.01 
TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59         0.69         1.41         0.16         3.91 

  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                        147.35                         210.67 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                         18.84                          20.28 
[1] "0.1 - 147.3 (18.8)" "0.0 - 210.7 (20.3)"
[1] "hr=" "1.8"
D63V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 35(XQ21.33) MUTATED    30  13   3   1
  DEL PEAK 35(XQ21.33) WILD-TYPE 104  55  18   7
D63V3, multiclass
    clus
vv   DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  T1                           30                            104
  T2                           13                             55
  T3                            3                             18
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                                cls
clus                               0   1
  DEL PEAK 35(XQ21.33) MUTATED    25  13
  DEL PEAK 35(XQ21.33) WILD-TYPE 102  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     25   13
  DEL PEAK 35(XQ21.33) WILD-TYPE  102   42
   clus
vv  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  0                           25                            102
  1                           13                             42
[1] 2 2
[1] FALSE
D63V5, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   17  3
  DEL PEAK 35(XQ21.33) WILD-TYPE 90  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     17    3
  DEL PEAK 35(XQ21.33) WILD-TYPE   90    7
   clus
vv  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  0                           17                             90
  1                            3                              7
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(XQ21.33) MUTATED               1                               48
  DEL PEAK 35(XQ21.33) WILD-TYPE             4                              193
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 35(XQ21.33) MUTATED                                               0
  DEL PEAK 35(XQ21.33) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 35(XQ21.33) MUTATED                                     3
  DEL PEAK 35(XQ21.33) WILD-TYPE                                  19
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 35(XQ21.33) MUTATED                                           2
  DEL PEAK 35(XQ21.33) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 35(XQ21.33) MUTATED                                              5
  DEL PEAK 35(XQ21.33) WILD-TYPE                                           10
D63V6, multiclass
                                               clus
vv                                              DEL PEAK 35(XQ21.33) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        48
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             5
                                               clus
vv                                              DEL PEAK 35(XQ21.33) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         193
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(XQ21.33) MUTATED     9  50
  DEL PEAK 35(XQ21.33) WILD-TYPE  21 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED      9   50
  DEL PEAK 35(XQ21.33) WILD-TYPE   21  212
     clus
vv    DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  NO                             9                             21
  YES                           50                            212
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(XQ21.33) MUTATED                                  1     3
  DEL PEAK 35(XQ21.33) WILD-TYPE                                7    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(XQ21.33) MUTATED                           5
  DEL PEAK 35(XQ21.33) WILD-TYPE                        23
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 35(XQ21.33) MUTATED                                           2
  DEL PEAK 35(XQ21.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 35(XQ21.33) MUTATED      43
  DEL PEAK 35(XQ21.33) WILD-TYPE   158
D63V10, multiclass
                                           clus
vv                                          DEL PEAK 35(XQ21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               43
                                           clus
vv                                          DEL PEAK 35(XQ21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, binary
                                cls
clus                               0   1
  DEL PEAK 35(XQ21.33) MUTATED     6  31
  DEL PEAK 35(XQ21.33) WILD-TYPE  17 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED      6   31
  DEL PEAK 35(XQ21.33) WILD-TYPE   17  130
                        clus
vv                       DEL PEAK 35(XQ21.33) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       DEL PEAK 35(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            130
[1] 2 2
[1] FALSE
D63V12, continuous
D63V13, binary
                                cls
clus                               0   1
  DEL PEAK 35(XQ21.33) MUTATED    23  12
  DEL PEAK 35(XQ21.33) WILD-TYPE 111  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     23   12
  DEL PEAK 35(XQ21.33) WILD-TYPE  111   29
            clus
vv           DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  TUMOR FREE                           23                            111
  WITH TUMOR                           12                             29
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 35(XQ21.33) MUTATED       12      0       0      3       1
  DEL PEAK 35(XQ21.33) WILD-TYPE     41      5       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 35(XQ21.33) MUTATED              41       2
  DEL PEAK 35(XQ21.33) WILD-TYPE           160      12
D63V14, multiclass
               clus
vv              DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  BRAZIL                                  12                             41
  CANADA                                   0                              5
  NIGERIA                                  0                              1
  RUSSIA                                   3                              8
  UKRAINE                                  1                              6
  UNITED STATES                           41                            160
  VIETNAM                                  2                             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 35(XQ21.33) MUTATED     4  21  25   0   7
  DEL PEAK 35(XQ21.33) WILD-TYPE  14 108  88   1  17
D63V15, multiclass
    clus
vv   DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  G1                            4                             14
  G2                           21                            108
  G3                           25                             88
  G4                            0                              1
  GX                            7                             17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V16, continuous
D63V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 35(XQ21.33) MUTATED                                             6
  DEL PEAK 35(XQ21.33) WILD-TYPE                                          31
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 35(XQ21.33) MUTATED                                        1
  DEL PEAK 35(XQ21.33) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 35(XQ21.33) MUTATED                                                 1
  DEL PEAK 35(XQ21.33) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 35(XQ21.33) MUTATED               15                  26
  DEL PEAK 35(XQ21.33) WILD-TYPE             47                 116
D63V18, multiclass
                                                 clus
vv                                                DEL PEAK 35(XQ21.33) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            15
  LIFELONG NON-SMOKER                                                       26
                                                 clus
vv                                                DEL PEAK 35(XQ21.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              47
  LIFELONG NON-SMOKER                                                        116
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V19, continuous
D63V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 35(XQ21.33) MUTATED             6       19             4        4
  DEL PEAK 35(XQ21.33) WILD-TYPE          13       83             8       21
D63V21, multiclass
               clus
vv              DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  COMBINATION                              6                             13
  EXTERNAL                                19                             83
  EXTERNAL BEAM                            4                              8
  INTERNAL                                 4                             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"
D63V22, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED    6  2
  DEL PEAK 35(XQ21.33) WILD-TYPE 19  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED      6    2
  DEL PEAK 35(XQ21.33) WILD-TYPE   19    1
                         clus
vv                        DEL PEAK 35(XQ21.33) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        DEL PEAK 35(XQ21.33) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
                                vv
clus                             DISTANT RECURRENCE LOCAL RECURRENCE
  DEL PEAK 35(XQ21.33) MUTATED                    1                1
  DEL PEAK 35(XQ21.33) WILD-TYPE                  1                1
                                vv
clus                             PRIMARY TUMOR FIELD REGIONAL SITE
  DEL PEAK 35(XQ21.33) MUTATED                     5             5
  DEL PEAK 35(XQ21.33) WILD-TYPE                  31            28
D63V23, multiclass
                     clus
vv                    DEL PEAK 35(XQ21.33) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            5
  REGIONAL SITE                                  5
                     clus
vv                    DEL PEAK 35(XQ21.33) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             31
  REGIONAL SITE                                   28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V24, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED    9  0
  DEL PEAK 35(XQ21.33) WILD-TYPE 47  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED      9    0
  DEL PEAK 35(XQ21.33) WILD-TYPE   47    5
     clus
vv    DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  CGY                            9                             47
  GY                             0                              5
[1] 2 2
[1] FALSE
D63V25, continuous
D63V26, continuous
D63V27, continuous
D63V28, continuous
D63V29, continuous
D63V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 35(XQ21.33) MUTATED                                     0
  DEL PEAK 35(XQ21.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 35(XQ21.33) MUTATED                                     4
  DEL PEAK 35(XQ21.33) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 35(XQ21.33) MUTATED                         5
  DEL PEAK 35(XQ21.33) WILD-TYPE                      30
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 35(XQ21.33) MUTATED                         0
  DEL PEAK 35(XQ21.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 35(XQ21.33) MUTATED                         3
  DEL PEAK 35(XQ21.33) WILD-TYPE                       5
D63V31, multiclass
                                     clus
vv                                    DEL PEAK 35(XQ21.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                        5
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        3
                                     clus
vv                                    DEL PEAK 35(XQ21.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              3
  OTHER LOCATION, SPECIFY                                         30
  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 35(XQ21.33) MUTATED                                               2
  DEL PEAK 35(XQ21.33) WILD-TYPE                                             0
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 35(XQ21.33) MUTATED                                                5
  DEL PEAK 35(XQ21.33) WILD-TYPE                                             20
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 35(XQ21.33) MUTATED                                                                                  13
  DEL PEAK 35(XQ21.33) WILD-TYPE                                                                                68
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 35(XQ21.33) MUTATED                                                                                             28
  DEL PEAK 35(XQ21.33) WILD-TYPE                                                                                           92
D63V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 35(XQ21.33) MUTATED
  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)                                      13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           28
                                                                                              clus
vv                                                                                             DEL PEAK 35(XQ21.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V33, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   12 14
  DEL PEAK 35(XQ21.33) WILD-TYPE 58 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     12   14
  DEL PEAK 35(XQ21.33) WILD-TYPE   58   59
         clus
vv        DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  ABSENT                            12                             58
  PRESENT                           14                             59
[1] 2 2
[1] FALSE
D63V34, continuous
D63V35, continuous
D63V36, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   16 21
  DEL PEAK 35(XQ21.33) WILD-TYPE 32 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     16   21
  DEL PEAK 35(XQ21.33) WILD-TYPE   32   95
                                          clus
vv                                         DEL PEAK 35(XQ21.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           21
                                          clus
vv                                         DEL PEAK 35(XQ21.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             95
[1] 2 2
[1] FALSE
D63V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 35(XQ21.33) MUTATED              4          11         20
  DEL PEAK 35(XQ21.33) WILD-TYPE           11          42         64
D63V38, multiclass
              clus
vv             DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  CURRENT USER                            4                             11
  FORMER USER                            11                             42
  NEVER USED                             20                             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V39, continuous
D63V40, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   21  1
  DEL PEAK 35(XQ21.33) WILD-TYPE 71 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     21    1
  DEL PEAK 35(XQ21.33) WILD-TYPE   71   16
         clus
vv        DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  ABSENT                            21                             71
  PRESENT                            1                             16
[1] 2 2
[1] FALSE
D63V41, continuous
                                vv
clus                             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A
  DEL PEAK 35(XQ21.33) MUTATED      0   7   15    8  2   2    0    2   7  0   0
  DEL PEAK 35(XQ21.33) WILD-TYPE    1  27   54   22  4   8    7    7  29  2   2
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 35(XQ21.33) MUTATED     3  1   0  2
  DEL PEAK 35(XQ21.33) WILD-TYPE  14  7   1 14
D63V42, multiclass
      clus
vv     DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  T1A1                            0                              1
  T1B                             7                             27
  T1B1                           15                             54
  T1B2                            8                             22
  T2                              2                              4
  T2A                             2                              8
  T2A1                            0                              7
  T2A2                            2                              7
  T2B                             7                             29
  T3                              0                              2
  T3A                             0                              2
  T3B                             3                             14
  T4                              1                              7
  TIS                             0                              1
  TX                              2                             14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 35(XQ21.33) MUTATED         2        0         0         1        6
  DEL PEAK 35(XQ21.33) WILD-TYPE       3        1         1         0       27
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 35(XQ21.33) MUTATED          16         9        0         2
  DEL PEAK 35(XQ21.33) WILD-TYPE        61        27        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 35(XQ21.33) MUTATED            0          1        10         0
  DEL PEAK 35(XQ21.33) WILD-TYPE          5          6        33         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 35(XQ21.33) MUTATED            0          8         0         3
  DEL PEAK 35(XQ21.33) WILD-TYPE          3         34         7         9
D63V44, multiclass
            clus
vv           DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              6                             27
  STAGE IB1                            16                             61
  STAGE IB2                             9                             27
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                            10                             33
  STAGE III                             0                              1
  STAGE IIIA                            0                              3
  STAGE IIIB                            8                             34
  STAGE IVA                             0                              7
  STAGE IVB                             3                              9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
