[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTCESC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/11541273/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/11555655/transformed.cor.cli.txt"

nPatients in clinical file=250, in cluster file=295, common to both=238
[1]  63 238
[1] "AMP PEAK  1(1P31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           81                           157 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           81                           157 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          128                           110 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          128                           110 
[1] "AMP PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        128                         110 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        128                         110 
[1] "AMP PEAK  4(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           65                           173 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           65                           173 
[1] "AMP PEAK  5(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           38                           200 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           38                           200 
[1] "AMP PEAK  6(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                           184                             54 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                           184                             54 
[1] "AMP PEAK  7(3Q28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                        183                          55 
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                        183                          55 
[1] "AMP PEAK  8(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                         16                         222 
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                         16                         222 
[1] "AMP PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           106                            132 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           106                            132 
[1] "AMP PEAK 10(6P21.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                            64                            174 
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                            64                            174 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           44                           194 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           44                           194 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            97                            141 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            97                            141 
[1] "AMP PEAK 13(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           51                           187 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           51                           187 
[1] "AMP PEAK 14(11P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                          19                          219 
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                          19                          219 
[1] "AMP PEAK 15(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            32                            206 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            32                            206 
[1] "AMP PEAK 16(11Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                            42                            196 
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                            42                            196 
[1] "AMP PEAK 17(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                            54                            184 
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                            54                            184 
[1] "AMP PEAK 18(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          58                          180 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          58                          180 
[1] "AMP PEAK 19(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                            61                            177 
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                            61                            177 
[1] "AMP PEAK 20(16P13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                             49                             189 
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                             49                             189 
[1] "AMP PEAK 21(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                          47                          191 
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                          47                          191 
[1] "AMP PEAK 22(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            65                            173 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            65                            173 
[1] "AMP PEAK 23(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                            30                            208 
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                            30                            208 
[1] "AMP PEAK 24(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                            37                            201 
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                            37                            201 
[1] "AMP PEAK 25(19Q13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                             76                             162 
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                             76                             162 
[1] "AMP PEAK 26(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                            110                             128 
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                            110                             128 
[1] "AMP PEAK 27(21Q22.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                             40                             198 
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                             40                             198 
[1] "AMP PEAK 28(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         59                         179 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         59                         179 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            32                            206 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            32                            206 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           30                           208 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           30                           208 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           48                           190 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           48                           190 
[1] "DEL PEAK  4(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          104                           134 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          104                           134 
[1] "DEL PEAK  5(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                          106                           132 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                          106                           132 
[1] "DEL PEAK  6(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                           81                           157 
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                           81                           157 
[1] "DEL PEAK  7(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           79                           159 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           79                           159 
[1] "DEL PEAK  8(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                           92                           146 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                           92                           146 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           61                           177 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           61                           177 
[1] "DEL PEAK 10(5Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                           58                           180 
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                           58                           180 
[1] "DEL PEAK 11(6P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                           36                           202 
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                           36                           202 
[1] "DEL PEAK 12(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         83                         155 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         83                         155 
[1] "DEL PEAK 13(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                         51                         187 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                         51                         187 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           85                           153 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           85                           153 
[1] "DEL PEAK 15(8P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                           78                           160 
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                           78                           160 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             71                             167 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             71                             167 
[1] "DEL PEAK 17(11P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            82                            156 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            82                            156 
[1] "DEL PEAK 18(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                           132                            106 
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                           132                            106 
[1] "DEL PEAK 19(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                         131                          107 
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                         131                          107 
[1] "DEL PEAK 20(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                             82                             156 
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                             82                             156 
[1] "DEL PEAK 21(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            96                            142 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            96                            142 
[1] "DEL PEAK 22(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                             40                             198 
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                             40                             198 
[1] "DEL PEAK 23(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            51                            187 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            51                            187 
[1] "DEL PEAK 24(16Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                            44                            194 
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                            44                            194 
[1] "DEL PEAK 25(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            45                            193 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            45                            193 
[1] "DEL PEAK 26(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                          86                          152 
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                          86                          152 
[1] "DEL PEAK 27(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                            40                            198 
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                            40                            198 
[1] "DEL PEAK 28(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            66                            172 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            66                            172 
[1] "DEL PEAK 29(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            82                            156 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            82                            156 
[1] "DEL PEAK 30(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                             31                             207 
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                             31                             207 
[1] "DEL PEAK 31(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            31                            207 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            31                            207 
[1] "DEL PEAK 32(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                            50                            188 
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                            50                            188 
[1] "DEL PEAK 33(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             69                             169 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             69                             169 
[1] "DEL PEAK 34(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           57                           181 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           57                           181 
[1] "DEL PEAK 35(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            45                            193 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            45                            193 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                    
 [2] "VITALSTATUS"                                     
 [3] "DAYSTODEATH"                                     
 [4] "DAYSTOLASTFOLLOWUP"                              
 [5] "PRIMARYSITEOFDISEASE"                            
 [6] "NEOPLASM.DISEASESTAGE"                           
 [7] "PATHOLOGY.T.STAGE"                               
 [8] "PATHOLOGY.N.STAGE"                               
 [9] "PATHOLOGY.M.STAGE"                               
[10] "DCCUPLOADDATE"                                   
[11] "GENDER"                                          
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                
[13] "HISTOLOGICALTYPE"                                
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"          
[15] "NUMBERPACKYEARSSMOKED"                           
[16] "NUMBER.OF.LYMPH.NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCHNUMBER"                                     
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASMHISTOLOGICGRADE"                         
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_TOTAL_DOSE"                            
[30] "RADIATION_THERAPY_TYPE"                          
[31] "RADIATION_THERAPY_STATUS"                        
[32] "RADIATION_THERAPY_SITE"                          
[33] "RADIATION_ADJUVANT_UNITS"                        
[34] "PREGNANCIES_COUNT_TOTAL"                         
[35] "PREGNANCIES_COUNT_STILLBIRTH"                    
[36] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[38] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[39] "PREGNANCIES_COUNT_ECTOPIC"                       
[40] "PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[41] "POS_LYMPH_NODE_LOCATION"                         
[42] "MENOPAUSE_STATUS"                                
[43] "LYMPHOVASCULAR_INVOLVEMENT"                      
[44] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[45] "LYMPH_NODES_EXAMINED"                            
[46] "KERATINIZATION_SQUAMOUS_CELL"                    
[47] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[48] "HYSTERECTOMY_TYPE"                               
[49] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[50] "HEIGHT_CM_AT_DIAGNOSIS"                          
[51] "FEDPET_OR_CT_RESULTS"                            
[52] "CORPUS_INVOLVEMENT"                              
[53] "CHEMO_CONCURRENT_TYPE"                           
[54] "CERVIX_SUV_RESULTS"                              
[55] "CAUSE_OF_DEATH"                                  
[56] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[57] "AGE_AT_DIAGNOSIS"                                
[58] "STAGE_EVENT.CLINICAL_STAGE"                      

Input Data has 58 rows and 238 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
        1505         1735          720           NA           NA           NA 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
        1112         4385         5385         5271           NA           NA 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
          NA           NA           NA         1409          919           NA 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
        1756         1617           NA           NA           NA           NA 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
          NA           NA          109         1345         2226         2234 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
        2526         2383           NA         1169           25         1582 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
         548           NA          621         5564         4694           NA 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
          NA           NA          619         4482           NA         2602 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
        1846           NA           NA           NA           83         1551 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
          NA          254         2305         3039           NA           NA 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
         186          636          136           34         1791         1544 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1367         1218         2669         1791           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        3589         3609          699          512           NA          533 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
          NA           23          376           53           40           25 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
          19          397           36          441           41           41 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
         441           55          385          390            8          453 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
          45          423          457          456          455          413 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
         410           11          383         1398          799          202 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
          46           NA           NA           13           18           18 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
          44            4          489            2          123            1 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
          11           36           NA          721           68            3 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
           2            3            3           NA            1          619 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
         241          211          447          602          186          144 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
          37          725           28           66           20           31 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
          44           48           45           25          107           41 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
          40           60           34          274          773          217 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
          NA          632          454          287         4483         4172 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
          NA         3571         2949         2394         2493          808 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
        1106          834           NA          747          652          623 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
         474          306          156          204           NA         5957 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AV TCGA-LP-A4AW TCGA-LP-A4AX 
         922          243          343           NA           27            2 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
           9           25            6          422            1          165 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
         904            2          132          167           90          474 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
         406          485          103          491          534          428 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
         483          179          190          316          596          118 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
          NA           NA           NA         1864           NA         1050 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
         883          615          428           NA         1628           NA 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
        1400          708           NA         1507           NA           NA 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
          NA           NA          707         1365         1295         1280 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
        1333         1197         1185          549 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=164,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBERPACKYEARSSMOKED':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TUMOR_SAMPLE_PROCUREMENT_COUNTRY':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASMHISTOLOGICGRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'RADIATION_TOTAL_DOSE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 31:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'RADIATION_THERAPY_SITE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 33:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 40:'PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 41:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 42:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 45:'LYMPH_NODES_EXAMINED':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 47:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 48:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 49:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 50:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 51:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 52:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 53:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 54:'CERVIX_SUV_RESULTS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 55:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 56:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 57:'AGE_AT_DIAGNOSIS':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 58:'STAGE_EVENT.CLINICAL_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                             
 [2] "PATHOLOGY.T.STAGE"                               
 [3] "PATHOLOGY.N.STAGE"                               
 [4] "PATHOLOGY.M.STAGE"                               
 [5] "HISTOLOGICAL.TYPE"                               
 [6] "RADIATIONS.RADIATION.REGIMENINDICATION"          
 [7] "NUMBERPACKYEARSSMOKED"                           
 [8] "NUMBER.OF.LYMPH.NODES"                           
 [9] "RACE"                                            
[10] "ETHNICITY"                                       
[11] "WEIGHT_KG_AT_DIAGNOSIS"                          
[12] "TUMOR_STATUS"                                    
[13] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[14] "NEOPLASMHISTOLOGICGRADE"                         
[15] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[16] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[17] "TOBACCO_SMOKING_HISTORY"                         
[18] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[19] "RADIATION_TOTAL_DOSE"                            
[20] "RADIATION_THERAPY_TYPE"                          
[21] "RADIATION_THERAPY_STATUS"                        
[22] "RADIATION_THERAPY_SITE"                          
[23] "RADIATION_ADJUVANT_UNITS"                        
[24] "PREGNANCIES_COUNT_TOTAL"                         
[25] "PREGNANCIES_COUNT_STILLBIRTH"                    
[26] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[27] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[28] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[29] "PREGNANCIES_COUNT_ECTOPIC"                       
[30] "POS_LYMPH_NODE_LOCATION"                         
[31] "MENOPAUSE_STATUS"                                
[32] "LYMPHOVASCULAR_INVOLVEMENT"                      
[33] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[34] "LYMPH_NODES_EXAMINED"                            
[35] "KERATINIZATION_SQUAMOUS_CELL"                    
[36] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[37] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[38] "HEIGHT_CM_AT_DIAGNOSIS"                          
[39] "CORPUS_INVOLVEMENT"                              
[40] "CERVIX_SUV_RESULTS"                              
[41] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[42] "AGE_AT_DIAGNOSIS"                                
[43] "STAGE_EVENT.CLINICAL_STAGE"                      
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 238 columns, 1 survival variables, and 43 non-survival variables.
AGE, nv=58, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
121  50   9   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  121    50    11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
121  50   9   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


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

Clustering(1) Variable = AMP PEAK  1(1P31.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P31.3) MUTATED    60  19
  AMP PEAK  1(1P31.3) WILD-TYPE 123  31
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           79                           154 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           19                            31 
$`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         0.76         1.74         0.62         1.18         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A97N 
       14.50         1.81        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 
        6.71       195.85        30.31         7.99         0.30         0.20 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       13.87         0.03         0.07         2.96        13.35         3.39 
TCGA-Q1-A6DW TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EG TCGA-VS-A8EJ 
       17.56        19.59        93.99        12.16        29.03        19.96 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 
       11.51        49.55        31.27        42.58        42.08        39.35 
TCGA-VS-A9U5 
       38.96 

$`AMP PEAK  1(1P31.3) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK 
       23.67        11.44        68.84        18.74       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 
      173.29         5.46        19.86        67.46        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       57.73        53.16        35.61        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.18        73.45        83.05        78.35        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7CL 
       52.01        18.02        20.42       182.93       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ 
        9.34         8.35        75.78        99.91         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        4.47        58.88        50.76        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       36.76       117.99        22.98        16.83        16.18        17.52 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
       12.36         1.32         0.82        13.05        14.50         1.35 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZE 
       12.66        12.82         0.26        14.89         1.48        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.43         1.45         0.13         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.36        23.70         0.10         0.10        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70         6.12         4.73         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.92         2.17         0.66         1.02         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        3.52         1.32         1.97         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
        7.13        21.67         9.44       147.39       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        78.71        81.96        26.56        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       24.56        21.44        15.58        10.06         5.13        21.11 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A8JM TCGA-MY-A5BD 
       11.28         0.89         0.07         0.82         5.42        29.72 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O 
        4.34         5.49        15.58        15.95        16.14        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       15.88         5.88         6.25        10.39         3.88        11.67 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL 
       61.28        10.03        34.52        20.22        14.07        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y 
       32.15        46.03        23.28        39.78        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A958 TCGA-WL-A834 
       23.24        44.88        43.82        18.05 

  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                        182.93 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                        14.93                         16.16 
[1] "0.0 - 195.8 (14.9)" "0.0 - 182.9 (16.2)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  1(1P31.3) MUTATED   37 20     3
  AMP PEAK  1(1P31.3) WILD-TYPE 84 30     8
D1V3, multiclass
       clus
vv      AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  T1                             37                            84
  T2                             20                            30
  T3+T4                           3                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   35 16
  AMP PEAK  1(1P31.3) WILD-TYPE 76 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     35   16
  AMP PEAK  1(1P31.3) WILD-TYPE   76   31
   clus
vv  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  0                          35                            76
  1                          16                            31
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  1(1P31.3) MUTATED   34  2 30
  AMP PEAK  1(1P31.3) WILD-TYPE 57  6 63
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  M0                          34                            57
  M1                           2                             6
  MX                          30                            63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1P31.3) MUTATED               1                               73
  AMP PEAK  1(1P31.3) WILD-TYPE             4                              124
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  1(1P31.3) MUTATED                                               1
  AMP PEAK  1(1P31.3) WILD-TYPE                                             4
                               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                                              2
  AMP PEAK  1(1P31.3) WILD-TYPE                                            4
D1V6, multiclass
                                               clus
vv                                              AMP PEAK  1(1P31.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       73
  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  1(1P31.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        124
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P31.3) MUTATED     9  72
  AMP PEAK  1(1P31.3) WILD-TYPE  21 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      9   72
  AMP PEAK  1(1P31.3) WILD-TYPE   21  136
     clus
vv    AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  NO                            9                            21
  YES                          72                           136
[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                           8
  AMP PEAK  1(1P31.3) WILD-TYPE                        16
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  1(1P31.3) MUTATED                                           0    56
  AMP PEAK  1(1P31.3) WILD-TYPE                                         1   113
D1V10, multiclass
                                           clus
vv                                          AMP PEAK  1(1P31.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              56
                                           clus
vv                                          AMP PEAK  1(1P31.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED    3 54
  AMP PEAK  1(1P31.3) WILD-TYPE 13 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      3   54
  AMP PEAK  1(1P31.3) WILD-TYPE   13   95
                        clus
vv                       AMP PEAK  1(1P31.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       AMP PEAK  1(1P31.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                            95
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   18 10
  AMP PEAK  1(1P31.3) WILD-TYPE 53 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     18   10
  AMP PEAK  1(1P31.3) WILD-TYPE   53   15
            clus
vv           AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  TUMOR FREE                          18                            53
  WITH TUMOR                          10                            15
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  1(1P31.3) MUTATED        9      2       1      5       3
  AMP PEAK  1(1P31.3) WILD-TYPE     14      3       0      5       4
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK  1(1P31.3) MUTATED              55       6
  AMP PEAK  1(1P31.3) WILD-TYPE           123       8
D1V14, multiclass
               clus
vv              AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  BRAZIL                                  9                            14
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  5                             5
  UKRAINE                                 3                             4
  UNITED STATES                          55                           123
  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 36 35  0  5
  AMP PEAK  1(1P31.3) WILD-TYPE 13 70 62  1  9
D1V15, multiclass
    clus
vv   AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  G1                           4                            13
  G2                          36                            70
  G3                          35                            62
  G4                           0                             1
  GX                           5                             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V16, continuous
D1V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  1(1P31.3) MUTATED                                             9
  AMP PEAK  1(1P31.3) WILD-TYPE                                          22
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  1(1P31.3) MUTATED                                        4
  AMP PEAK  1(1P31.3) WILD-TYPE                                      4
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  1(1P31.3) MUTATED                                                 0
  AMP PEAK  1(1P31.3) WILD-TYPE                                               2
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  1(1P31.3) MUTATED               18                  39
  AMP PEAK  1(1P31.3) WILD-TYPE             34                  73
D1V18, multiclass
                                                 clus
vv                                                AMP PEAK  1(1P31.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           18
  LIFELONG NON-SMOKER                                                      39
                                                 clus
vv                                                AMP PEAK  1(1P31.3) 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                                                             34
  LIFELONG NON-SMOKER                                                        73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V19, continuous
D1V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  1(1P31.3) MUTATED             7       22             2        3
  AMP PEAK  1(1P31.3) WILD-TYPE          12       53            10        9
D1V21, multiclass
               clus
vv              AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               22                            53
  EXTERNAL BEAM                           2                            10
  INTERNAL                                3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     9             6
  AMP PEAK  1(1P31.3) WILD-TYPE                  19            10
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                           9                            19
  REGIONAL SITE                                 6                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V24, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   12  1
  AMP PEAK  1(1P31.3) WILD-TYPE 22  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     12    1
  AMP PEAK  1(1P31.3) WILD-TYPE   22    2
     clus
vv    AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  CGY                          12                            22
  GY                            1                             2
[1] 2 2
[1] FALSE
D1V25, continuous
D1V26, continuous
D1V27, continuous
D1V28, continuous
D1V29, continuous
D1V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  1(1P31.3) MUTATED                                     1
  AMP PEAK  1(1P31.3) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  1(1P31.3) MUTATED                                     0
  AMP PEAK  1(1P31.3) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  1(1P31.3) MUTATED                        10                       0
  AMP PEAK  1(1P31.3) WILD-TYPE                      19                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  1(1P31.3) MUTATED                         2
  AMP PEAK  1(1P31.3) WILD-TYPE                       5
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                             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)
  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                                                5
  AMP PEAK  1(1P31.3) WILD-TYPE                                             11
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  1(1P31.3) MUTATED                                                                                  31
  AMP PEAK  1(1P31.3) WILD-TYPE                                                                                37
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  1(1P31.3) MUTATED                                                                                             31
  AMP PEAK  1(1P31.3) WILD-TYPE                                                                                           74
D1V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  1(1P31.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     31
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          31
                                                                                              clus
vv                                                                                             AMP PEAK  1(1P31.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       37
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V33, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   21 24
  AMP PEAK  1(1P31.3) WILD-TYPE 47 46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     21   24
  AMP PEAK  1(1P31.3) WILD-TYPE   47   46
         clus
vv        AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  ABSENT                           21                            47
  PRESENT                          24                            46
[1] 2 2
[1] FALSE
D1V34, continuous
D1V35, continuous
D1V36, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   17 31
  AMP PEAK  1(1P31.3) WILD-TYPE 26 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     17   31
  AMP PEAK  1(1P31.3) WILD-TYPE   26   63
                                          clus
vv                                         AMP PEAK  1(1P31.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          31
                                          clus
vv                                         AMP PEAK  1(1P31.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            63
[1] 2 2
[1] FALSE
D1V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  1(1P31.3) MUTATED              3           9         21
  AMP PEAK  1(1P31.3) WILD-TYPE            7          40         36
D1V38, multiclass
              clus
vv             AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  CURRENT USER                           3                             7
  FORMER USER                            9                            40
  NEVER USED                            21                            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V39, continuous
D1V40, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   26  6
  AMP PEAK  1(1P31.3) WILD-TYPE 63 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     26    6
  AMP PEAK  1(1P31.3) WILD-TYPE   63   10
         clus
vv        AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  ABSENT                           26                            63
  PRESENT                           6                            10
[1] 2 2
[1] FALSE
D1V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  1(1P31.3) MUTATED     0    1   8   22    6  2   5    3    2   8  1
  AMP PEAK  1(1P31.3) WILD-TYPE   1    0  22   43   18  2   3    4    7  14  0
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK  1(1P31.3) MUTATED     2  0   0  7
  AMP PEAK  1(1P31.3) WILD-TYPE   6  2   1  7
D1V42, multiclass
      clus
vv     AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  T1A                            0                             1
  T1A1                           1                             0
  T1B                            8                            22
  T1B1                          22                            43
  T1B2                           6                            18
  T2                             2                             2
  T2A                            5                             3
  T2A1                           3                             4
  T2A2                           2                             7
  T2B                            8                            14
  T3                             1                             0
  T3B                            2                             6
  T4                             0                             2
  TIS                            0                             1
  TX                             7                             7
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  1(1P31.3) MUTATED         2        0         1         0       12
  AMP PEAK  1(1P31.3) WILD-TYPE       2        2         0         1       19
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  1(1P31.3) MUTATED          24         6        2         2
  AMP PEAK  1(1P31.3) WILD-TYPE        45        26        1         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  1(1P31.3) MUTATED            2          3         9         1
  AMP PEAK  1(1P31.3) WILD-TYPE          3          4        18         0
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  1(1P31.3) MUTATED           12         1         2
  AMP PEAK  1(1P31.3) WILD-TYPE         22         2         5
D1V44, multiclass
            clus
vv           AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                             0                             2
  STAGE IA1                            1                             0
  STAGE IA2                            0                             1
  STAGE IB                            12                            19
  STAGE IB1                           24                            45
  STAGE IB2                            6                            26
  STAGE II                             2                             1
  STAGE IIA                            2                             4
  STAGE IIA1                           2                             3
  STAGE IIA2                           3                             4
  STAGE IIB                            9                            18
  STAGE III                            1                             0
  STAGE IIIB                          12                            22
  STAGE IVA                            1                             2
  STAGE IVB                            2                             5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   94 30
  AMP PEAK  2(1Q21.3) WILD-TYPE 89 20
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          124                           109 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           30                            20 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        57.04        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF 
      173.29        82.85         5.46        31.40        46.32        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP 
       38.99        35.61         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7CJ 
       44.22        78.35       100.14        17.85       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH 
      134.33        15.48        94.95        13.61         2.73        45.83 
TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DR-A0ZL 
        8.35        23.51        27.52         1.12        44.94        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-DS-A7WI 
       58.88         2.66       117.99        22.98        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 
        0.76         1.74         1.32         0.82         0.62         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.50         1.81        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 
       13.58         0.36        12.59         1.51         0.59         0.59 
TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK 
       16.08         1.18        23.70         2.24         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        0.03         6.94        14.70        19.79         6.12         4.73 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A40J TCGA-HG-A2PA TCGA-HG-A9SC 
       23.84         2.17         1.45         1.35        25.41         7.13 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
       20.78        14.93         9.44       117.40        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       36.36        21.44        20.48         5.13         6.71       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y 
       30.31         7.99        11.28         0.30         0.82        13.87 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-Q1-A73Q 
        0.07         2.96        13.35        15.95        17.56         5.88 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH 
        6.25        19.59        93.99        12.16        10.03        20.22 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        53.52        32.15        46.03        11.51        49.55 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       31.27        16.64         4.73        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 
       23.67        11.44        68.84        19.86        67.46        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       35.01        57.73        40.93        73.18        73.45        83.05 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43         0.82        52.01        18.02        20.42       182.93 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19        85.55        60.69         9.34 
TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       50.99        75.78        99.91         6.12        20.91         4.47 
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         1.18        14.50         1.35 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A78R 
       12.66        12.82         0.26        14.89         1.48        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         0.66         1.02 
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        26.56        27.42         3.29        24.56        15.58 
TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MU-A5YI 
       10.06        21.11         0.89         0.07         0.20         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A6DT 
        5.42        29.72         4.34         5.49        15.58         3.39 
TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       16.14        14.07        15.88        10.39         3.88        11.67 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8QA TCGA-VS-A8QH 
       61.28        34.52        29.03        14.07        23.28        39.78 
TCGA-VS-A94Z 
       23.24 

  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                        182.93 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        16.36                         15.58 
[1] "0.0 - 195.8 (16.4)" "0.0 - 182.9 (15.6)"
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  2(1Q21.3) MUTATED   56 35     6
  AMP PEAK  2(1Q21.3) WILD-TYPE 65 15     5
D2V3, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                             56                            65
  T2                             35                            15
  T3+T4                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   57 26
  AMP PEAK  2(1Q21.3) WILD-TYPE 54 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     57   26
  AMP PEAK  2(1Q21.3) WILD-TYPE   54   21
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                          57                            54
  1                          26                            21
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  2(1Q21.3) MUTATED   50  6 50
  AMP PEAK  2(1Q21.3) WILD-TYPE 41  2 43
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                          50                            41
  M1                           6                             2
  MX                          50                            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED               3                              109
  AMP PEAK  2(1Q21.3) WILD-TYPE             2                               88
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                               2
  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                                              3
  AMP PEAK  2(1Q21.3) WILD-TYPE                                            3
D2V6, multiclass
                                               clus
vv                                              AMP PEAK  2(1Q21.3) MUTATED
  ADENOSQUAMOUS                                                           3
  CERVICAL SQUAMOUS CELL CARCINOMA                                      109
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              AMP PEAK  2(1Q21.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         88
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    17 111
  AMP PEAK  2(1Q21.3) WILD-TYPE  13  97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     17  111
  AMP PEAK  2(1Q21.3) WILD-TYPE   13   97
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           17                            13
  YES                         111                            97
[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                          17
  AMP PEAK  2(1Q21.3) WILD-TYPE                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           0    89
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         1    80
D2V10, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                              12
  BLACK OR AFRICAN AMERICAN                                          17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              89
                                           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                             1
  WHITE                                                                80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED    5 78
  AMP PEAK  2(1Q21.3) WILD-TYPE 11 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      5   78
  AMP PEAK  2(1Q21.3) WILD-TYPE   11   71
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          78
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                            71
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   37 15
  AMP PEAK  2(1Q21.3) WILD-TYPE 34 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     37   15
  AMP PEAK  2(1Q21.3) WILD-TYPE   34   10
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  TUMOR FREE                          37                            34
  WITH TUMOR                          15                            10
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  2(1Q21.3) MUTATED       17      2       1      6       3
  AMP PEAK  2(1Q21.3) WILD-TYPE      6      3       0      4       4
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK  2(1Q21.3) MUTATED              90       9
  AMP PEAK  2(1Q21.3) WILD-TYPE            88       5
D2V14, multiclass
               clus
vv              AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  BRAZIL                                 17                             6
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  6                             4
  UKRAINE                                 3                             4
  UNITED STATES                          90                            88
  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 57 55  1  7
  AMP PEAK  2(1Q21.3) WILD-TYPE 10 49 42  0  7
D2V15, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  G1                           7                            10
  G2                          57                            49
  G3                          55                            42
  G4                           1                             0
  GX                           7                             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V16, continuous
D2V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  2(1Q21.3) MUTATED                                            15
  AMP PEAK  2(1Q21.3) WILD-TYPE                                          16
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  2(1Q21.3) MUTATED                                        4
  AMP PEAK  2(1Q21.3) WILD-TYPE                                      4
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  2(1Q21.3) MUTATED                                                 1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  2(1Q21.3) MUTATED               31                  62
  AMP PEAK  2(1Q21.3) WILD-TYPE             21                  50
D2V18, multiclass
                                                 clus
vv                                                AMP PEAK  2(1Q21.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           31
  LIFELONG NON-SMOKER                                                      62
                                                 clus
vv                                                AMP PEAK  2(1Q21.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             21
  LIFELONG NON-SMOKER                                                        50
[1] 5 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       42             3        5
  AMP PEAK  2(1Q21.3) WILD-TYPE           5       33             9        7
D2V21, multiclass
               clus
vv              AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  COMBINATION                            14                             5
  EXTERNAL                               42                            33
  EXTERNAL BEAM                           3                             9
  INTERNAL                                5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    15            10
  AMP PEAK  2(1Q21.3) WILD-TYPE                  13             6
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                          15                            13
  REGIONAL SITE                                10                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V24, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   20  2
  AMP PEAK  2(1Q21.3) WILD-TYPE 14  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     20    2
  AMP PEAK  2(1Q21.3) WILD-TYPE   14    1
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  CGY                          20                            14
  GY                            2                             1
[1] 2 2
[1] FALSE
D2V25, continuous
D2V26, continuous
D2V27, continuous
D2V28, continuous
D2V29, continuous
D2V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  2(1Q21.3) MUTATED                                     1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  2(1Q21.3) MUTATED                                     1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  2(1Q21.3) MUTATED                        15                       0
  AMP PEAK  2(1Q21.3) WILD-TYPE                      14                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  2(1Q21.3) MUTATED                         4
  AMP PEAK  2(1Q21.3) WILD-TYPE                       3
D2V31, multiclass
                                     clus
vv                                    AMP PEAK  2(1Q21.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                      15
  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                                        14
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  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                                                9
  AMP PEAK  2(1Q21.3) WILD-TYPE                                              7
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  2(1Q21.3) MUTATED                                                                                  40
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                                28
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  2(1Q21.3) MUTATED                                                                                             57
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                                           48
D2V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  2(1Q21.3) 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)                                     40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          57
                                                                                              clus
vv                                                                                             AMP PEAK  2(1Q21.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V33, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   34 38
  AMP PEAK  2(1Q21.3) WILD-TYPE 34 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     34   38
  AMP PEAK  2(1Q21.3) WILD-TYPE   34   32
         clus
vv        AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ABSENT                           34                            34
  PRESENT                          38                            32
[1] 2 2
[1] FALSE
D2V34, continuous
D2V35, continuous
D2V36, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   22 49
  AMP PEAK  2(1Q21.3) WILD-TYPE 21 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     22   49
  AMP PEAK  2(1Q21.3) WILD-TYPE   21   45
                                          clus
vv                                         AMP PEAK  2(1Q21.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          49
                                          clus
vv                                         AMP PEAK  2(1Q21.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            45
[1] 2 2
[1] FALSE
D2V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  2(1Q21.3) MUTATED              5          23         32
  AMP PEAK  2(1Q21.3) WILD-TYPE            5          26         25
D2V38, multiclass
              clus
vv             AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  CURRENT USER                           5                             5
  FORMER USER                           23                            26
  NEVER USED                            32                            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V39, continuous
D2V40, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   42  9
  AMP PEAK  2(1Q21.3) WILD-TYPE 47  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     42    9
  AMP PEAK  2(1Q21.3) WILD-TYPE   47    7
         clus
vv        AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ABSENT                           42                            47
  PRESENT                           9                             7
[1] 2 2
[1] FALSE
D2V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  2(1Q21.3) MUTATED     1    0  11   33   11  2   7    7    2  17  1
  AMP PEAK  2(1Q21.3) WILD-TYPE   0    1  19   32   13  2   1    0    7   5  0
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK  2(1Q21.3) MUTATED     5  0   0 11
  AMP PEAK  2(1Q21.3) WILD-TYPE   3  2   1  3
D2V42, multiclass
      clus
vv     AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1A                            1                             0
  T1A1                           0                             1
  T1B                           11                            19
  T1B1                          33                            32
  T1B2                          11                            13
  T2                             2                             2
  T2A                            7                             1
  T2A1                           7                             0
  T2A2                           2                             7
  T2B                           17                             5
  T3                             1                             0
  T3B                            5                             3
  T4                             0                             2
  TIS                            0                             1
  TX                            11                             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"
D2V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  2(1Q21.3) MUTATED         3        1         0         0       18
  AMP PEAK  2(1Q21.3) WILD-TYPE       1        1         1         1       13
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED          31        13        2         3
  AMP PEAK  2(1Q21.3) WILD-TYPE        38        19        1         3
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  2(1Q21.3) MUTATED            5          3        17         1
  AMP PEAK  2(1Q21.3) WILD-TYPE          0          4        10         0
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  2(1Q21.3) MUTATED           20         2         5
  AMP PEAK  2(1Q21.3) WILD-TYPE         14         1         2
D2V44, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              3                             1
  STAGE IA                             1                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            18                            13
  STAGE IB1                           31                            38
  STAGE IB2                           13                            19
  STAGE II                             2                             1
  STAGE IIA                            3                             3
  STAGE IIA1                           5                             0
  STAGE IIA2                           3                             4
  STAGE IIB                           17                            10
  STAGE III                            1                             0
  STAGE IIIB                          20                            14
  STAGE IVA                            2                             1
  STAGE IVB                            5                             2
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(1Q44) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  3(1Q44) MUTATED   94 30
  AMP PEAK  3(1Q44) WILD-TYPE 89 20
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        124                         109 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         30                          20 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       49.48        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH 
       82.85         5.46        31.40        46.32        53.16        38.99 
TCGA-C5-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-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CH 
       83.05        78.35       100.14        52.01        17.85       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A7XC 
      101.82       134.33        15.48        94.95         2.73        50.99 
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-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A411 
        8.28         1.74         1.32         0.62        13.05         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.50         1.81        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG 
       13.58        13.48         0.36        12.59        45.96         1.51 
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        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.10         0.03         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A40J 
        6.12         4.73        23.84         2.17         1.45         1.35 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LC 
       25.41         7.13        20.78        14.93         9.44       117.40 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 
       81.96        26.56        36.36        21.44        20.48         5.13 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 
        6.71       195.85        30.31         7.99        11.28         0.30 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.82        13.87         0.07         2.96        13.35        15.95 
TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG 
       17.56         5.88         6.25        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        34.52        20.22        19.96        53.52        32.15 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A954 
       11.51        49.55        31.27        16.64         4.73        42.58 
TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.08        39.35        38.96        18.05 

$`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         0.82        18.02        20.42       182.93        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19        85.55        60.69         9.34        13.61 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
       75.78        99.91         6.12        20.91         4.47        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 
        0.76        12.36         0.82         1.18        14.50         1.35 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2H1 
       12.66        12.82         0.26        14.89         1.48        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         0.66         1.02         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-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        10.06        21.11 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.89         0.07         0.20         0.03         5.42        29.72 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O 
        4.34         5.49        15.58         3.39        16.14        14.07 
TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EG 
       15.88        10.39         3.88        11.67        61.28        29.03 
TCGA-VS-A8EI TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94Z TCGA-VS-A952 
       14.07        46.03        23.28        39.78        23.24        44.88 
TCGA-VS-A958 
       43.82 

  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                      182.93 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                      17.08                       14.89 
[1] "0.0 - 195.8 (17.1)" "0.0 - 182.9 (14.9)"
[1] "hr=" "1.2"
D3V2, continuous
                             vv
clus                          T1 T2 T3+T4
  AMP PEAK  3(1Q44) MUTATED   56 34     7
  AMP PEAK  3(1Q44) WILD-TYPE 65 16     4
D3V3, multiclass
       clus
vv      AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  T1                           56                          65
  T2                           34                          16
  T3+T4                         7                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   54 28
  AMP PEAK  3(1Q44) WILD-TYPE 57 19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     54   28
  AMP PEAK  3(1Q44) WILD-TYPE   57   19
   clus
vv  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  0                        54                          57
  1                        28                          19
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK  3(1Q44) MUTATED   51  6 48
  AMP PEAK  3(1Q44) WILD-TYPE 40  2 45
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  M0                        51                          40
  M1                         6                           2
  MX                        48                          45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(1Q44) MUTATED               3                              110
  AMP PEAK  3(1Q44) WILD-TYPE             2                               87
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  3(1Q44) MUTATED                                               2
  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                                              2
  AMP PEAK  3(1Q44) WILD-TYPE                                            4
D3V6, multiclass
                                               clus
vv                                              AMP PEAK  3(1Q44) MUTATED
  ADENOSQUAMOUS                                                         3
  CERVICAL SQUAMOUS CELL CARCINOMA                                    110
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                  11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          2
                                               clus
vv                                              AMP PEAK  3(1Q44) WILD-TYPE
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    20 108
  AMP PEAK  3(1Q44) WILD-TYPE  10 100
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     20  108
  AMP PEAK  3(1Q44) WILD-TYPE   10  100
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         20                          10
  YES                       108                         100
[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                          15
  AMP PEAK  3(1Q44) WILD-TYPE                         9
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q44) MUTATED                                           0    90
  AMP PEAK  3(1Q44) WILD-TYPE                                         1    79
D3V10, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                            13
  BLACK OR AFRICAN AMERICAN                                        15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            90
                                           clus
vv                                          AMP PEAK  3(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    7
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED    5 79
  AMP PEAK  3(1Q44) WILD-TYPE 11 70
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED      5   79
  AMP PEAK  3(1Q44) WILD-TYPE   11   70
                        clus
vv                       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             5                          11
  NOT HISPANIC OR LATINO                        79                          70
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   40 16
  AMP PEAK  3(1Q44) WILD-TYPE 31  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     40   16
  AMP PEAK  3(1Q44) WILD-TYPE   31    9
            clus
vv           AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  TUMOR FREE                        40                          31
  WITH TUMOR                        16                           9
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  3(1Q44) MUTATED       15      2       1      4       3
  AMP PEAK  3(1Q44) WILD-TYPE      8      3       0      6       4
                             vv
clus                          UNITED STATES VIETNAM
  AMP PEAK  3(1Q44) MUTATED              93      10
  AMP PEAK  3(1Q44) WILD-TYPE            85       4
D3V14, multiclass
               clus
vv              AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  BRAZIL                               15                           8
  CANADA                                2                           3
  NIGERIA                               1                           0
  RUSSIA                                4                           6
  UKRAINE                               3                           4
  UNITED STATES                        93                          85
  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 58 56  0  7
  AMP PEAK  3(1Q44) WILD-TYPE 11 48 41  1  7
D3V15, multiclass
    clus
vv   AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  G1                         6                          11
  G2                        58                          48
  G3                        56                          41
  G4                         0                           1
  GX                         7                           7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V16, continuous
D3V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  3(1Q44) MUTATED                                            15
  AMP PEAK  3(1Q44) WILD-TYPE                                          16
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  3(1Q44) MUTATED                                        4
  AMP PEAK  3(1Q44) WILD-TYPE                                      4
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  3(1Q44) MUTATED                                                 1
  AMP PEAK  3(1Q44) WILD-TYPE                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  3(1Q44) MUTATED               32                  60
  AMP PEAK  3(1Q44) WILD-TYPE             20                  52
D3V18, multiclass
                                                 clus
vv                                                AMP PEAK  3(1Q44) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                            15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         1
  CURRENT SMOKER                                                         32
  LIFELONG NON-SMOKER                                                    60
                                                 clus
vv                                                AMP PEAK  3(1Q44) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           20
  LIFELONG NON-SMOKER                                                      52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V19, continuous
D3V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  3(1Q44) MUTATED            16       42             4        4
  AMP PEAK  3(1Q44) WILD-TYPE           3       33             8        8
D3V21, multiclass
               clus
vv              AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  COMBINATION                          16                           3
  EXTERNAL                             42                          33
  EXTERNAL BEAM                         4                           8
  INTERNAL                              4                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    12            10
  AMP PEAK  3(1Q44) WILD-TYPE                  16             6
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                        12                          16
  REGIONAL SITE                              10                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V24, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   18  2
  AMP PEAK  3(1Q44) WILD-TYPE 16  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     18    2
  AMP PEAK  3(1Q44) WILD-TYPE   16    1
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  CGY                        18                          16
  GY                          2                           1
[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                                     2
  AMP PEAK  3(1Q44) WILD-TYPE                                   4
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  3(1Q44) MUTATED                        16                       0
  AMP PEAK  3(1Q44) WILD-TYPE                      13                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  3(1Q44) MUTATED                         4
  AMP PEAK  3(1Q44) WILD-TYPE                       3
D3V31, multiclass
                                     clus
vv                                    AMP PEAK  3(1Q44) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         2
  OTHER LOCATION, SPECIFY                                    16
  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                                      13
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  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                                               11
  AMP PEAK  3(1Q44) WILD-TYPE                                              5
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  3(1Q44) MUTATED                                                                                  40
  AMP PEAK  3(1Q44) WILD-TYPE                                                                                28
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  3(1Q44) MUTATED                                                                                             54
  AMP PEAK  3(1Q44) WILD-TYPE                                                                                           51
D3V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  3(1Q44) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                      11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        54
                                                                                              clus
vv                                                                                             AMP PEAK  3(1Q44) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V33, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   29 41
  AMP PEAK  3(1Q44) WILD-TYPE 39 29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     29   41
  AMP PEAK  3(1Q44) WILD-TYPE   39   29
         clus
vv        AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  ABSENT                         29                          39
  PRESENT                        41                          29
[1] 2 2
[1] FALSE
D3V34, continuous
D3V35, continuous
D3V36, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   21 50
  AMP PEAK  3(1Q44) WILD-TYPE 22 44
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     21   50
  AMP PEAK  3(1Q44) WILD-TYPE   22   44
                                          clus
vv                                         AMP PEAK  3(1Q44) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        50
                                          clus
vv                                         AMP PEAK  3(1Q44) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          44
[1] 2 2
[1] FALSE
D3V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  3(1Q44) MUTATED              5          26         29
  AMP PEAK  3(1Q44) WILD-TYPE            5          23         28
D3V38, multiclass
              clus
vv             AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  CURRENT USER                         5                           5
  FORMER USER                         26                          23
  NEVER USED                          29                          28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V39, continuous
D3V40, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   42  9
  AMP PEAK  3(1Q44) WILD-TYPE 47  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     42    9
  AMP PEAK  3(1Q44) WILD-TYPE   47    7
         clus
vv        AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  ABSENT                         42                          47
  PRESENT                         9                           7
[1] 2 2
[1] FALSE
D3V41, continuous
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  3(1Q44) MUTATED     1    0  10   33   12  3   7    6    2  16  1
  AMP PEAK  3(1Q44) WILD-TYPE   0    1  20   32   12  1   1    1    7   6  0
                             vv
clus                          T3B T4 TIS TX
  AMP PEAK  3(1Q44) MUTATED     6  0   0 10
  AMP PEAK  3(1Q44) WILD-TYPE   2  2   1  4
D3V42, multiclass
      clus
vv     AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  T1A                          1                           0
  T1A1                         0                           1
  T1B                         10                          20
  T1B1                        33                          32
  T1B2                        12                          12
  T2                           3                           1
  T2A                          7                           1
  T2A1                         6                           1
  T2A2                         2                           7
  T2B                         16                           6
  T3                           1                           0
  T3B                          6                           2
  T4                           0                           2
  TIS                          0                           1
  TX                          10                           4
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  3(1Q44) MUTATED         3        1         0         0       16
  AMP PEAK  3(1Q44) WILD-TYPE       1        1         1         1       15
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK  3(1Q44) MUTATED          31        14        2         3          4
  AMP PEAK  3(1Q44) WILD-TYPE        38        18        1         3          1
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIB
  AMP PEAK  3(1Q44) MUTATED            3        18         1         22
  AMP PEAK  3(1Q44) WILD-TYPE          4         9         0         12
                             vv
clus                          STAGE IVA STAGE IVB
  AMP PEAK  3(1Q44) MUTATED           2         4
  AMP PEAK  3(1Q44) WILD-TYPE         1         3
D3V44, multiclass
            clus
vv           AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  STAGE I                            3                           1
  STAGE IA                           1                           1
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                          16                          15
  STAGE IB1                         31                          38
  STAGE IB2                         14                          18
  STAGE II                           2                           1
  STAGE IIA                          3                           3
  STAGE IIA1                         4                           1
  STAGE IIA2                         3                           4
  STAGE IIB                         18                           9
  STAGE III                          1                           0
  STAGE IIIB                        22                          12
  STAGE IVA                          2                           1
  STAGE IVB                          4                           3
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(2P24.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P24.3) MUTATED    50  14
  AMP PEAK  4(2P24.3) WILD-TYPE 133  36
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           64                           169 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           14                            36 
$`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         0.82        60.69         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         1.32         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF 
       14.50         1.81        12.66        14.89        13.91        14.96 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
       12.59        26.27         1.51        16.08         1.18         2.24 
TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY 
        0.10         7.92         6.94        23.84         0.92         0.66 
TCGA-FU-A40J TCGA-IR-A3LA TCGA-IR-A3LC TCGA-JW-A5VJ TCGA-JX-A5QV TCGA-LP-A7HU 
        1.35       137.16       117.40        21.44         7.99         0.20 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73S TCGA-UC-A7PD 
        5.49        15.58        13.35        15.95        10.39        11.67 
TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y 
       93.99        14.07        19.96        49.55        16.64         4.73 
TCGA-VS-A952 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       44.88        39.35        38.96        18.05 

$`AMP PEAK  4(2P24.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      177.04       173.29        82.85        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML 
       30.21        35.01        53.16        38.99         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       40.93         3.58        44.22        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      182.93       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A8XI TCGA-C5-A8XJ 
      147.35        17.19        85.55        94.95         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KM 
       99.91         6.12        20.91         4.47        50.76        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18         8.28         0.76        12.36         1.74 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       12.82         0.26         1.48        15.02        14.99        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
       13.48         0.36        45.96         6.64         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         1.45         0.13         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
        0.36        23.70         0.10         0.07         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       20.35        14.70        19.79         6.12         4.73         1.22 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        3.52         1.32         1.97         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        7.13        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
        5.13         6.71        21.11       195.85        30.31        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.89         0.07         0.30         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A6DT 
        5.42        29.72         0.07         4.34         2.96         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         5.88         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59         3.88        12.16        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       29.03        20.22        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 
       11.51        39.78        31.27        23.24        42.58        42.08 
TCGA-VS-A958 
       43.82 

  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                        195.85 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                       14.925                        16.180 
[1] "0.1 - 137.2 (14.9)" "0.0 - 195.8 (16.2)"
[1] "hr=" "1.3"
D4V2, continuous
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  4(2P24.3) MUTATED   31 16     2
  AMP PEAK  4(2P24.3) WILD-TYPE 90 34     9
D4V3, multiclass
       clus
vv      AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  T1                             31                            90
  T2                             16                            34
  T3+T4                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   32 10
  AMP PEAK  4(2P24.3) WILD-TYPE 79 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     32   10
  AMP PEAK  4(2P24.3) WILD-TYPE   79   37
   clus
vv  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  0                          32                            79
  1                          10                            37
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  4(2P24.3) MUTATED   28  2 20
  AMP PEAK  4(2P24.3) WILD-TYPE 63  6 73
D4V5, multiclass
    clus
vv   AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  M0                          28                            63
  M1                           2                             6
  MX                          20                            73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(2P24.3) MUTATED               2                               51
  AMP PEAK  4(2P24.3) WILD-TYPE             3                              146
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  4(2P24.3) MUTATED                                               0
  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                                              3
  AMP PEAK  4(2P24.3) WILD-TYPE                                            3
D4V6, multiclass
                                               clus
vv                                              AMP PEAK  4(2P24.3) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       51
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              AMP PEAK  4(2P24.3) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        146
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED     5  60
  AMP PEAK  4(2P24.3) WILD-TYPE  25 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      5   60
  AMP PEAK  4(2P24.3) WILD-TYPE   25  148
     clus
vv    AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  NO                            5                            25
  YES                          60                           148
[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                        19
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(2P24.3) MUTATED                                           1    47
  AMP PEAK  4(2P24.3) WILD-TYPE                                         0   122
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                                                              47
                                           clus
vv                                          AMP PEAK  4(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                            19
  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"
D4V11, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED     3  38
  AMP PEAK  4(2P24.3) WILD-TYPE  13 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      3   38
  AMP PEAK  4(2P24.3) WILD-TYPE   13  111
                        clus
vv                       AMP PEAK  4(2P24.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          38
                        clus
vv                       AMP PEAK  4(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           111
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   18  7
  AMP PEAK  4(2P24.3) WILD-TYPE 53 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     18    7
  AMP PEAK  4(2P24.3) WILD-TYPE   53   18
            clus
vv           AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  TUMOR FREE                          18                            53
  WITH TUMOR                           7                            18
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  4(2P24.3) MUTATED        8      3       0      3       3
  AMP PEAK  4(2P24.3) WILD-TYPE     15      2       1      7       4
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK  4(2P24.3) MUTATED              45       3
  AMP PEAK  4(2P24.3) WILD-TYPE           133      11
D4V14, multiclass
               clus
vv              AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  BRAZIL                                  8                            15
  CANADA                                  3                             2
  NIGERIA                                 0                             1
  RUSSIA                                  3                             7
  UKRAINE                                 3                             4
  UNITED STATES                          45                           133
  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 26 32  0  3
  AMP PEAK  4(2P24.3) WILD-TYPE 14 80 65  1 11
D4V15, multiclass
    clus
vv   AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  G1                           3                            14
  G2                          26                            80
  G3                          32                            65
  G4                           0                             1
  GX                           3                            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V16, continuous
D4V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  4(2P24.3) MUTATED                                             9
  AMP PEAK  4(2P24.3) WILD-TYPE                                          22
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  4(2P24.3) MUTATED                                        1
  AMP PEAK  4(2P24.3) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  4(2P24.3) MUTATED                                                 1
  AMP PEAK  4(2P24.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  4(2P24.3) MUTATED               13                  31
  AMP PEAK  4(2P24.3) WILD-TYPE             39                  81
D4V18, multiclass
                                                 clus
vv                                                AMP PEAK  4(2P24.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           13
  LIFELONG NON-SMOKER                                                      31
                                                 clus
vv                                                AMP PEAK  4(2P24.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             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"
D4V19, continuous
D4V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  4(2P24.3) MUTATED             3       23             2        5
  AMP PEAK  4(2P24.3) WILD-TYPE          16       52            10        7
D4V21, multiclass
               clus
vv              AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  COMBINATION                             3                            16
  EXTERNAL                               23                            52
  EXTERNAL BEAM                           2                            10
  INTERNAL                                5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    10             4
  AMP PEAK  4(2P24.3) WILD-TYPE                  18            12
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                          10                            18
  REGIONAL SITE                                 4                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V24, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   10  1
  AMP PEAK  4(2P24.3) WILD-TYPE 24  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     10    1
  AMP PEAK  4(2P24.3) WILD-TYPE   24    2
     clus
vv    AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  CGY                          10                            24
  GY                            1                             2
[1] 2 2
[1] FALSE
D4V25, continuous
D4V26, continuous
D4V27, continuous
D4V28, continuous
D4V29, continuous
D4V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                     1
  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                      21                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  4(2P24.3) MUTATED                         1
  AMP PEAK  4(2P24.3) WILD-TYPE                       6
D4V31, multiclass
                                     clus
vv                                    AMP PEAK  4(2P24.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  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                                        21
  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  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                                                4
  AMP PEAK  4(2P24.3) WILD-TYPE                                             12
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  4(2P24.3) MUTATED                                                                                  18
  AMP PEAK  4(2P24.3) WILD-TYPE                                                                                50
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  4(2P24.3) MUTATED                                                                                             28
  AMP PEAK  4(2P24.3) WILD-TYPE                                                                                           77
D4V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  4(2P24.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          28
                                                                                              clus
vv                                                                                             AMP PEAK  4(2P24.3) 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)                                       50
  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"
D4V33, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   20 18
  AMP PEAK  4(2P24.3) WILD-TYPE 48 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     20   18
  AMP PEAK  4(2P24.3) WILD-TYPE   48   52
         clus
vv        AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  ABSENT                           20                            48
  PRESENT                          18                            52
[1] 2 2
[1] FALSE
D4V34, continuous
D4V35, continuous
D4V36, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED    9 25
  AMP PEAK  4(2P24.3) WILD-TYPE 34 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      9   25
  AMP PEAK  4(2P24.3) WILD-TYPE   34   69
                                          clus
vv                                         AMP PEAK  4(2P24.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          25
                                          clus
vv                                         AMP PEAK  4(2P24.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            69
[1] 2 2
[1] FALSE
D4V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  4(2P24.3) MUTATED              6          15         15
  AMP PEAK  4(2P24.3) WILD-TYPE            4          34         42
D4V38, multiclass
              clus
vv             AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  CURRENT USER                           6                             4
  FORMER USER                           15                            34
  NEVER USED                            15                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V39, continuous
D4V40, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.3) MUTATED   22  6
  AMP PEAK  4(2P24.3) WILD-TYPE 67 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     22    6
  AMP PEAK  4(2P24.3) WILD-TYPE   67   10
         clus
vv        AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  ABSENT                           22                            67
  PRESENT                           6                            10
[1] 2 2
[1] FALSE
D4V41, continuous
[1] "Remove cluster labels:"      "AMP PEAK  4(2P24.3) MUTATED"
clus
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                            2                            11 
                   TCGA-C5-A1MH                    TCGA-C5-A1ML 
"AMP PEAK  4(2P24.3) WILD-TYPE" "AMP PEAK  4(2P24.3) WILD-TYPE" 
                   TCGA-C5-A1MN                    TCGA-C5-A1MP 
"AMP PEAK  4(2P24.3) WILD-TYPE" "AMP PEAK  4(2P24.3) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-GH-A9DA 
"AMP PEAK  4(2P24.3) WILD-TYPE" "AMP PEAK  4(2P24.3) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-JW-A852 
"AMP PEAK  4(2P24.3) WILD-TYPE" "AMP PEAK  4(2P24.3) WILD-TYPE" 
                   TCGA-JX-A3Q8                    TCGA-MU-A51Y 
"AMP PEAK  4(2P24.3) WILD-TYPE" "AMP PEAK  4(2P24.3) WILD-TYPE" 
                   TCGA-MU-A8JM 
"AMP PEAK  4(2P24.3) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  4(2P24.3) MUTATED     0    0   6   22    3  1   3    4    2   6  0
  AMP PEAK  4(2P24.3) WILD-TYPE   1    1  24   43   21  3   5    3    7  16  1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK  4(2P24.3) MUTATED     2  0   1  3
  AMP PEAK  4(2P24.3) WILD-TYPE   6  2   0 11
D4V42, multiclass
      clus
vv     AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                            6                            24
  T1B1                          22                            43
  T1B2                           3                            21
  T2                             1                             3
  T2A                            3                             5
  T2A1                           4                             3
  T2A2                           2                             7
  T2B                            6                            16
  T3                             0                             1
  T3B                            2                             6
  T4                             0                             2
  TIS                            1                             0
  TX                             3                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        2         1         1       26
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  4(2P24.3) MUTATED          24         6        2         2
  AMP PEAK  4(2P24.3) WILD-TYPE        45        26        1         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  4(2P24.3) MUTATED            3          1         9         0
  AMP PEAK  4(2P24.3) WILD-TYPE          2          6        18         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  4(2P24.3) MUTATED            8         0         1
  AMP PEAK  4(2P24.3) WILD-TYPE         26         3         6
D4V44, multiclass
            clus
vv           AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                             0                             2
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             5                            26
  STAGE IB1                           24                            45
  STAGE IB2                            6                            26
  STAGE II                             2                             1
  STAGE IIA                            2                             4
  STAGE IIA1                           3                             2
  STAGE IIA2                           1                             6
  STAGE IIB                            9                            18
  STAGE III                            0                             1
  STAGE IIIB                           8                            26
  STAGE IVA                            0                             3
  STAGE IVB                            1                             6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(2Q33.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(2Q33.1) MUTATED    27   9
  AMP PEAK  5(2Q33.1) WILD-TYPE 156  41
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           36                           197 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                            9                            41 
$`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         0.82 
TCGA-C5-A3HD TCGA-C5-A7CK TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK 
       52.01       134.33        60.69         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         1.81        14.96        13.58 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PM TCGA-EK-A2RM TCGA-FU-A3NI 
       12.59        45.96        26.27         0.59         2.24         1.45 
TCGA-FU-A40J TCGA-HG-A9SC TCGA-JW-A5VL TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-Q1-A73S 
        1.35         7.13        15.58         0.07         0.30        10.39 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A959 
       11.67        93.99        10.03        14.07        49.55        39.35 

$`AMP PEAK  5(2Q33.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HE 
       73.18        73.45        83.05       100.14        38.43        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CL 
       17.85        20.42       182.93       154.32       101.82        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35        17.19        85.55        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR 
       13.61        50.99         8.35        75.78        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
        6.12        20.91         4.47         1.12        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
      118.65        22.98        16.83        16.18        17.52         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       12.36         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA 
        1.18        14.50         1.35         1.35        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.26        14.89         1.48        13.91        15.02        14.99 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 
       13.48         0.36         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-A2RO TCGA-EK-A3GJ 
        0.36         1.18        23.70         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        3.52         1.32         1.97         1.12         9.01        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        7.99        11.28         0.89         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
        0.03         5.42        29.72         0.07         4.34         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
       17.56        14.07        15.88         5.88         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
        3.88        12.16        61.28        34.52        29.03        20.22 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       19.96        53.52        32.15        46.03        23.28        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        16.64         4.73        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        38.96        18.05 

  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                       134.33                        195.85 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                       14.285                        16.140 
[1] "0.1 - 134.3 (14.3)" "0.0 - 195.8 (16.1)"
[1] "hr=" "1.2"
D5V2, continuous
                               vv
clus                             T1  T2 T3+T4
  AMP PEAK  5(2Q33.1) MUTATED    15   7     2
  AMP PEAK  5(2Q33.1) WILD-TYPE 106  43     9
D5V3, multiclass
       clus
vv      AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  T1                             15                           106
  T2                              7                            43
  T3+T4                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED     9  10
  AMP PEAK  5(2Q33.1) WILD-TYPE 102  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      9   10
  AMP PEAK  5(2Q33.1) WILD-TYPE  102   37
   clus
vv  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  0                           9                           102
  1                          10                            37
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  5(2Q33.1) MUTATED   13  1 11
  AMP PEAK  5(2Q33.1) WILD-TYPE 78  7 82
D5V5, multiclass
    clus
vv   AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  M0                          13                            78
  M1                           1                             7
  MX                          11                            82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(2Q33.1) MUTATED               2                               30
  AMP PEAK  5(2Q33.1) WILD-TYPE             3                              167
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  5(2Q33.1) MUTATED                                               1
  AMP PEAK  5(2Q33.1) WILD-TYPE                                             4
                               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                                              1
  AMP PEAK  5(2Q33.1) WILD-TYPE                                            5
D5V6, multiclass
                                               clus
vv                                              AMP PEAK  5(2Q33.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              AMP PEAK  5(2Q33.1) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        167
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED     5  33
  AMP PEAK  5(2Q33.1) WILD-TYPE  25 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      5   33
  AMP PEAK  5(2Q33.1) WILD-TYPE   25  175
     clus
vv    AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  NO                            5                            25
  YES                          33                           175
[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                        22
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  5(2Q33.1) MUTATED                                           0    26
  AMP PEAK  5(2Q33.1) WILD-TYPE                                         1   143
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                                                              26
                                           clus
vv                                          AMP PEAK  5(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               143
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED     2  21
  AMP PEAK  5(2Q33.1) WILD-TYPE  14 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      2   21
  AMP PEAK  5(2Q33.1) WILD-TYPE   14  128
                        clus
vv                       AMP PEAK  5(2Q33.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          21
                        clus
vv                       AMP PEAK  5(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           128
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    9  5
  AMP PEAK  5(2Q33.1) WILD-TYPE 62 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      9    5
  AMP PEAK  5(2Q33.1) WILD-TYPE   62   20
            clus
vv           AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  TUMOR FREE                           9                            62
  WITH TUMOR                           5                            20
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  5(2Q33.1) MUTATED        4      1       0      0       1
  AMP PEAK  5(2Q33.1) WILD-TYPE     19      4       1     10       6
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK  5(2Q33.1) MUTATED              27       5
  AMP PEAK  5(2Q33.1) WILD-TYPE           151       9
D5V14, multiclass
               clus
vv              AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  BRAZIL                                  4                            19
  CANADA                                  1                             4
  NIGERIA                                 0                             1
  RUSSIA                                  0                            10
  UKRAINE                                 1                             6
  UNITED STATES                          27                           151
  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 18 16  0  2
  AMP PEAK  5(2Q33.1) WILD-TYPE 16 88 81  1 12
D5V15, multiclass
    clus
vv   AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  G1                           1                            16
  G2                          18                            88
  G3                          16                            81
  G4                           0                             1
  GX                           2                            12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                                          26
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  5(2Q33.1) MUTATED                                        0
  AMP PEAK  5(2Q33.1) WILD-TYPE                                      8
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  5(2Q33.1) MUTATED                                                 1
  AMP PEAK  5(2Q33.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  5(2Q33.1) MUTATED                7                  17
  AMP PEAK  5(2Q33.1) WILD-TYPE             45                  95
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                                                            7
  LIFELONG NON-SMOKER                                                      17
                                                 clus
vv                                                AMP PEAK  5(2Q33.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             45
  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"
D5V19, continuous
D5V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  5(2Q33.1) MUTATED             4       10             1        2
  AMP PEAK  5(2Q33.1) WILD-TYPE          15       65            11       10
D5V21, multiclass
               clus
vv              AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  COMBINATION                             4                            15
  EXTERNAL                               10                            65
  EXTERNAL BEAM                           1                            11
  INTERNAL                                2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     3             3
  AMP PEAK  5(2Q33.1) WILD-TYPE                  25            13
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                           3                            25
  REGIONAL SITE                                 3                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V24, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    3  0
  AMP PEAK  5(2Q33.1) WILD-TYPE 31  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      3    0
  AMP PEAK  5(2Q33.1) WILD-TYPE   31    3
     clus
vv    AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  CGY                           3                            31
  GY                            0                             3
[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                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  5(2Q33.1) MUTATED                         4                       0
  AMP PEAK  5(2Q33.1) WILD-TYPE                      25                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  5(2Q33.1) MUTATED                         0
  AMP PEAK  5(2Q33.1) WILD-TYPE                       7
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                             6
  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)
  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                                                4
  AMP PEAK  5(2Q33.1) WILD-TYPE                                             12
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  5(2Q33.1) MUTATED                                                                                   7
  AMP PEAK  5(2Q33.1) WILD-TYPE                                                                                61
                               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                                                                                           87
D5V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  5(2Q33.1) 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)                                      7
  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)                                                                          12
  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)                            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"
D5V33, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    5 14
  AMP PEAK  5(2Q33.1) WILD-TYPE 63 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      5   14
  AMP PEAK  5(2Q33.1) WILD-TYPE   63   56
         clus
vv        AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  ABSENT                            5                            63
  PRESENT                          14                            56
[1] 2 2
[1] FALSE
D5V34, continuous
D5V35, continuous
D5V36, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    6 12
  AMP PEAK  5(2Q33.1) WILD-TYPE 37 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      6   12
  AMP PEAK  5(2Q33.1) WILD-TYPE   37   82
                                          clus
vv                                         AMP PEAK  5(2Q33.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          12
                                          clus
vv                                         AMP PEAK  5(2Q33.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            82
[1] 2 2
[1] FALSE
D5V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  5(2Q33.1) MUTATED              0           9          6
  AMP PEAK  5(2Q33.1) WILD-TYPE           10          40         51
D5V38, multiclass
              clus
vv             AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  CURRENT USER                           0                            10
  FORMER USER                            9                            40
  NEVER USED                             6                            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V39, continuous
D5V40, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q33.1) MUTATED    9  3
  AMP PEAK  5(2Q33.1) WILD-TYPE 80 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      9    3
  AMP PEAK  5(2Q33.1) WILD-TYPE   80   13
         clus
vv        AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  ABSENT                            9                            80
  PRESENT                           3                            13
[1] 2 2
[1] FALSE
D5V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  5(2Q33.1) MUTATED     0    0   2   12    1  0   2    2    1   2  0
  AMP PEAK  5(2Q33.1) WILD-TYPE   1    1  28   53   23  4   6    5    8  20  1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK  5(2Q33.1) MUTATED     2  0   0  1
  AMP PEAK  5(2Q33.1) WILD-TYPE   6  2   1 13
D5V42, multiclass
      clus
vv     AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                            2                            28
  T1B1                          12                            53
  T1B2                           1                            23
  T2                             0                             4
  T2A                            2                             6
  T2A1                           2                             5
  T2A2                           1                             8
  T2B                            2                            20
  T3                             0                             1
  T3B                            2                             6
  T4                             0                             2
  TIS                            0                             1
  TX                             1                            13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        2         1         1       28
                               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        58        29        3         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  5(2Q33.1) MUTATED            1          1         8         0
  AMP PEAK  5(2Q33.1) WILD-TYPE          4          6        19         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  5(2Q33.1) MUTATED            8         1         0
  AMP PEAK  5(2Q33.1) WILD-TYPE         26         2         7
D5V44, multiclass
            clus
vv           AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                             0                             2
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             3                            28
  STAGE IB1                           11                            58
  STAGE IB2                            3                            29
  STAGE II                             0                             3
  STAGE IIA                            1                             5
  STAGE IIA1                           1                             4
  STAGE IIA2                           1                             6
  STAGE IIB                            8                            19
  STAGE III                            0                             1
  STAGE IIIB                           8                            26
  STAGE IVA                            1                             2
  STAGE IVB                            0                             7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(3Q26.31) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(3Q26.31) MUTATED   141  40
  AMP PEAK  6(3Q26.31) WILD-TYPE  42  10
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                           181                             52 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            40                             10 
$`AMP PEAK  6(3Q26.31) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85         5.46        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       31.40        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-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         0.82        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        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       60.69        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-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 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 
       13.05         1.35        14.50        12.66         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R 
        1.48        13.91        15.02        14.99        14.96        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
        0.36        12.59        26.27         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-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        0.03        23.70         2.24         0.10         0.07         0.03 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI 
       20.35         6.94        19.79         6.12        23.84         1.45 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-GH-A9DA 
        1.48         0.82         3.52         1.35         1.97         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41         7.13        21.67        20.78        14.93         9.44 
TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VJ 
      137.16       117.40        78.71        81.96        36.36        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       20.48        15.58         5.13         6.71       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         0.20 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        5.49         2.96        15.58        13.35        15.95         3.39 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       17.56        14.07         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
        3.88        11.67        93.99        12.16        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       29.03        20.22        14.07        19.96        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X 
       46.03        23.28        11.51        49.55        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
        4.73        23.24        42.58        42.08        39.35        38.96 
TCGA-WL-A834 
       18.05 

$`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       182.93        17.19 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DR-A0ZM 
       75.78        99.91        27.52         6.12         4.47        58.88 
TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA 
       16.18         1.18        14.50         1.35         1.81        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         4.73         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-FU-A770 
        2.17         0.66         1.02         1.58         1.32         1.12 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH 
      147.39        66.81        96.95        26.56        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-Q1-A6DV TCGA-Q1-A73P 
       24.56        10.06        21.11         0.07        16.14        15.88 
TCGA-UC-A7PI TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A958 
       61.28        39.78        44.88        43.82 

  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                        195.85                         182.93 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                         16.08                          14.60 
[1] "0.0 - 195.8 (16.1)" "0.1 - 182.9 (14.6)"
[1] "hr=" "1"  
D6V2, continuous
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK  6(3Q26.31) MUTATED   89 39    10
  AMP PEAK  6(3Q26.31) WILD-TYPE 32 11     1
D6V3, multiclass
       clus
vv      AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  T1                              89                             32
  T2                              39                             11
  T3+T4                           10                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   77 42
  AMP PEAK  6(3Q26.31) WILD-TYPE 34  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     77   42
  AMP PEAK  6(3Q26.31) WILD-TYPE   34    5
   clus
vv  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  0                           77                             34
  1                           42                              5
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  6(3Q26.31) MUTATED   73  6 69
  AMP PEAK  6(3Q26.31) WILD-TYPE 18  2 24
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  M0                           73                             18
  M1                            6                              2
  MX                           69                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(3Q26.31) MUTATED               4                              160
  AMP PEAK  6(3Q26.31) WILD-TYPE             1                               37
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  6(3Q26.31) MUTATED                                               3
  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                                              3
  AMP PEAK  6(3Q26.31) WILD-TYPE                                            3
D6V6, multiclass
                                               clus
vv                                              AMP PEAK  6(3Q26.31) MUTATED
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       160
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             3
                                               clus
vv                                              AMP PEAK  6(3Q26.31) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                          37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    26 158
  AMP PEAK  6(3Q26.31) WILD-TYPE   4  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     26  158
  AMP PEAK  6(3Q26.31) WILD-TYPE    4   50
     clus
vv    AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  NO                            26                              4
  YES                          158                             50
[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                          23
  AMP PEAK  6(3Q26.31) WILD-TYPE                         1
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  6(3Q26.31) MUTATED                                           0
  AMP PEAK  6(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK  6(3Q26.31) MUTATED     124
  AMP PEAK  6(3Q26.31) WILD-TYPE    45
D6V10, multiclass
                                           clus
vv                                          AMP PEAK  6(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                           23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              124
                                           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                                                                 45
[1] 5 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    11 116
  AMP PEAK  6(3Q26.31) WILD-TYPE   5  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     11  116
  AMP PEAK  6(3Q26.31) WILD-TYPE    5   33
                        clus
vv                       AMP PEAK  6(3Q26.31) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       AMP PEAK  6(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             33
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   58 21
  AMP PEAK  6(3Q26.31) WILD-TYPE 13  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     58   21
  AMP PEAK  6(3Q26.31) WILD-TYPE   13    4
            clus
vv           AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  TUMOR FREE                           58                             13
  WITH TUMOR                           21                              4
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  6(3Q26.31) MUTATED       20      5       1      8       4
  AMP PEAK  6(3Q26.31) WILD-TYPE      3      0       0      2       3
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK  6(3Q26.31) MUTATED             134      12
  AMP PEAK  6(3Q26.31) WILD-TYPE            44       2
D6V14, multiclass
               clus
vv              AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  BRAZIL                                  20                              3
  CANADA                                   5                              0
  NIGERIA                                  1                              0
  RUSSIA                                   8                              2
  UKRAINE                                  4                              3
  UNITED STATES                          134                             44
  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   12 82 74  1 13
  AMP PEAK  6(3Q26.31) WILD-TYPE  5 24 23  0  1
D6V15, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  G1                           12                              5
  G2                           82                             24
  G3                           74                             23
  G4                            1                              0
  GX                           13                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V16, continuous
D6V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  6(3Q26.31) MUTATED                                            26
  AMP PEAK  6(3Q26.31) WILD-TYPE                                           5
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  6(3Q26.31) MUTATED                                        7
  AMP PEAK  6(3Q26.31) WILD-TYPE                                      1
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  6(3Q26.31) MUTATED                                                 2
  AMP PEAK  6(3Q26.31) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  6(3Q26.31) MUTATED               43                  84
  AMP PEAK  6(3Q26.31) WILD-TYPE              9                  28
D6V18, multiclass
                                                 clus
vv                                                AMP PEAK  6(3Q26.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            43
  LIFELONG NON-SMOKER                                                       84
                                                 clus
vv                                                AMP PEAK  6(3Q26.31) WILD-TYPE
  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                                                         28
[1] 5 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       58            10       10
  AMP PEAK  6(3Q26.31) WILD-TYPE           2       17             2        2
D6V21, multiclass
               clus
vv              AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  COMBINATION                             17                              2
  EXTERNAL                                58                             17
  EXTERNAL BEAM                           10                              2
  INTERNAL                                10                              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"
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                    21            14
  AMP PEAK  6(3Q26.31) WILD-TYPE                   7             2
D6V23, multiclass
                     clus
vv                    AMP PEAK  6(3Q26.31) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                           21
  REGIONAL SITE                                 14
                     clus
vv                    AMP PEAK  6(3Q26.31) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                              7
  REGIONAL SITE                                    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"
D6V24, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   27  3
  AMP PEAK  6(3Q26.31) WILD-TYPE  7  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     27    3
  AMP PEAK  6(3Q26.31) WILD-TYPE    7    0
     clus
vv    AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  CGY                           27                              7
  GY                             3                              0
[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                                     5
  AMP PEAK  6(3Q26.31) WILD-TYPE                                   1
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  6(3Q26.31) MUTATED                        26
  AMP PEAK  6(3Q26.31) WILD-TYPE                       3
                                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                         6
  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                            5
  OTHER LOCATION, SPECIFY                                       26
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        6
                                     clus
vv                                    AMP PEAK  6(3Q26.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  OTHER LOCATION, SPECIFY                                          3
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                               13
  AMP PEAK  6(3Q26.31) WILD-TYPE                                              3
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  6(3Q26.31) MUTATED                                                                                  57
  AMP PEAK  6(3Q26.31) WILD-TYPE                                                                                11
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  6(3Q26.31) MUTATED                                                                                             79
  AMP PEAK  6(3Q26.31) WILD-TYPE                                                                                           26
D6V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  6(3Q26.31) MUTATED
  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)                                      57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           79
                                                                                              clus
vv                                                                                             AMP PEAK  6(3Q26.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D6V33, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   50 56
  AMP PEAK  6(3Q26.31) WILD-TYPE 18 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     50   56
  AMP PEAK  6(3Q26.31) WILD-TYPE   18   14
         clus
vv        AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  ABSENT                            50                             18
  PRESENT                           56                             14
[1] 2 2
[1] FALSE
D6V34, continuous
D6V35, continuous
D6V36, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   35 72
  AMP PEAK  6(3Q26.31) WILD-TYPE  8 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     35   72
  AMP PEAK  6(3Q26.31) WILD-TYPE    8   22
                                          clus
vv                                         AMP PEAK  6(3Q26.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           72
                                          clus
vv                                         AMP PEAK  6(3Q26.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             22
[1] 2 2
[1] FALSE
D6V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  6(3Q26.31) MUTATED              7          37         42
  AMP PEAK  6(3Q26.31) WILD-TYPE            3          12         15
D6V38, multiclass
              clus
vv             AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  CURRENT USER                            7                              3
  FORMER USER                            37                             12
  NEVER USED                             42                             15
[1] 3 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   67 13
  AMP PEAK  6(3Q26.31) WILD-TYPE 22  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     67   13
  AMP PEAK  6(3Q26.31) WILD-TYPE   22    3
         clus
vv        AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  ABSENT                            67                             22
  PRESENT                           13                              3
[1] 2 2
[1] FALSE
D6V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  6(3Q26.31) MUTATED     1    1  22   48   17  4   7    6    5  17  1
  AMP PEAK  6(3Q26.31) WILD-TYPE   0    0   8   17    7  0   1    1    4   5  0
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK  6(3Q26.31) MUTATED     8  1   1 12
  AMP PEAK  6(3Q26.31) WILD-TYPE   0  1   0  2
D6V42, multiclass
      clus
vv     AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  T1A                             1                              0
  T1A1                            1                              0
  T1B                            22                              8
  T1B1                           48                             17
  T1B2                           17                              7
  T2                              4                              0
  T2A                             7                              1
  T2A1                            6                              1
  T2A2                            5                              4
  T2B                            17                              5
  T3                              1                              0
  T3B                             8                              0
  T4                              1                              1
  TIS                             1                              0
  TX                             12                              2
[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         4        2         1         0       23
  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          50        24        3         4
  AMP PEAK  6(3Q26.31) WILD-TYPE        19         8        0         2
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  6(3Q26.31) MUTATED            5          5        22         1
  AMP PEAK  6(3Q26.31) WILD-TYPE          0          2         5         0
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  6(3Q26.31) MUTATED           28         3         5
  AMP PEAK  6(3Q26.31) WILD-TYPE          6         0         2
D6V44, multiclass
            clus
vv           AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  STAGE I                               4                              0
  STAGE IA                              2                              0
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                             23                              8
  STAGE IB1                            50                             19
  STAGE IB2                            24                              8
  STAGE II                              3                              0
  STAGE IIA                             4                              2
  STAGE IIA1                            5                              0
  STAGE IIA2                            5                              2
  STAGE IIB                            22                              5
  STAGE III                             1                              0
  STAGE IIIB                           28                              6
  STAGE IVA                             3                              0
  STAGE IVB                             5                              2
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(3Q28) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(3Q28) MUTATED   141  38
  AMP PEAK  7(3Q28) WILD-TYPE  42  12
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                        179                          54 
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                         38                          12 
$`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         0.82        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        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       60.69        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-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 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 
       13.05         1.35        14.50        12.66         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R 
        1.48        13.91        15.02        14.99        14.96        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
        0.36        12.59        26.27         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-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        0.03        23.70         2.24         0.10         0.07         0.03 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI 
       20.35         6.94        19.79         6.12        23.84         1.45 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-GH-A9DA 
        1.48         0.82         3.52         1.35         1.97         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LC 
       25.41         7.13        20.78        14.93       137.16       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK 
       78.71        81.96        36.36        27.42        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       15.58         5.13         6.71       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       11.28         0.89         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
        0.03         5.42        29.72         0.07         4.34         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
        2.96        15.58        13.35        15.95         3.39        17.56 
TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07         5.88         6.25        10.39        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        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       20.22        14.07        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       11.51        49.55        31.27        16.64         4.73        23.24 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        39.35        38.96        18.05 

$`AMP PEAK  7(3Q28) WILD-TYPE`
TCGA-C5-A1BF TCGA-C5-A1BQ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7UC 
       18.74        19.86        38.43        52.01       182.93        17.19 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DR-A0ZM 
       75.78        99.91        27.52         6.12         4.47        58.88 
TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA 
       16.18         1.18        14.50         1.35         1.81        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         4.73         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-FU-A770 
        2.17         0.66         1.02         1.58         1.32         1.12 
TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK 
       21.67         9.44       147.39        66.81        96.95        26.56 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-Q1-A6DV 
        3.29        24.56        10.06        21.11         0.07        16.14 
TCGA-Q1-A73P TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A958 
       15.88        61.28        19.96        39.78        44.88        43.82 

  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                       0.03                        0.07 
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                     195.85                      182.93 
  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE 
                      16.08                       14.60 
[1] "0.0 - 195.8 (16.1)" "0.1 - 182.9 (14.6)"
[1] "hr=" "1.2"
D7V2, continuous
                             vv
clus                          T1 T2 T3+T4
  AMP PEAK  7(3Q28) MUTATED   89 38    10
  AMP PEAK  7(3Q28) WILD-TYPE 32 12     1
D7V3, multiclass
       clus
vv      AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  T1                           89                          32
  T2                           38                          12
  T3+T4                        10                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   77 41
  AMP PEAK  7(3Q28) WILD-TYPE 34  6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     77   41
  AMP PEAK  7(3Q28) WILD-TYPE   34    6
   clus
vv  AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  0                        77                          34
  1                        41                           6
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK  7(3Q28) MUTATED   73  4 70
  AMP PEAK  7(3Q28) WILD-TYPE 18  4 23
D7V5, multiclass
    clus
vv   AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  M0                        73                          18
  M1                         4                           4
  MX                        70                          23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(3Q28) MUTATED               3                              160
  AMP PEAK  7(3Q28) WILD-TYPE             2                               37
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  7(3Q28) MUTATED                                               3
  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                                              3
  AMP PEAK  7(3Q28) WILD-TYPE                                            3
D7V6, multiclass
                                               clus
vv                                              AMP PEAK  7(3Q28) MUTATED
  ADENOSQUAMOUS                                                         3
  CERVICAL SQUAMOUS CELL CARCINOMA                                    160
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                  12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          3
                                               clus
vv                                              AMP PEAK  7(3Q28) WILD-TYPE
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(3Q28) MUTATED    25 158
  AMP PEAK  7(3Q28) WILD-TYPE   5  50
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     25  158
  AMP PEAK  7(3Q28) WILD-TYPE    5   50
     clus
vv    AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  NO                         25                           5
  YES                       158                          50
[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                          21
  AMP PEAK  7(3Q28) WILD-TYPE                         3
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(3Q28) MUTATED                                           0   124
  AMP PEAK  7(3Q28) WILD-TYPE                                         1    45
D7V10, multiclass
                                           clus
vv                                          AMP PEAK  7(3Q28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  6
  ASIAN                                                            15
  BLACK OR AFRICAN AMERICAN                                        21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                           124
                                           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                                                              45
[1] 5 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    12 115
  AMP PEAK  7(3Q28) WILD-TYPE   4  34
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     12  115
  AMP PEAK  7(3Q28) WILD-TYPE    4   34
                        clus
vv                       AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  HISPANIC OR LATINO                            12                           4
  NOT HISPANIC OR LATINO                       115                          34
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   58 20
  AMP PEAK  7(3Q28) WILD-TYPE 13  5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     58   20
  AMP PEAK  7(3Q28) WILD-TYPE   13    5
            clus
vv           AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  TUMOR FREE                        58                          13
  WITH TUMOR                        20                           5
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  7(3Q28) MUTATED       19      5       1      8       4
  AMP PEAK  7(3Q28) WILD-TYPE      4      0       0      2       3
                             vv
clus                          UNITED STATES VIETNAM
  AMP PEAK  7(3Q28) MUTATED             134      12
  AMP PEAK  7(3Q28) WILD-TYPE            44       2
D7V14, multiclass
               clus
vv              AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  BRAZIL                               19                           4
  CANADA                                5                           0
  NIGERIA                               1                           0
  RUSSIA                                8                           2
  UKRAINE                               4                           3
  UNITED STATES                       134                          44
  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   12 82 73  1 13
  AMP PEAK  7(3Q28) WILD-TYPE  5 24 24  0  1
D7V15, multiclass
    clus
vv   AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  G1                        12                           5
  G2                        82                          24
  G3                        73                          24
  G4                         1                           0
  GX                        13                           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"
D7V16, continuous
D7V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  7(3Q28) MUTATED                                            26
  AMP PEAK  7(3Q28) WILD-TYPE                                           5
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  7(3Q28) MUTATED                                        7
  AMP PEAK  7(3Q28) WILD-TYPE                                      1
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  7(3Q28) MUTATED                                                 2
  AMP PEAK  7(3Q28) WILD-TYPE                                               0
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  7(3Q28) MUTATED               42                  84
  AMP PEAK  7(3Q28) WILD-TYPE             10                  28
D7V18, multiclass
                                                 clus
vv                                                AMP PEAK  7(3Q28) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                            26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         2
  CURRENT SMOKER                                                         42
  LIFELONG NON-SMOKER                                                    84
                                                 clus
vv                                                AMP PEAK  7(3Q28) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           10
  LIFELONG NON-SMOKER                                                      28
[1] 5 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       57             9       10
  AMP PEAK  7(3Q28) WILD-TYPE           2       18             3        2
D7V21, multiclass
               clus
vv              AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  COMBINATION                          17                           2
  EXTERNAL                             57                          18
  EXTERNAL BEAM                         9                           3
  INTERNAL                             10                           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"
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                    22            14
  AMP PEAK  7(3Q28) WILD-TYPE                   6             2
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                        22                           6
  REGIONAL SITE                              14                           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"
D7V24, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   27  3
  AMP PEAK  7(3Q28) WILD-TYPE  7  0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     27    3
  AMP PEAK  7(3Q28) WILD-TYPE    7    0
     clus
vv    AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  CGY                        27                           7
  GY                          3                           0
[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                                     5
  AMP PEAK  7(3Q28) WILD-TYPE                                   1
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  7(3Q28) MUTATED                        26                       1
  AMP PEAK  7(3Q28) WILD-TYPE                       3                       0
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  7(3Q28) MUTATED                         6
  AMP PEAK  7(3Q28) WILD-TYPE                       1
D7V31, multiclass
                                     clus
vv                                    AMP PEAK  7(3Q28) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         5
  OTHER LOCATION, SPECIFY                                    26
  POSITIVE BLADDER MARGIN                                     1
  POSITIVE VAGINAL MARGIN                                     6
                                     clus
vv                                    AMP PEAK  7(3Q28) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                       3
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                               13
  AMP PEAK  7(3Q28) WILD-TYPE                                              3
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  7(3Q28) MUTATED                                                                                  57
  AMP PEAK  7(3Q28) WILD-TYPE                                                                                11
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  7(3Q28) MUTATED                                                                                             78
  AMP PEAK  7(3Q28) WILD-TYPE                                                                                           27
D7V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  7(3Q28) MUTATED
  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)                                   57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        78
                                                                                              clus
vv                                                                                             AMP PEAK  7(3Q28) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          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"
D7V33, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   51 54
  AMP PEAK  7(3Q28) WILD-TYPE 17 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     51   54
  AMP PEAK  7(3Q28) WILD-TYPE   17   16
         clus
vv        AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  ABSENT                         51                          17
  PRESENT                        54                          16
[1] 2 2
[1] FALSE
D7V34, continuous
D7V35, continuous
D7V36, binary
                             cls
clus                           0  1
  AMP PEAK  7(3Q28) MUTATED   35 73
  AMP PEAK  7(3Q28) WILD-TYPE  8 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     35   73
  AMP PEAK  7(3Q28) WILD-TYPE    8   21
                                          clus
vv                                         AMP PEAK  7(3Q28) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        73
                                          clus
vv                                         AMP PEAK  7(3Q28) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          21
[1] 2 2
[1] FALSE
D7V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  7(3Q28) MUTATED              7          35         43
  AMP PEAK  7(3Q28) WILD-TYPE            3          14         14
D7V38, multiclass
              clus
vv             AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  CURRENT USER                         7                           3
  FORMER USER                         35                          14
  NEVER USED                          43                          14
[1] 3 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   67 13
  AMP PEAK  7(3Q28) WILD-TYPE 22  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(3Q28) MUTATED     67   13
  AMP PEAK  7(3Q28) WILD-TYPE   22    3
         clus
vv        AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  ABSENT                         67                          22
  PRESENT                        13                           3
[1] 2 2
[1] FALSE
D7V41, continuous
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  7(3Q28) MUTATED     1    1  22   48   17  4   7    6    5  16  1
  AMP PEAK  7(3Q28) WILD-TYPE   0    0   8   17    7  0   1    1    4   6  0
                             vv
clus                          T3B T4 TIS TX
  AMP PEAK  7(3Q28) MUTATED     8  1   1 12
  AMP PEAK  7(3Q28) WILD-TYPE   0  1   0  2
D7V42, multiclass
      clus
vv     AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  T1A                          1                           0
  T1A1                         1                           0
  T1B                         22                           8
  T1B1                        48                          17
  T1B2                        17                           7
  T2                           4                           0
  T2A                          7                           1
  T2A1                         6                           1
  T2A2                         5                           4
  T2B                         16                           6
  T3                           1                           0
  T3B                          8                           0
  T4                           1                           1
  TIS                          1                           0
  TX                          12                           2
[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         4        2         1         1       23
  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          49        24        3         5          5
  AMP PEAK  7(3Q28) WILD-TYPE        20         8        0         1          0
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIB
  AMP PEAK  7(3Q28) MUTATED            5        21         1         28
  AMP PEAK  7(3Q28) WILD-TYPE          2         6         0          6
                             vv
clus                          STAGE IVA STAGE IVB
  AMP PEAK  7(3Q28) MUTATED           3         4
  AMP PEAK  7(3Q28) WILD-TYPE         0         3
D7V44, multiclass
            clus
vv           AMP PEAK  7(3Q28) MUTATED AMP PEAK  7(3Q28) WILD-TYPE
  STAGE I                            4                           0
  STAGE IA                           2                           0
  STAGE IA1                          1                           0
  STAGE IA2                          1                           0
  STAGE IB                          23                           8
  STAGE IB1                         49                          20
  STAGE IB2                         24                           8
  STAGE II                           3                           0
  STAGE IIA                          5                           1
  STAGE IIA1                         5                           0
  STAGE IIA2                         5                           2
  STAGE IIB                         21                           6
  STAGE III                          1                           0
  STAGE IIIB                        28                           6
  STAGE IVA                          3                           0
  STAGE IVB                          4                           3
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(4Q12) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  8(4Q12) MUTATED    13   2
  AMP PEAK  8(4Q12) WILD-TYPE 170  48
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                         15                         218 
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                          2                          48 
$`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         4.47 
TCGA-DS-A3LQ TCGA-EK-A2GZ TCGA-EK-A3GK TCGA-FU-A23K TCGA-IR-A3LF TCGA-IR-A3LH 
       22.98        12.59         0.10         1.22        96.95        78.71 
TCGA-JX-A3Q8 TCGA-MY-A5BF TCGA-VS-A8EC 
       30.31         4.34        34.52 

$`AMP PEAK  8(4Q12) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        30.21        57.73 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A2LS 
       38.99        35.61         0.46         2.43        20.91        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19        85.55        60.69        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99        45.83        75.78        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       27.52         6.12        20.91         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-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99       118.65        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
        0.36        45.96        26.27         6.64         1.51         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         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-A23L 
        6.94        14.70        19.79         6.12         4.73        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       117.40 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85         7.99        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         5.49         2.96        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        12.16        61.28        10.03        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       14.07        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  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                      195.85 
  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE 
                      22.98                       15.73 
[1] "0.1 - 97.0 (23.0)"  "0.0 - 195.8 (15.7)"
[1] "hr=" "1.7"
D8V2, continuous
                             vv
clus                           T1  T2 T3+T4
  AMP PEAK  8(4Q12) MUTATED     7   2     3
  AMP PEAK  8(4Q12) WILD-TYPE 114  48     8
D8V3, multiclass
       clus
vv      AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  T1                            7                         114
  T2                            2                          48
  T3+T4                         3                           8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                             cls
clus                            0   1
  AMP PEAK  8(4Q12) MUTATED     7   4
  AMP PEAK  8(4Q12) WILD-TYPE 104  43
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      7    4
  AMP PEAK  8(4Q12) WILD-TYPE  104   43
   clus
vv  AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  0                         7                         104
  1                         4                          43
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK  8(4Q12) MUTATED    5  0  7
  AMP PEAK  8(4Q12) WILD-TYPE 86  8 86
D8V5, multiclass
    clus
vv   AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  M0                         5                          86
  M1                         0                           8
  MX                         7                          86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(4Q12) MUTATED               0                               12
  AMP PEAK  8(4Q12) WILD-TYPE             5                              185
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  8(4Q12) MUTATED                                               1
  AMP PEAK  8(4Q12) WILD-TYPE                                             4
                             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                                            6
D8V6, multiclass
                                               clus
vv                                              AMP PEAK  8(4Q12) MUTATED
  ADENOSQUAMOUS                                                         0
  CERVICAL SQUAMOUS CELL CARCINOMA                                     12
  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                                      185
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                             cls
clus                            0   1
  AMP PEAK  8(4Q12) MUTATED     4  12
  AMP PEAK  8(4Q12) WILD-TYPE  26 196
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      4   12
  AMP PEAK  8(4Q12) WILD-TYPE   26  196
     clus
vv    AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  NO                          4                          26
  YES                        12                         196
[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                        20
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(4Q12) MUTATED                                           0    10
  AMP PEAK  8(4Q12) WILD-TYPE                                         1   159
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                                                            10
                                           clus
vv                                          AMP PEAK  8(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    8
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                          20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  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"
D8V11, binary
                             cls
clus                            0   1
  AMP PEAK  8(4Q12) MUTATED     0   9
  AMP PEAK  8(4Q12) WILD-TYPE  16 140
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      0    9
  AMP PEAK  8(4Q12) WILD-TYPE   16  140
                        clus
vv                       AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                          16
  NOT HISPANIC OR LATINO                         9                         140
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    5  2
  AMP PEAK  8(4Q12) WILD-TYPE 66 23
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      5    2
  AMP PEAK  8(4Q12) WILD-TYPE   66   23
            clus
vv           AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  TUMOR FREE                         5                          66
  WITH TUMOR                         2                          23
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  8(4Q12) MUTATED        1      0       0      0       0
  AMP PEAK  8(4Q12) WILD-TYPE     22      5       1     10       7
                             vv
clus                          UNITED STATES VIETNAM
  AMP PEAK  8(4Q12) MUTATED              15       0
  AMP PEAK  8(4Q12) WILD-TYPE           163      14
D8V14, multiclass
               clus
vv              AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  BRAZIL                                1                          22
  CANADA                                0                           5
  NIGERIA                               0                           1
  RUSSIA                                0                          10
  UKRAINE                               0                           7
  UNITED STATES                        15                         163
  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  7  7  1  0
  AMP PEAK  8(4Q12) WILD-TYPE 16 99 90  0 14
D8V15, multiclass
    clus
vv   AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  G1                         1                          16
  G2                         7                          99
  G3                         7                          90
  G4                         1                           0
  GX                         0                          14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V16, continuous
D8V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  8(4Q12) MUTATED                                             3
  AMP PEAK  8(4Q12) WILD-TYPE                                          28
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  8(4Q12) MUTATED                                        1
  AMP PEAK  8(4Q12) WILD-TYPE                                      7
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  8(4Q12) MUTATED                                                 0
  AMP PEAK  8(4Q12) WILD-TYPE                                               2
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  8(4Q12) MUTATED                2                   6
  AMP PEAK  8(4Q12) WILD-TYPE             50                 106
D8V18, multiclass
                                                 clus
vv                                                AMP PEAK  8(4Q12) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         0
  CURRENT SMOKER                                                          2
  LIFELONG NON-SMOKER                                                     6
                                                 clus
vv                                                AMP PEAK  8(4Q12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           50
  LIFELONG NON-SMOKER                                                     106
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V19, continuous
D8V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  8(4Q12) MUTATED             2        5             2        0
  AMP PEAK  8(4Q12) WILD-TYPE          17       70            10       12
D8V21, multiclass
               clus
vv              AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  COMBINATION                           2                          17
  EXTERNAL                              5                          70
  EXTERNAL BEAM                         2                          10
  INTERNAL                              0                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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             1
  AMP PEAK  8(4Q12) WILD-TYPE                  25            15
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                          25
  REGIONAL SITE                               1                          15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V24, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    4  0
  AMP PEAK  8(4Q12) WILD-TYPE 30  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      4    0
  AMP PEAK  8(4Q12) WILD-TYPE   30    3
     clus
vv    AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  CGY                         4                          30
  GY                          0                           3
[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                                   6
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  8(4Q12) MUTATED                         5                       0
  AMP PEAK  8(4Q12) WILD-TYPE                      24                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  8(4Q12) MUTATED                         1
  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                                     1
                                     clus
vv                                    AMP PEAK  8(4Q12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           6
  OTHER LOCATION, SPECIFY                                      24
  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                                             15
                             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                                                                                64
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  8(4Q12) MUTATED                                                                                              8
  AMP PEAK  8(4Q12) WILD-TYPE                                                                                           97
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)                         8
                                                                                              clus
vv                                                                                             AMP PEAK  8(4Q12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          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"
D8V33, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    3  7
  AMP PEAK  8(4Q12) WILD-TYPE 65 63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      3    7
  AMP PEAK  8(4Q12) WILD-TYPE   65   63
         clus
vv        AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  ABSENT                          3                          65
  PRESENT                         7                          63
[1] 2 2
[1] FALSE
D8V34, continuous
D8V35, continuous
D8V36, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    2  4
  AMP PEAK  8(4Q12) WILD-TYPE 41 90
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      2    4
  AMP PEAK  8(4Q12) WILD-TYPE   41   90
                                          clus
vv                                         AMP PEAK  8(4Q12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         4
                                          clus
vv                                         AMP PEAK  8(4Q12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          90
[1] 2 2
[1] FALSE
D8V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  8(4Q12) MUTATED              1           7          1
  AMP PEAK  8(4Q12) WILD-TYPE            9          42         56
D8V38, multiclass
              clus
vv             AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  CURRENT USER                         1                           9
  FORMER USER                          7                          42
  NEVER USED                           1                          56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V39, continuous
D8V40, binary
                             cls
clus                           0  1
  AMP PEAK  8(4Q12) MUTATED    6  0
  AMP PEAK  8(4Q12) WILD-TYPE 83 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(4Q12) MUTATED      6    0
  AMP PEAK  8(4Q12) WILD-TYPE   83   16
         clus
vv        AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  ABSENT                          6                          83
  PRESENT                         0                          16
[1] 2 2
[1] FALSE
D8V41, continuous
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  8(4Q12) MUTATED     0    0   0    4    3  0   0    1    1   0  0
  AMP PEAK  8(4Q12) WILD-TYPE   1    1  30   61   21  4   8    6    8  22  1
                             vv
clus                          T3B T4 TIS TX
  AMP PEAK  8(4Q12) MUTATED     3  0   0  0
  AMP PEAK  8(4Q12) WILD-TYPE   5  2   1 14
D8V42, multiclass
      clus
vv     AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  T1A                          0                           1
  T1A1                         0                           1
  T1B                          0                          30
  T1B1                         4                          61
  T1B2                         3                          21
  T2                           0                           4
  T2A                          0                           8
  T2A1                         1                           6
  T2A2                         1                           8
  T2B                          0                          22
  T3                           0                           1
  T3B                          3                           5
  T4                           0                           2
  TIS                          0                           1
  TX                           0                          14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        2         1         1       31
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK  8(4Q12) MUTATED           4         4        0         0          1
  AMP PEAK  8(4Q12) WILD-TYPE        65        28        3         6          4
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIB
  AMP PEAK  8(4Q12) MUTATED            1         0         0          6
  AMP PEAK  8(4Q12) WILD-TYPE          6        27         1         28
                             vv
clus                          STAGE IVA STAGE IVB
  AMP PEAK  8(4Q12) MUTATED           0         0
  AMP PEAK  8(4Q12) WILD-TYPE         3         7
D8V44, multiclass
            clus
vv           AMP PEAK  8(4Q12) MUTATED AMP PEAK  8(4Q12) WILD-TYPE
  STAGE I                            0                           4
  STAGE IA                           0                           2
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           0                          31
  STAGE IB1                          4                          65
  STAGE IB2                          4                          28
  STAGE II                           0                           3
  STAGE IIA                          0                           6
  STAGE IIA1                         1                           4
  STAGE IIA2                         1                           6
  STAGE IIB                          0                          27
  STAGE III                          0                           1
  STAGE IIIB                         6                          28
  STAGE IVA                          0                           3
  STAGE IVB                          0                           7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(5P15.33) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(5P15.33) MUTATED    80  21
  AMP PEAK  9(5P15.33) WILD-TYPE 103  29
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           101                            132 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                            21                             29 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BQ 
       49.48        57.04        11.44       144.16       173.29        19.86 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       31.40        46.32        57.73        20.91        40.93         3.58 
TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL 
       73.18       100.14        38.43        52.01        18.02        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19        85.55        60.69         9.34 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR 
        2.73        50.99        45.83        75.78        99.91        27.52 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VL TCGA-DS-A0VM 
        4.47         1.12        58.88        44.94         2.66       117.99 
TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3Y4 TCGA-EA-A439 TCGA-EA-A43B 
       22.98         0.76         1.32        14.50        14.50         1.81 
TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2PG 
       14.89        13.91        14.96        13.48        45.96         1.51 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
        0.43         0.59         0.59        16.08         1.18         2.24 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L 
        0.10         0.10         0.03        20.35         6.94        19.79 
TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA 
        4.73        23.84         0.66         1.45         1.97         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL 
       25.41         7.13        21.67        78.71        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A4AW 
       27.42        24.56         5.13         6.71         7.99         0.89 
TCGA-LP-A5U3 TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.82         0.07         2.96        13.35        15.95         3.39 
TCGA-Q1-A6DW TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EH 
       17.56        11.67        12.16        61.28        10.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X 
       14.07        19.96        53.52        11.51        49.55        16.64 
TCGA-VS-A94Y TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
        4.73        43.82        39.35        38.96        18.05 

$`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         0.82        17.85        20.42       182.93       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 
        6.12        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         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35         1.35        12.66        12.82         0.26         1.48 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-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        23.70         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 
        6.12         1.22         0.92         2.17         1.02         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
        1.48         0.82         3.52         1.35         1.32         1.12 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
      117.40        96.95        81.96         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
       15.58        10.06        21.11       195.85        30.31        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.07         0.30         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73O 
       29.72         4.34         5.49        15.58        16.14        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         5.88         6.25        10.39        19.59         3.88 
TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       93.99        34.52        29.03        32.15        46.03        23.28 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       39.78        31.27        23.24        44.88        42.58        42.08 

  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                         195.85 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                         16.64                          15.30 
[1] "0.0 - 173.3 (16.6)" "0.0 - 195.8 (15.3)"
[1] "hr=" "1"  
D9V2, continuous
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK  9(5P15.33) MUTATED   46 24     5
  AMP PEAK  9(5P15.33) WILD-TYPE 75 26     6
D9V3, multiclass
       clus
vv      AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T1                              46                             75
  T2                              24                             26
  T3+T4                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   43 18
  AMP PEAK  9(5P15.33) WILD-TYPE 68 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     43   18
  AMP PEAK  9(5P15.33) WILD-TYPE   68   29
   clus
vv  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  0                           43                             68
  1                           18                             29
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  9(5P15.33) MUTATED   43  2 35
  AMP PEAK  9(5P15.33) WILD-TYPE 48  6 58
D9V5, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  M0                           43                             48
  M1                            2                              6
  MX                           35                             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(5P15.33) MUTATED               2                               96
  AMP PEAK  9(5P15.33) WILD-TYPE             3                              101
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  9(5P15.33) MUTATED                                               1
  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                                              1
  AMP PEAK  9(5P15.33) WILD-TYPE                                            5
D9V6, multiclass
                                               clus
vv                                              AMP PEAK  9(5P15.33) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        96
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK  9(5P15.33) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         101
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  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"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED    12  94
  AMP PEAK  9(5P15.33) WILD-TYPE  18 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     12   94
  AMP PEAK  9(5P15.33) WILD-TYPE   18  114
     clus
vv    AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  NO                            12                             18
  YES                           94                            114
[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                          11
  AMP PEAK  9(5P15.33) WILD-TYPE                        13
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  9(5P15.33) MUTATED                                           0
  AMP PEAK  9(5P15.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK  9(5P15.33) MUTATED      78
  AMP PEAK  9(5P15.33) WILD-TYPE    91
D9V10, multiclass
                                           clus
vv                                          AMP PEAK  9(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               78
                                           clus
vv                                          AMP PEAK  9(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED    7 62
  AMP PEAK  9(5P15.33) WILD-TYPE  9 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED      7   62
  AMP PEAK  9(5P15.33) WILD-TYPE    9   87
                        clus
vv                       AMP PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       AMP PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                             87
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   31 10
  AMP PEAK  9(5P15.33) WILD-TYPE 40 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     31   10
  AMP PEAK  9(5P15.33) WILD-TYPE   40   15
            clus
vv           AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  TUMOR FREE                           31                             40
  WITH TUMOR                           10                             15
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK  9(5P15.33) MUTATED       12      3       1      3       3
  AMP PEAK  9(5P15.33) WILD-TYPE     11      2       0      7       4
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK  9(5P15.33) MUTATED              78       6
  AMP PEAK  9(5P15.33) WILD-TYPE           100       8
D9V14, multiclass
               clus
vv              AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  BRAZIL                                  12                             11
  CANADA                                   3                              2
  NIGERIA                                  1                              0
  RUSSIA                                   3                              7
  UKRAINE                                  3                              4
  UNITED STATES                           78                            100
  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 40 51  1  6
  AMP PEAK  9(5P15.33) WILD-TYPE 12 66 46  0  8
D9V15, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  G1                            5                             12
  G2                           40                             66
  G3                           51                             46
  G4                            1                              0
  GX                            6                              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V16, continuous
D9V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  9(5P15.33) MUTATED                                            15
  AMP PEAK  9(5P15.33) WILD-TYPE                                          16
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  9(5P15.33) MUTATED                                        2
  AMP PEAK  9(5P15.33) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  9(5P15.33) MUTATED                                                 0
  AMP PEAK  9(5P15.33) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  9(5P15.33) MUTATED               26                  45
  AMP PEAK  9(5P15.33) WILD-TYPE             26                  67
D9V18, multiclass
                                                 clus
vv                                                AMP PEAK  9(5P15.33) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            26
  LIFELONG NON-SMOKER                                                       45
                                                 clus
vv                                                AMP PEAK  9(5P15.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              26
  LIFELONG NON-SMOKER                                                         67
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V19, continuous
D9V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  9(5P15.33) MUTATED             6       38             5        8
  AMP PEAK  9(5P15.33) WILD-TYPE          13       37             7        4
D9V21, multiclass
               clus
vv              AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  COMBINATION                              6                             13
  EXTERNAL                                38                             37
  EXTERNAL BEAM                            5                              7
  INTERNAL                                 8                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    18             9
  AMP PEAK  9(5P15.33) WILD-TYPE                  10             7
D9V23, multiclass
                     clus
vv                    AMP PEAK  9(5P15.33) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                           18
  REGIONAL SITE                                  9
                     clus
vv                    AMP PEAK  9(5P15.33) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             10
  REGIONAL SITE                                    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"
D9V24, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   21  1
  AMP PEAK  9(5P15.33) WILD-TYPE 13  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     21    1
  AMP PEAK  9(5P15.33) WILD-TYPE   13    2
     clus
vv    AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  CGY                           21                             13
  GY                             1                              2
[1] 2 2
[1] FALSE
D9V25, continuous
D9V26, continuous
D9V27, continuous
D9V28, continuous
D9V29, continuous
D9V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                     3
  AMP PEAK  9(5P15.33) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  9(5P15.33) MUTATED                        15
  AMP PEAK  9(5P15.33) WILD-TYPE                      14
                                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                       5
D9V31, multiclass
                                     clus
vv                                    AMP PEAK  9(5P15.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                       15
  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                                         14
  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  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                                                6
  AMP PEAK  9(5P15.33) WILD-TYPE                                             10
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  9(5P15.33) MUTATED                                                                                  25
  AMP PEAK  9(5P15.33) WILD-TYPE                                                                                43
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  9(5P15.33) MUTATED                                                                                             48
  AMP PEAK  9(5P15.33) WILD-TYPE                                                                                           57
D9V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  9(5P15.33) 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)                                      25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           48
                                                                                              clus
vv                                                                                             AMP PEAK  9(5P15.33) 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)                                        43
  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"
D9V33, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   24 29
  AMP PEAK  9(5P15.33) WILD-TYPE 44 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     24   29
  AMP PEAK  9(5P15.33) WILD-TYPE   44   41
         clus
vv        AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  ABSENT                            24                             44
  PRESENT                           29                             41
[1] 2 2
[1] FALSE
D9V34, continuous
D9V35, continuous
D9V36, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   15 46
  AMP PEAK  9(5P15.33) WILD-TYPE 28 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     15   46
  AMP PEAK  9(5P15.33) WILD-TYPE   28   48
                                          clus
vv                                         AMP PEAK  9(5P15.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           46
                                          clus
vv                                         AMP PEAK  9(5P15.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             48
[1] 2 2
[1] FALSE
D9V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  9(5P15.33) MUTATED              5          21         21
  AMP PEAK  9(5P15.33) WILD-TYPE            5          28         36
D9V38, multiclass
              clus
vv             AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  CURRENT USER                            5                              5
  FORMER USER                            21                             28
  NEVER USED                             21                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V39, continuous
D9V40, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   31  5
  AMP PEAK  9(5P15.33) WILD-TYPE 58 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     31    5
  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                            31                             58
  PRESENT                            5                             11
[1] 2 2
[1] FALSE
D9V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK  9(5P15.33) MUTATED     1    0  13   24    8  0   4    5    1  14  0
  AMP PEAK  9(5P15.33) WILD-TYPE   0    1  17   41   16  4   4    2    8   8  1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK  9(5P15.33) MUTATED     5  0   0  7
  AMP PEAK  9(5P15.33) WILD-TYPE   3  2   1  7
D9V42, multiclass
      clus
vv     AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T1A                             1                              0
  T1A1                            0                              1
  T1B                            13                             17
  T1B1                           24                             41
  T1B2                            8                             16
  T2                              0                              4
  T2A                             4                              4
  T2A1                            5                              2
  T2A2                            1                              8
  T2B                            14                              8
  T3                              0                              1
  T3B                             5                              3
  T4                              0                              2
  TIS                             0                              1
  TX                              7                              7
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  9(5P15.33) MUTATED         2        2         0         1       14
  AMP PEAK  9(5P15.33) WILD-TYPE       2        0         1         0       17
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  9(5P15.33) MUTATED          25        12        1         3
  AMP PEAK  9(5P15.33) WILD-TYPE        44        20        2         3
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  9(5P15.33) MUTATED            4          1        19         0
  AMP PEAK  9(5P15.33) WILD-TYPE          1          6         8         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  9(5P15.33) MUTATED           16         1         0
  AMP PEAK  9(5P15.33) WILD-TYPE         18         2         7
D9V44, multiclass
            clus
vv           AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                              2                              0
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             14                             17
  STAGE IB1                            25                             44
  STAGE IB2                            12                             20
  STAGE II                              1                              2
  STAGE IIA                             3                              3
  STAGE IIA1                            4                              1
  STAGE IIA2                            1                              6
  STAGE IIB                            19                              8
  STAGE III                             0                              1
  STAGE IIIB                           16                             18
  STAGE IVA                             1                              2
  STAGE IVB                             0                              7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(6P21.33) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(6P21.33) MUTATED    45  17
  AMP PEAK 10(6P21.33) WILD-TYPE 138  33
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                            62                            171 
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                            17                             33 
$`AMP PEAK 10(6P21.33) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        57.04        11.44         5.46        31.40        46.32 
TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LY TCGA-C5-A3HD 
       35.01        38.99        35.61        20.91        78.35        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       18.02        17.85       154.32        85.55        60.69        94.95 
TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VM TCGA-DS-A7WH 
        2.73        45.83        58.88        44.94       117.99        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A5O9 
        8.28         0.76        14.50         1.81        14.89        13.91 
TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
       14.96         0.36         0.59        16.08         1.18         2.24 
TCGA-EK-A3GJ TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A57G TCGA-HG-A2PA 
        0.10         6.12         1.22        23.84         1.32        25.41 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX 
       96.95        78.71        21.11        30.31        11.28         0.07 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD 
        0.03        29.72         5.49         2.96        13.35        11.67 
TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A952 
       93.99        14.07        19.96        11.51        39.78        44.88 
TCGA-VS-A959 TCGA-VS-A9U5 
       39.35        38.96 

$`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         0.82 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93       101.82       134.33        15.48        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 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        4.47         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         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA 
        1.18        14.50         1.35         1.35        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        0.26         1.48        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        23.70         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         4.73 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.35         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        9.01         7.13        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        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58        10.06         5.13         6.71       195.85         7.99 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM 
        0.89         0.30         0.82         0.20        13.87         5.42 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        0.07         4.34        15.58        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59         3.88        12.16        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       29.03        20.22        53.52        32.15        46.03        23.28 
TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 
       49.55        31.27        16.64         4.73        23.24        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-WL-A834 
       42.08        43.82        18.05 

  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                        154.32                         195.85 
  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE 
                         18.99                          15.02 
[1] "0.0 - 154.3 (19.0)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1.3"
D10V2, continuous
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 10(6P21.33) MUTATED   31 14     2
  AMP PEAK 10(6P21.33) WILD-TYPE 90 36     9
D10V3, multiclass
       clus
vv      AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  T1                              31                             90
  T2                              14                             36
  T3+T4                            2                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   31 11
  AMP PEAK 10(6P21.33) WILD-TYPE 80 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     31   11
  AMP PEAK 10(6P21.33) WILD-TYPE   80   36
   clus
vv  AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  0                           31                             80
  1                           11                             36
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 10(6P21.33) MUTATED   29  2 19
  AMP PEAK 10(6P21.33) WILD-TYPE 62  6 74
D10V5, multiclass
    clus
vv   AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  M0                           29                             62
  M1                            2                              6
  MX                           19                             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"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(6P21.33) MUTATED               0                               54
  AMP PEAK 10(6P21.33) WILD-TYPE             5                              143
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 10(6P21.33) MUTATED                                               1
  AMP PEAK 10(6P21.33) WILD-TYPE                                             4
                                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                                              4
  AMP PEAK 10(6P21.33) WILD-TYPE                                            2
D10V6, multiclass
                                               clus
vv                                              AMP PEAK 10(6P21.33) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        54
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              AMP PEAK 10(6P21.33) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         143
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(6P21.33) MUTATED    10  54
  AMP PEAK 10(6P21.33) WILD-TYPE  20 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     10   54
  AMP PEAK 10(6P21.33) WILD-TYPE   20  154
     clus
vv    AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  NO                            10                             20
  YES                           54                            154
[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                           6
  AMP PEAK 10(6P21.33) WILD-TYPE                        18
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 10(6P21.33) MUTATED                                           1
  AMP PEAK 10(6P21.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 10(6P21.33) MUTATED      46
  AMP PEAK 10(6P21.33) WILD-TYPE   123
D10V10, multiclass
                                           clus
vv                                          AMP PEAK 10(6P21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               46
                                           clus
vv                                          AMP PEAK 10(6P21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D10V11, binary
                                cls
clus                               0   1
  AMP PEAK 10(6P21.33) MUTATED     3  38
  AMP PEAK 10(6P21.33) WILD-TYPE  13 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED      3   38
  AMP PEAK 10(6P21.33) WILD-TYPE   13  111
                        clus
vv                       AMP PEAK 10(6P21.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           38
                        clus
vv                       AMP PEAK 10(6P21.33) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            111
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   18 11
  AMP PEAK 10(6P21.33) WILD-TYPE 53 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     18   11
  AMP PEAK 10(6P21.33) WILD-TYPE   53   14
            clus
vv           AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  TUMOR FREE                           18                             53
  WITH TUMOR                           11                             14
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 10(6P21.33) MUTATED        7      2       1      2       3
  AMP PEAK 10(6P21.33) WILD-TYPE     16      3       0      8       4
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 10(6P21.33) MUTATED              45       4
  AMP PEAK 10(6P21.33) WILD-TYPE           133      10
D10V14, multiclass
               clus
vv              AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  BRAZIL                                   7                             16
  CANADA                                   2                              3
  NIGERIA                                  1                              0
  RUSSIA                                   2                              8
  UKRAINE                                  3                              4
  UNITED STATES                           45                            133
  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 26 33  1  1
  AMP PEAK 10(6P21.33) WILD-TYPE 15 80 64  0 13
D10V15, multiclass
    clus
vv   AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  G1                            2                             15
  G2                           26                             80
  G3                           33                             64
  G4                            1                              0
  GX                            1                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V16, continuous
D10V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 10(6P21.33) MUTATED                                             6
  AMP PEAK 10(6P21.33) WILD-TYPE                                          25
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 10(6P21.33) MUTATED                                        2
  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                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 10(6P21.33) MUTATED               15                  32
  AMP PEAK 10(6P21.33) WILD-TYPE             37                  80
D10V18, multiclass
                                                 clus
vv                                                AMP PEAK 10(6P21.33) 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                                                            15
  LIFELONG NON-SMOKER                                                       32
                                                 clus
vv                                                AMP PEAK 10(6P21.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              37
  LIFELONG NON-SMOKER                                                         80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V19, continuous
D10V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 10(6P21.33) MUTATED             8       20             2        3
  AMP PEAK 10(6P21.33) WILD-TYPE          11       55            10        9
D10V21, multiclass
               clus
vv              AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  COMBINATION                              8                             11
  EXTERNAL                                20                             55
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     9             3
  AMP PEAK 10(6P21.33) WILD-TYPE                  19            13
D10V23, multiclass
                     clus
vv                    AMP PEAK 10(6P21.33) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            9
  REGIONAL SITE                                  3
                     clus
vv                    AMP PEAK 10(6P21.33) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             19
  REGIONAL SITE                                   13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V24, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   10  1
  AMP PEAK 10(6P21.33) WILD-TYPE 24  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     10    1
  AMP PEAK 10(6P21.33) WILD-TYPE   24    2
     clus
vv    AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  CGY                           10                             24
  GY                             1                              2
[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                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 10(6P21.33) MUTATED                         7
  AMP PEAK 10(6P21.33) WILD-TYPE                      22
                                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                       5
D10V31, multiclass
                                     clus
vv                                    AMP PEAK 10(6P21.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        7
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK 10(6P21.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         22
  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 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                                                5
  AMP PEAK 10(6P21.33) WILD-TYPE                                             11
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 10(6P21.33) MUTATED                                                                                  18
  AMP PEAK 10(6P21.33) WILD-TYPE                                                                                50
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 10(6P21.33) MUTATED                                                                                             26
  AMP PEAK 10(6P21.33) WILD-TYPE                                                                                           79
D10V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 10(6P21.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           26
                                                                                              clus
vv                                                                                             AMP PEAK 10(6P21.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        50
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V33, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   15 19
  AMP PEAK 10(6P21.33) WILD-TYPE 53 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     15   19
  AMP PEAK 10(6P21.33) WILD-TYPE   53   51
         clus
vv        AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  ABSENT                            15                             53
  PRESENT                           19                             51
[1] 2 2
[1] FALSE
D10V34, continuous
D10V35, continuous
D10V36, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   10 24
  AMP PEAK 10(6P21.33) WILD-TYPE 33 70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     10   24
  AMP PEAK 10(6P21.33) WILD-TYPE   33   70
                                          clus
vv                                         AMP PEAK 10(6P21.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           24
                                          clus
vv                                         AMP PEAK 10(6P21.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             70
[1] 2 2
[1] FALSE
D10V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 10(6P21.33) MUTATED              0          14         15
  AMP PEAK 10(6P21.33) WILD-TYPE           10          35         42
D10V38, multiclass
              clus
vv             AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  CURRENT USER                            0                             10
  FORMER USER                            14                             35
  NEVER USED                             15                             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V39, continuous
D10V40, binary
                                cls
clus                              0  1
  AMP PEAK 10(6P21.33) MUTATED   19  7
  AMP PEAK 10(6P21.33) WILD-TYPE 70  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(6P21.33) MUTATED     19    7
  AMP PEAK 10(6P21.33) WILD-TYPE   70    9
         clus
vv        AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  ABSENT                            19                             70
  PRESENT                            7                              9
[1] 2 2
[1] FALSE
D10V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 10(6P21.33) MUTATED     0    1   6   17    7  1   2    3    2   6  0
  AMP PEAK 10(6P21.33) WILD-TYPE   1    0  24   48   17  3   6    4    7  16  1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 10(6P21.33) MUTATED     2  0   1  3
  AMP PEAK 10(6P21.33) WILD-TYPE   6  2   0 11
D10V42, multiclass
      clus
vv     AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  T1A                             0                              1
  T1A1                            1                              0
  T1B                             6                             24
  T1B1                           17                             48
  T1B2                            7                             17
  T2                              1                              3
  T2A                             2                              6
  T2A1                            3                              4
  T2A2                            2                              7
  T2B                             6                             16
  T3                              0                              1
  T3B                             2                              6
  T4                              0                              2
  TIS                             1                              0
  TX                              3                             11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        2         0         1       25
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 10(6P21.33) MUTATED          20        11        0         2
  AMP PEAK 10(6P21.33) WILD-TYPE        49        21        3         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 10(6P21.33) MUTATED            3          2        10         0
  AMP PEAK 10(6P21.33) WILD-TYPE          2          5        17         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 10(6P21.33) MUTATED            7         1         0
  AMP PEAK 10(6P21.33) WILD-TYPE         27         2         7
D10V44, multiclass
            clus
vv           AMP PEAK 10(6P21.33) MUTATED AMP PEAK 10(6P21.33) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              0                              2
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                              6                             25
  STAGE IB1                            20                             49
  STAGE IB2                            11                             21
  STAGE II                              0                              3
  STAGE IIA                             2                              4
  STAGE IIA1                            3                              2
  STAGE IIA2                            2                              5
  STAGE IIB                            10                             17
  STAGE III                             0                              1
  STAGE IIIB                            7                             27
  STAGE IVA                             1                              2
  STAGE IVB                             0                              7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7P11.2) MUTATED    29  15
  AMP PEAK 11(7P11.2) WILD-TYPE 154  35
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           44                           189 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           15                            35 
$`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        60.69        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         0.26 
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         4.73        23.84         1.35        21.67        78.71 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ TCGA-MY-A913 
       36.36        21.44        20.48        10.06        21.11         5.49 
TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC 
        3.39        19.59        12.16        14.07        19.96        11.51 
TCGA-VS-A8QF TCGA-VS-A9U5 
       49.55        38.96 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       31.40        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         0.46        20.91         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       73.45        83.05        38.43         0.82        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       182.93       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       20.35        17.19        85.55        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR 
        2.73        50.99         8.35        75.78        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
        6.12        20.91         4.47         1.12        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       40.04        58.88         2.66       117.99       118.65        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18        17.52         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 
        1.35        14.50         1.81        12.66        12.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
       13.48         0.36        45.96        26.27         6.64         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.59         0.59         1.45         0.13        16.08         4.04 
TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.03        23.70         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03        20.35         7.92        14.70        19.79         6.12 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12         9.01        25.41         7.13        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VL 
       81.96        26.56        27.42         3.29        24.56        15.58 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        5.13         6.71       195.85        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        13.35        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       15.88         5.88         6.25        10.39         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM 
       53.52        32.15        46.03        23.28        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  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                        195.85 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                       20.795                        15.480 
[1] "0.1 - 173.3 (20.8)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.5"
D11V2, continuous
                               vv
clus                             T1  T2 T3+T4
  AMP PEAK 11(7P11.2) MUTATED    15  10     4
  AMP PEAK 11(7P11.2) WILD-TYPE 106  40     7
D11V3, multiclass
       clus
vv      AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1                             15                           106
  T2                             10                            40
  T3+T4                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   14 10
  AMP PEAK 11(7P11.2) WILD-TYPE 97 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     14   10
  AMP PEAK 11(7P11.2) WILD-TYPE   97   37
   clus
vv  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  0                          14                            97
  1                          10                            37
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 11(7P11.2) MUTATED   15  2 16
  AMP PEAK 11(7P11.2) WILD-TYPE 76  6 77
D11V5, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  M0                          15                            76
  M1                           2                             6
  MX                          16                            77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(7P11.2) MUTATED               0                               42
  AMP PEAK 11(7P11.2) WILD-TYPE             5                              155
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 11(7P11.2) MUTATED                                               0
  AMP PEAK 11(7P11.2) WILD-TYPE                                             5
                               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                                              0
  AMP PEAK 11(7P11.2) WILD-TYPE                                            6
D11V6, multiclass
                                               clus
vv                                              AMP PEAK 11(7P11.2) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       42
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            0
                                               clus
vv                                              AMP PEAK 11(7P11.2) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED     8  36
  AMP PEAK 11(7P11.2) WILD-TYPE  22 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      8   36
  AMP PEAK 11(7P11.2) WILD-TYPE   22  172
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  NO                            8                            22
  YES                          36                           172
[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                           7
  AMP PEAK 11(7P11.2) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(7P11.2) MUTATED                                           0    32
  AMP PEAK 11(7P11.2) WILD-TYPE                                         1   137
D11V10, multiclass
                                           clus
vv                                          AMP PEAK 11(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              32
                                           clus
vv                                          AMP PEAK 11(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D11V11, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED     3  27
  AMP PEAK 11(7P11.2) WILD-TYPE  13 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      3   27
  AMP PEAK 11(7P11.2) WILD-TYPE   13  122
                        clus
vv                       AMP PEAK 11(7P11.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          27
                        clus
vv                       AMP PEAK 11(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           122
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   11  9
  AMP PEAK 11(7P11.2) WILD-TYPE 60 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     11    9
  AMP PEAK 11(7P11.2) WILD-TYPE   60   16
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  TUMOR FREE                          11                            60
  WITH TUMOR                           9                            16
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 11(7P11.2) MUTATED        5      1       0      0       0
  AMP PEAK 11(7P11.2) WILD-TYPE     18      4       1     10       7
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK 11(7P11.2) MUTATED              37       1
  AMP PEAK 11(7P11.2) WILD-TYPE           141      13
D11V14, multiclass
               clus
vv              AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  BRAZIL                                  5                            18
  CANADA                                  1                             4
  NIGERIA                                 0                             1
  RUSSIA                                  0                            10
  UKRAINE                                 0                             7
  UNITED STATES                          37                           141
  VIETNAM                                 1                            13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK 11(7P11.2) MUTATED    1 15 23  1  3
  AMP PEAK 11(7P11.2) WILD-TYPE 16 91 74  0 11
D11V15, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  G1                           1                            16
  G2                          15                            91
  G3                          23                            74
  G4                           1                             0
  GX                           3                            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V16, continuous
D11V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 11(7P11.2) MUTATED                                             5
  AMP PEAK 11(7P11.2) WILD-TYPE                                          26
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 11(7P11.2) MUTATED                                        3
  AMP PEAK 11(7P11.2) WILD-TYPE                                      5
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 11(7P11.2) MUTATED                                                 1
  AMP PEAK 11(7P11.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 11(7P11.2) MUTATED                7                  21
  AMP PEAK 11(7P11.2) WILD-TYPE             45                  91
D11V18, multiclass
                                                 clus
vv                                                AMP PEAK 11(7P11.2) 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                                                            7
  LIFELONG NON-SMOKER                                                      21
                                                 clus
vv                                                AMP PEAK 11(7P11.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             45
  LIFELONG NON-SMOKER                                                        91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V19, continuous
D11V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 11(7P11.2) MUTATED             4       16             5        3
  AMP PEAK 11(7P11.2) WILD-TYPE          15       59             7        9
D11V21, multiclass
               clus
vv              AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  COMBINATION                             4                            15
  EXTERNAL                               16                            59
  EXTERNAL BEAM                           5                             7
  INTERNAL                                3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    10             4
  AMP PEAK 11(7P11.2) WILD-TYPE                  18            12
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                          10                            18
  REGIONAL SITE                                 4                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V24, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   12  2
  AMP PEAK 11(7P11.2) WILD-TYPE 22  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     12    2
  AMP PEAK 11(7P11.2) WILD-TYPE   22    1
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  CGY                          12                            22
  GY                            2                             1
[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                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 11(7P11.2) MUTATED                         3                       1
  AMP PEAK 11(7P11.2) WILD-TYPE                      26                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK 11(7P11.2) MUTATED                         2
  AMP PEAK 11(7P11.2) WILD-TYPE                       5
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                             5
  OTHER LOCATION, SPECIFY                                        26
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             13
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 11(7P11.2) MUTATED                                                                                  12
  AMP PEAK 11(7P11.2) WILD-TYPE                                                                                56
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 11(7P11.2) MUTATED                                                                                             22
  AMP PEAK 11(7P11.2) WILD-TYPE                                                                                           83
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)                                     12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          22
                                                                                              clus
vv                                                                                             AMP PEAK 11(7P11.2) 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)                                       56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V33, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED    6 16
  AMP PEAK 11(7P11.2) WILD-TYPE 62 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      6   16
  AMP PEAK 11(7P11.2) WILD-TYPE   62   54
         clus
vv        AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  ABSENT                            6                            62
  PRESENT                          16                            54
[1] 2 2
[1] FALSE
D11V34, continuous
D11V35, continuous
D11V36, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   10 17
  AMP PEAK 11(7P11.2) WILD-TYPE 33 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     10   17
  AMP PEAK 11(7P11.2) WILD-TYPE   33   77
                                          clus
vv                                         AMP PEAK 11(7P11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          17
                                          clus
vv                                         AMP PEAK 11(7P11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            77
[1] 2 2
[1] FALSE
D11V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK 11(7P11.2) MUTATED              2           7         10
  AMP PEAK 11(7P11.2) WILD-TYPE            8          42         47
D11V38, multiclass
              clus
vv             AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  CURRENT USER                           2                             8
  FORMER USER                            7                            42
  NEVER USED                            10                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V39, continuous
D11V40, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   14  2
  AMP PEAK 11(7P11.2) WILD-TYPE 75 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     14    2
  AMP PEAK 11(7P11.2) WILD-TYPE   75   14
         clus
vv        AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  ABSENT                           14                            75
  PRESENT                           2                            14
[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                            11 
                   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-MU-A51Y 
"AMP PEAK 11(7P11.2) WILD-TYPE" "AMP PEAK 11(7P11.2) WILD-TYPE" 
                   TCGA-MU-A8JM 
"AMP PEAK 11(7P11.2) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 11(7P11.2) MUTATED     0    0   6    6    3  0   0    5    2   3  0
  AMP PEAK 11(7P11.2) WILD-TYPE   1    1  24   59   21  4   8    2    7  19  1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK 11(7P11.2) MUTATED     3  1   1  3
  AMP PEAK 11(7P11.2) WILD-TYPE   5  1   0 11
D11V42, multiclass
      clus
vv     AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                            6                            24
  T1B1                           6                            59
  T1B2                           3                            21
  T2                             0                             4
  T2A                            0                             8
  T2A1                           5                             2
  T2A2                           2                             7
  T2B                            3                            19
  T3                             0                             1
  T3B                            3                             5
  T4                             1                             1
  TIS                            1                             0
  TX                             3                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        2         1         1       24
                               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        63        27        3         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 11(7P11.2) MUTATED            3          1         6         0
  AMP PEAK 11(7P11.2) WILD-TYPE          2          6        21         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 11(7P11.2) MUTATED            9         2         1
  AMP PEAK 11(7P11.2) WILD-TYPE         25         1         6
D11V44, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                             0                             2
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             7                            24
  STAGE IB1                            6                            63
  STAGE IB2                            5                            27
  STAGE II                             0                             3
  STAGE IIA                            2                             4
  STAGE IIA1                           3                             2
  STAGE IIA2                           1                             6
  STAGE IIB                            6                            21
  STAGE III                            0                             1
  STAGE IIIB                           9                            25
  STAGE IVA                            2                             1
  STAGE IVB                            1                             6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED    74  21
  AMP PEAK 12(8Q24.21) WILD-TYPE 109  29
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            95                            138 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            21                             29 
$`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 
      182.93       154.32        60.69        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         1.74        13.05 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 
       14.50         1.35        12.82         0.26        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         6.12         4.73 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A40J 
        1.22        23.84         0.66         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         7.13         9.44       137.16        26.56        36.36 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
       21.44        15.58         5.13        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MY-A5BF 
        0.07         0.30         0.82         0.20         0.03         4.34 
TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-Q1-A73S 
        5.49        13.35         3.39        17.56         5.88        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EJ 
       19.59         3.88        12.16        10.03        20.22        19.96 
TCGA-VS-A94X TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       16.64        42.58        43.82        38.96        18.05 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
      144.16       173.29         5.46        46.32        30.21        57.73 
TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX 
        0.46        20.91        40.93        44.22        73.18        83.05 
TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       78.35         0.82        20.42       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35        17.19        85.55        94.95         9.34 
TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A907 
        2.73        45.83        75.78        99.91         6.12         4.47 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VN 
       50.76        44.94        40.04        58.88        36.76       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HR 
       16.83        16.18        17.52         8.28         0.76         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B 
        0.82         0.62         1.18         1.35        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.66         1.48        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       13.48        12.59        26.27         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        1.18        23.70         2.24        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ 
       14.70        19.79         0.92         2.17         1.02         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-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC 
       21.67        20.78        14.93       147.39        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       96.95        78.71        81.96        27.42         3.29        24.56 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       20.48        10.06         6.71        21.11       195.85         7.99 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 
       13.87         5.42        29.72         0.07         2.96        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PD 
       15.95        16.14        14.07        15.88         6.25        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL 
       93.99        61.28        34.52        29.03        14.07        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        23.28        11.51        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A959 
       31.27         4.73        23.24        44.88        42.08        39.35 

  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 
                        182.93                         195.85 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        13.610                         16.505 
[1] "0.0 - 182.9 (13.6)" "0.0 - 195.8 (16.5)"
[1] "hr=" "1.3"
D12V2, continuous
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 12(8Q24.21) MUTATED   48 18     7
  AMP PEAK 12(8Q24.21) WILD-TYPE 73 32     4
D12V3, multiclass
       clus
vv      AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  T1                              48                             73
  T2                              18                             32
  T3+T4                            7                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   43 21
  AMP PEAK 12(8Q24.21) WILD-TYPE 68 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     43   21
  AMP PEAK 12(8Q24.21) WILD-TYPE   68   26
   clus
vv  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  0                           43                             68
  1                           21                             26
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 12(8Q24.21) MUTATED   35  4 37
  AMP PEAK 12(8Q24.21) WILD-TYPE 56  4 56
D12V5, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  M0                           35                             56
  M1                            4                              4
  MX                           37                             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8Q24.21) MUTATED               4                               81
  AMP PEAK 12(8Q24.21) WILD-TYPE             1                              116
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 12(8Q24.21) MUTATED                                               1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                             4
                                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                                              1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                            5
D12V6, multiclass
                                               clus
vv                                              AMP PEAK 12(8Q24.21) MUTATED
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        81
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 12(8Q24.21) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         116
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       14
  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"
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    11  86
  AMP PEAK 12(8Q24.21) WILD-TYPE  19 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     11   86
  AMP PEAK 12(8Q24.21) WILD-TYPE   19  122
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            11                             19
  YES                           86                            122
[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                          11
  AMP PEAK 12(8Q24.21) WILD-TYPE                        13
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 12(8Q24.21) MUTATED                                           1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 12(8Q24.21) MUTATED      68
  AMP PEAK 12(8Q24.21) WILD-TYPE   101
D12V10, multiclass
                                           clus
vv                                          AMP PEAK 12(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               68
                                           clus
vv                                          AMP PEAK 12(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED    5 64
  AMP PEAK 12(8Q24.21) WILD-TYPE 11 85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      5   64
  AMP PEAK 12(8Q24.21) WILD-TYPE   11   85
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                             85
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   29 12
  AMP PEAK 12(8Q24.21) WILD-TYPE 42 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     29   12
  AMP PEAK 12(8Q24.21) WILD-TYPE   42   13
            clus
vv           AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  TUMOR FREE                           29                             42
  WITH TUMOR                           12                             13
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 12(8Q24.21) MUTATED        7      2       0      4       4
  AMP PEAK 12(8Q24.21) WILD-TYPE     16      3       1      6       3
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 12(8Q24.21) MUTATED              73       7
  AMP PEAK 12(8Q24.21) WILD-TYPE           105       7
D12V14, multiclass
               clus
vv              AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  BRAZIL                                   7                             16
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   4                              6
  UKRAINE                                  4                              3
  UNITED STATES                           73                            105
  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    6 35 50  0  6
  AMP PEAK 12(8Q24.21) WILD-TYPE 11 71 47  1  8
D12V15, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  G1                            6                             11
  G2                           35                             71
  G3                           50                             47
  G4                            0                              1
  GX                            6                              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V16, continuous
D12V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 12(8Q24.21) MUTATED                                            10
  AMP PEAK 12(8Q24.21) WILD-TYPE                                          21
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 12(8Q24.21) MUTATED                                        3
  AMP PEAK 12(8Q24.21) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 12(8Q24.21) MUTATED                                                 1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 12(8Q24.21) MUTATED               18                  52
  AMP PEAK 12(8Q24.21) WILD-TYPE             34                  60
D12V18, multiclass
                                                 clus
vv                                                AMP PEAK 12(8Q24.21) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            18
  LIFELONG NON-SMOKER                                                       52
                                                 clus
vv                                                AMP PEAK 12(8Q24.21) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              34
  LIFELONG NON-SMOKER                                                         60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V19, continuous
D12V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 12(8Q24.21) MUTATED             9       30             3        6
  AMP PEAK 12(8Q24.21) WILD-TYPE          10       45             9        6
D12V21, multiclass
               clus
vv              AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  COMBINATION                              9                             10
  EXTERNAL                                30                             45
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 6                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     9             6
  AMP PEAK 12(8Q24.21) WILD-TYPE                  19            10
D12V23, multiclass
                     clus
vv                    AMP PEAK 12(8Q24.21) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            9
  REGIONAL SITE                                  6
                     clus
vv                    AMP PEAK 12(8Q24.21) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             19
  REGIONAL SITE                                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V24, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED    8  2
  AMP PEAK 12(8Q24.21) WILD-TYPE 26  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      8    2
  AMP PEAK 12(8Q24.21) WILD-TYPE   26    1
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  CGY                            8                             26
  GY                             2                              1
[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                                     1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 12(8Q24.21) MUTATED                        13
  AMP PEAK 12(8Q24.21) WILD-TYPE                      16
                                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                       6
D12V31, multiclass
                                     clus
vv                                    AMP PEAK 12(8Q24.21) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                       13
  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                                         16
  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 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                                                6
  AMP PEAK 12(8Q24.21) WILD-TYPE                                             10
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 12(8Q24.21) MUTATED                                                                                  32
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                                                36
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 12(8Q24.21) MUTATED                                                                                             43
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                                                           62
D12V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 12(8Q24.21) 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)                                      32
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           43
                                                                                              clus
vv                                                                                             AMP PEAK 12(8Q24.21) 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)                                        36
  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"
D12V33, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   22 29
  AMP PEAK 12(8Q24.21) WILD-TYPE 46 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     22   29
  AMP PEAK 12(8Q24.21) WILD-TYPE   46   41
         clus
vv        AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  ABSENT                            22                             46
  PRESENT                           29                             41
[1] 2 2
[1] FALSE
D12V34, continuous
D12V35, continuous
D12V36, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   18 41
  AMP PEAK 12(8Q24.21) WILD-TYPE 25 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     18   41
  AMP PEAK 12(8Q24.21) WILD-TYPE   25   53
                                          clus
vv                                         AMP PEAK 12(8Q24.21) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           41
                                          clus
vv                                         AMP PEAK 12(8Q24.21) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             53
[1] 2 2
[1] FALSE
D12V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 12(8Q24.21) MUTATED              1          20         22
  AMP PEAK 12(8Q24.21) WILD-TYPE            9          29         35
D12V38, multiclass
              clus
vv             AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  CURRENT USER                            1                              9
  FORMER USER                            20                             29
  NEVER USED                             22                             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V39, continuous
D12V40, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   34  4
  AMP PEAK 12(8Q24.21) WILD-TYPE 55 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     34    4
  AMP PEAK 12(8Q24.21) WILD-TYPE   55   12
         clus
vv        AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  ABSENT                            34                             55
  PRESENT                            4                             12
[1] 2 2
[1] FALSE
D12V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 12(8Q24.21) MUTATED     1    1  11   23   12  3   3    3    1   8  0
  AMP PEAK 12(8Q24.21) WILD-TYPE   0    0  19   42   12  1   5    4    8  14  1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 12(8Q24.21) MUTATED     6  1   1  5
  AMP PEAK 12(8Q24.21) WILD-TYPE   2  1   0  9
D12V42, multiclass
      clus
vv     AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  T1A                             1                              0
  T1A1                            1                              0
  T1B                            11                             19
  T1B1                           23                             42
  T1B2                           12                             12
  T2                              3                              1
  T2A                             3                              5
  T2A1                            3                              4
  T2A2                            1                              8
  T2B                             8                             14
  T3                              0                              1
  T3B                             6                              2
  T4                              1                              1
  TIS                             1                              0
  TX                              5                              9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 12(8Q24.21) MUTATED         3        2         1         1       13
  AMP PEAK 12(8Q24.21) WILD-TYPE       1        0         0         0       18
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 12(8Q24.21) MUTATED          21        13        2         1
  AMP PEAK 12(8Q24.21) WILD-TYPE        48        19        1         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 12(8Q24.21) MUTATED            1          1        15         0
  AMP PEAK 12(8Q24.21) WILD-TYPE          4          6        12         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 12(8Q24.21) MUTATED           17         1         2
  AMP PEAK 12(8Q24.21) WILD-TYPE         17         2         5
D12V44, multiclass
            clus
vv           AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                              2                              0
  STAGE IA1                             1                              0
  STAGE IA2                             1                              0
  STAGE IB                             13                             18
  STAGE IB1                            21                             48
  STAGE IB2                            13                             19
  STAGE II                              2                              1
  STAGE IIA                             1                              5
  STAGE IIA1                            1                              4
  STAGE IIA2                            1                              6
  STAGE IIB                            15                             12
  STAGE III                             0                              1
  STAGE IIIB                           17                             17
  STAGE IVA                             1                              2
  STAGE IVB                             2                              5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(9P24.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(9P24.1) MUTATED    41   9
  AMP PEAK 13(9P24.1) WILD-TYPE 142  41
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           50                           183 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                            9                            41 
$`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 
        0.82        52.01       182.93       134.33        15.48       147.35 
TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VM 
       85.55         2.73        75.78        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        10.06        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         0.07         5.49         2.96        13.35 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC 
       11.67        93.99        12.16        53.52        32.15        11.51 
TCGA-VS-A94X TCGA-VS-A9U5 
       16.64        38.96 

$`AMP PEAK 13(9P24.1) WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       57.04        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       31.40        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF 
       44.22        78.35       100.14        38.43        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH 
       20.42       154.32       101.82        20.35        17.19        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34        13.61        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        58.88        50.76        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
        2.66       118.65        16.18        17.52         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
       12.36         1.74         1.32         0.82         0.62         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZF 
       12.82         0.26        14.89         1.48        15.02        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       13.58        13.48         0.36        12.59        45.96         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-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A2QG 
       14.70        19.79         6.12         4.73        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41         7.13        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
      147.39       137.16        66.81       117.40        96.95        81.96 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX 
        5.13         6.71       195.85         7.99         0.89         0.07 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.82         0.20        13.87         0.03         5.42        29.72 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34        15.58        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
        3.88        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       14.07        19.96        46.03        23.28        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       31.27         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                       182.93                        195.85 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                       16.735                        15.580 
[1] "0.1 - 182.9 (16.7)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.7"
D13V2, continuous
                               vv
clus                             T1  T2 T3+T4
  AMP PEAK 13(9P24.1) MUTATED    21  14     2
  AMP PEAK 13(9P24.1) WILD-TYPE 100  36     9
D13V3, multiclass
       clus
vv      AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  T1                             21                           100
  T2                             14                            36
  T3+T4                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   17 16
  AMP PEAK 13(9P24.1) WILD-TYPE 94 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     17   16
  AMP PEAK 13(9P24.1) WILD-TYPE   94   31
   clus
vv  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  0                          17                            94
  1                          16                            31
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 13(9P24.1) MUTATED   19  1 20
  AMP PEAK 13(9P24.1) WILD-TYPE 72  7 73
D13V5, multiclass
    clus
vv   AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  M0                          19                            72
  M1                           1                             7
  MX                          20                            73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(9P24.1) MUTATED               0                               45
  AMP PEAK 13(9P24.1) WILD-TYPE             5                              152
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 13(9P24.1) MUTATED                                               1
  AMP PEAK 13(9P24.1) WILD-TYPE                                             4
                               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                                              1
  AMP PEAK 13(9P24.1) WILD-TYPE                                            5
D13V6, multiclass
                                               clus
vv                                              AMP PEAK 13(9P24.1) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       45
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              AMP PEAK 13(9P24.1) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        152
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED     4  47
  AMP PEAK 13(9P24.1) WILD-TYPE  26 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED      4   47
  AMP PEAK 13(9P24.1) WILD-TYPE   26  161
     clus
vv    AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  NO                            4                            26
  YES                          47                           161
[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                          10
  AMP PEAK 13(9P24.1) WILD-TYPE                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(9P24.1) MUTATED                                           0    31
  AMP PEAK 13(9P24.1) WILD-TYPE                                         1   138
D13V10, multiclass
                                           clus
vv                                          AMP PEAK 13(9P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                          10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              31
                                           clus
vv                                          AMP PEAK 13(9P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D13V11, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED     3  27
  AMP PEAK 13(9P24.1) WILD-TYPE  13 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED      3   27
  AMP PEAK 13(9P24.1) WILD-TYPE   13  122
                        clus
vv                       AMP PEAK 13(9P24.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          27
                        clus
vv                       AMP PEAK 13(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           122
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   20  0
  AMP PEAK 13(9P24.1) WILD-TYPE 51 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     20    0
  AMP PEAK 13(9P24.1) WILD-TYPE   51   25
            clus
vv           AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  TUMOR FREE                          20                            51
  WITH TUMOR                           0                            25
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 13(9P24.1) MUTATED        5      2       1      0       1
  AMP PEAK 13(9P24.1) WILD-TYPE     18      3       0     10       6
                               vv
clus                            UNITED STATES VIETNAM
  AMP PEAK 13(9P24.1) MUTATED              39       3
  AMP PEAK 13(9P24.1) WILD-TYPE           139      11
D13V14, multiclass
               clus
vv              AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  BRAZIL                                  5                            18
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  0                            10
  UKRAINE                                 1                             6
  UNITED STATES                          39                           139
  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    3 21 24  1  1
  AMP PEAK 13(9P24.1) WILD-TYPE 14 85 73  0 13
D13V15, multiclass
    clus
vv   AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  G1                           3                            14
  G2                          21                            85
  G3                          24                            73
  G4                           1                             0
  GX                           1                            13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V16, continuous
D13V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 13(9P24.1) MUTATED                                             4
  AMP PEAK 13(9P24.1) WILD-TYPE                                          27
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 13(9P24.1) MUTATED                                        2
  AMP PEAK 13(9P24.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 13(9P24.1) MUTATED                                                 2
  AMP PEAK 13(9P24.1) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 13(9P24.1) MUTATED               12                  25
  AMP PEAK 13(9P24.1) WILD-TYPE             40                  87
D13V18, multiclass
                                                 clus
vv                                                AMP PEAK 13(9P24.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           12
  LIFELONG NON-SMOKER                                                      25
                                                 clus
vv                                                AMP PEAK 13(9P24.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             40
  LIFELONG NON-SMOKER                                                        87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V19, continuous
D13V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 13(9P24.1) MUTATED             2       20             2        5
  AMP PEAK 13(9P24.1) WILD-TYPE          17       55            10        7
D13V21, multiclass
               clus
vv              AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  COMBINATION                             2                            17
  EXTERNAL                               20                            55
  EXTERNAL BEAM                           2                            10
  INTERNAL                                5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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             5
  AMP PEAK 13(9P24.1) WILD-TYPE                  18            11
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                            18
  REGIONAL SITE                                 5                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V24, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   10  2
  AMP PEAK 13(9P24.1) WILD-TYPE 24  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     10    2
  AMP PEAK 13(9P24.1) WILD-TYPE   24    1
     clus
vv    AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  CGY                          10                            24
  GY                            2                             1
[1] 2 2
[1] FALSE
D13V25, continuous
D13V26, continuous
D13V27, continuous
D13V28, continuous
D13V29, continuous
D13V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 13(9P24.1) MUTATED                         8                       0
  AMP PEAK 13(9P24.1) WILD-TYPE                      21                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK 13(9P24.1) MUTATED                         3
  AMP PEAK 13(9P24.1) WILD-TYPE                       4
D13V31, multiclass
                                     clus
vv                                    AMP PEAK 13(9P24.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       8
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    AMP PEAK 13(9P24.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  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)
  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                                             13
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 13(9P24.1) MUTATED                                                                                  13
  AMP PEAK 13(9P24.1) WILD-TYPE                                                                                55
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 13(9P24.1) MUTATED                                                                                             24
  AMP PEAK 13(9P24.1) WILD-TYPE                                                                                           81
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)                                     13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          24
                                                                                              clus
vv                                                                                             AMP PEAK 13(9P24.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            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"
D13V33, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   12 19
  AMP PEAK 13(9P24.1) WILD-TYPE 56 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     12   19
  AMP PEAK 13(9P24.1) WILD-TYPE   56   51
         clus
vv        AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  ABSENT                           12                            56
  PRESENT                          19                            51
[1] 2 2
[1] FALSE
D13V34, continuous
D13V35, continuous
D13V36, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   11 15
  AMP PEAK 13(9P24.1) WILD-TYPE 32 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     11   15
  AMP PEAK 13(9P24.1) WILD-TYPE   32   79
                                          clus
vv                                         AMP PEAK 13(9P24.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          15
                                          clus
vv                                         AMP PEAK 13(9P24.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            79
[1] 2 2
[1] FALSE
D13V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK 13(9P24.1) MUTATED              2          15          7
  AMP PEAK 13(9P24.1) WILD-TYPE            8          34         50
D13V38, multiclass
              clus
vv             AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  CURRENT USER                           2                             8
  FORMER USER                           15                            34
  NEVER USED                             7                            50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V39, continuous
D13V40, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   17  2
  AMP PEAK 13(9P24.1) WILD-TYPE 72 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     17    2
  AMP PEAK 13(9P24.1) WILD-TYPE   72   14
         clus
vv        AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  ABSENT                           17                            72
  PRESENT                           2                            14
[1] 2 2
[1] FALSE
D13V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 13(9P24.1) MUTATED     0    0   7   10    4  2   3    3    0   6  0
  AMP PEAK 13(9P24.1) WILD-TYPE   1    1  23   55   20  2   5    4    9  16  1
                               vv
clus                            T3B T4 TIS TX
  AMP PEAK 13(9P24.1) MUTATED     2  0   1  2
  AMP PEAK 13(9P24.1) WILD-TYPE   6  2   0 12
D13V42, multiclass
      clus
vv     AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                            7                            23
  T1B1                          10                            55
  T1B2                           4                            20
  T2                             2                             2
  T2A                            3                             5
  T2A1                           3                             4
  T2A2                           0                             9
  T2B                            6                            16
  T3                             0                             1
  T3B                            2                             6
  T4                             0                             2
  TIS                            1                             0
  TX                             2                            12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 13(9P24.1) MUTATED         0        0         0         0       10
  AMP PEAK 13(9P24.1) WILD-TYPE       4        2         1         1       21
                               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        57        25        3         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 13(9P24.1) MUTATED            2          0         5         0
  AMP PEAK 13(9P24.1) WILD-TYPE          3          7        22         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 13(9P24.1) MUTATED            9         2         0
  AMP PEAK 13(9P24.1) WILD-TYPE         25         1         7
D13V44, multiclass
            clus
vv           AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                             0                             2
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            10                            21
  STAGE IB1                           12                            57
  STAGE IB2                            7                            25
  STAGE II                             0                             3
  STAGE IIA                            2                             4
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                            5                            22
  STAGE III                            0                             1
  STAGE IIIB                           9                            25
  STAGE IVA                            2                             1
  STAGE IVB                            0                             7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(11P12) MUTATION ANALYSIS
D14V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 14(11P12) MUTATED    14   4
  AMP PEAK 14(11P12) WILD-TYPE 169  46
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                          18                          215 
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                           4                           46 
$`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-FU-A40J TCGA-FU-A770 TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-MY-A913 
       26.27         1.35         1.12        24.56        21.44         5.49 
TCGA-PN-A8MA TCGA-Q1-A6DW TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 
        2.96        17.56        34.52        14.07        32.15        46.03 

$`AMP PEAK 14(11P12) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       36.56       144.16       177.04       173.29        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       67.46        46.32        30.21        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19        85.55        60.69        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       58.88        50.76        44.94        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35        14.50         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG 
       13.58        13.48         0.36        12.59         6.64         1.51 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.73         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.32         1.97         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       27.42         3.29        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        6.71        21.11       195.85        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
        0.03         5.42        29.72         0.07         4.34        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P 
       13.35        15.95         3.39        16.14        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        12.16        61.28        10.03        29.03        20.22 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       19.96        53.52        23.28        11.51        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       31.27        16.64         4.73        23.24        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.08        43.82        39.35        38.96        18.05 

  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                       195.85 
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                      25.415                       15.480 
[1] "1.1 - 73.2 (25.4)"  "0.0 - 195.8 (15.5)"
[1] "hr=" "1"  
D14V2, continuous
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 14(11P12) MUTATED     3   5     3
  AMP PEAK 14(11P12) WILD-TYPE 118  45     8
D14V3, multiclass
       clus
vv      AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  T1                             3                          118
  T2                             5                           45
  T3+T4                          3                            8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                              cls
clus                             0   1
  AMP PEAK 14(11P12) MUTATED     4   4
  AMP PEAK 14(11P12) WILD-TYPE 107  43
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      4    4
  AMP PEAK 14(11P12) WILD-TYPE  107   43
   clus
vv  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  0                          4                          107
  1                          4                           43
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  AMP PEAK 14(11P12) MUTATED    6  1  7
  AMP PEAK 14(11P12) WILD-TYPE 85  7 86
D14V5, multiclass
    clus
vv   AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  M0                          6                           85
  M1                          1                            7
  MX                          7                           86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(11P12) MUTATED               0                               16
  AMP PEAK 14(11P12) WILD-TYPE             5                              181
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 14(11P12) MUTATED                                               1
  AMP PEAK 14(11P12) WILD-TYPE                                             4
                              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                                            6
D14V6, multiclass
                                               clus
vv                                              AMP PEAK 14(11P12) MUTATED
  ADENOSQUAMOUS                                                          0
  CERVICAL SQUAMOUS CELL CARCINOMA                                      16
  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                                       181
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                              cls
clus                             0   1
  AMP PEAK 14(11P12) MUTATED     5  14
  AMP PEAK 14(11P12) WILD-TYPE  25 194
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      5   14
  AMP PEAK 14(11P12) WILD-TYPE   25  194
     clus
vv    AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  NO                           5                           25
  YES                         14                          194
[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                        22
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 14(11P12) MUTATED                                           0    14
  AMP PEAK 14(11P12) WILD-TYPE                                         1   155
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                                                             14
                                           clus
vv                                          AMP PEAK 14(11P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  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"
D14V11, binary
                              cls
clus                             0   1
  AMP PEAK 14(11P12) MUTATED     3   7
  AMP PEAK 14(11P12) WILD-TYPE  13 142
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      3    7
  AMP PEAK 14(11P12) WILD-TYPE   13  142
                        clus
vv                       AMP PEAK 14(11P12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                          7
                        clus
vv                       AMP PEAK 14(11P12) WILD-TYPE
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          142
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    3  5
  AMP PEAK 14(11P12) WILD-TYPE 68 20
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      3    5
  AMP PEAK 14(11P12) WILD-TYPE   68   20
            clus
vv           AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  TUMOR FREE                          3                           68
  WITH TUMOR                          5                           20
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 14(11P12) MUTATED        4      1       1      0       0
  AMP PEAK 14(11P12) WILD-TYPE     19      4       0     10       7
                              vv
clus                           UNITED STATES VIETNAM
  AMP PEAK 14(11P12) MUTATED              13       0
  AMP PEAK 14(11P12) WILD-TYPE           165      14
D14V14, multiclass
               clus
vv              AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  BRAZIL                                 4                           19
  CANADA                                 1                            4
  NIGERIA                                1                            0
  RUSSIA                                 0                           10
  UKRAINE                                0                            7
  UNITED STATES                         13                          165
  VIETNAM                                0                           14
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            G1  G2  G3  G4  GX
  AMP PEAK 14(11P12) MUTATED     0   6  11   0   2
  AMP PEAK 14(11P12) WILD-TYPE  17 100  86   1  12
D14V15, multiclass
    clus
vv   AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  G1                          0                           17
  G2                          6                          100
  G3                         11                           86
  G4                          0                            1
  GX                          2                           12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V16, continuous
[1] "Remove cluster labels:"     "AMP PEAK 14(11P12) MUTATED"
clus
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                           1                           33 
                  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-MU-A5YI                   TCGA-MU-A8JM 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-Q1-A73S                   TCGA-RA-A741 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-VS-A8QF                   TCGA-VS-A94Z 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-WL-A834 
"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                                          30
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 14(11P12) MUTATED                                        0
  AMP PEAK 14(11P12) WILD-TYPE                                      8
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 14(11P12) MUTATED                                                 1
  AMP PEAK 14(11P12) WILD-TYPE                                               1
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 14(11P12) MUTATED                4                   8
  AMP PEAK 14(11P12) WILD-TYPE             48                 104
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                                                           4
  LIFELONG NON-SMOKER                                                      8
                                                 clus
vv                                                AMP PEAK 14(11P12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            48
  LIFELONG NON-SMOKER                                                      104
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V19, continuous
D14V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 14(11P12) MUTATED             2        7             3        2
  AMP PEAK 14(11P12) WILD-TYPE          17       68             9       10
D14V21, multiclass
               clus
vv              AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  COMBINATION                            2                           17
  EXTERNAL                               7                           68
  EXTERNAL BEAM                          3                            9
  INTERNAL                               2                           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                  25            14
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                           25
  REGIONAL SITE                                2                           14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V24, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    4  1
  AMP PEAK 14(11P12) WILD-TYPE 30  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      4    1
  AMP PEAK 14(11P12) WILD-TYPE   30    2
     clus
vv    AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  CGY                          4                           30
  GY                           1                            2
[1] 2 2
[1] FALSE
D14V25, continuous
D14V26, continuous
D14V27, continuous
D14V28, continuous
D14V29, continuous
D14V30, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   6
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 14(11P12) MUTATED                         2                       0
  AMP PEAK 14(11P12) WILD-TYPE                      27                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 14(11P12) MUTATED                         0
  AMP PEAK 14(11P12) WILD-TYPE                       7
D14V31, multiclass
[1] "Remove cluster labels:"     "AMP PEAK 14(11P12) MUTATED"
clus
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                           2                           43 
                  TCGA-BI-A20A                   TCGA-C5-A0TN 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1BE                   TCGA-C5-A1BM 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1M5                   TCGA-C5-A1M7 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1M8                   TCGA-C5-A1ME 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1MF                   TCGA-C5-A1MJ 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1MP                   TCGA-C5-A2LS 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A2LV                   TCGA-C5-A2LX 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A2M1                   TCGA-C5-A3HE 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A3HL                   TCGA-C5-A7CJ 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A7UC                   TCGA-C5-A7X8 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A7XC                   TCGA-C5-A8XH 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A8XI                   TCGA-DG-A2KL 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-DR-A0ZM                   TCGA-DS-A0VK 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-DS-A0VL                   TCGA-DS-A0VM 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-DS-A0VN                   TCGA-DS-A3LQ 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-EA-A50E                   TCGA-EK-A2RN 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-EK-A2RO                   TCGA-EX-A1H5 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-EX-A449                   TCGA-FU-A3EO 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-HM-A4S6                   TCGA-IR-A3LH 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-IR-A3LI                   TCGA-IR-A3LK 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-MU-A8JM                   TCGA-UC-A7PD 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-VS-A8QA 
"AMP PEAK 14(11P12) WILD-TYPE" 
                              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                                                1
  AMP PEAK 14(11P12) WILD-TYPE                                             15
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 14(11P12) MUTATED                                                                                   3
  AMP PEAK 14(11P12) WILD-TYPE                                                                                65
                              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                                                                                           92
D14V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 14(11P12) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         13
                                                                                              clus
vv                                                                                             AMP PEAK 14(11P12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V33, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    6  3
  AMP PEAK 14(11P12) WILD-TYPE 62 67
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      6    3
  AMP PEAK 14(11P12) WILD-TYPE   62   67
         clus
vv        AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  ABSENT                           6                           62
  PRESENT                          3                           67
[1] 2 2
[1] FALSE
D14V34, continuous
D14V35, continuous
D14V36, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    1  6
  AMP PEAK 14(11P12) WILD-TYPE 42 88
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      1    6
  AMP PEAK 14(11P12) WILD-TYPE   42   88
                                          clus
vv                                         AMP PEAK 14(11P12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              1
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          6
                                          clus
vv                                         AMP PEAK 14(11P12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           88
[1] 2 2
[1] FALSE
D14V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 14(11P12) MUTATED              1           8          3
  AMP PEAK 14(11P12) WILD-TYPE            9          41         54
D14V38, multiclass
              clus
vv             AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  CURRENT USER                          1                            9
  FORMER USER                           8                           41
  NEVER USED                            3                           54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V39, continuous
D14V40, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P12) MUTATED    6  0
  AMP PEAK 14(11P12) WILD-TYPE 83 16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P12) MUTATED      6    0
  AMP PEAK 14(11P12) WILD-TYPE   83   16
         clus
vv        AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  ABSENT                           6                           83
  PRESENT                          0                           16
[1] 2 2
[1] FALSE
D14V41, continuous
[1] "Remove cluster labels:"     "AMP PEAK 14(11P12) MUTATED"
clus
  AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE 
                           2                           11 
                  TCGA-C5-A1MH                   TCGA-C5-A1ML 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-C5-A1MN                   TCGA-C5-A1MP 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-EK-A2RO                   TCGA-GH-A9DA 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-HM-A3JK                   TCGA-JW-A852 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-JX-A3Q8                   TCGA-MU-A51Y 
"AMP PEAK 14(11P12) WILD-TYPE" "AMP PEAK 14(11P12) WILD-TYPE" 
                  TCGA-MU-A8JM 
"AMP PEAK 14(11P12) WILD-TYPE" 
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 14(11P12) MUTATED     0    0   2    1    0  0   0    1    1   3  0
  AMP PEAK 14(11P12) WILD-TYPE   1    1  28   64   24  4   8    6    8  19  1
                              vv
clus                           T3B T4 TIS TX
  AMP PEAK 14(11P12) MUTATED     3  0   1  2
  AMP PEAK 14(11P12) WILD-TYPE   5  2   0 12
D14V42, multiclass
      clus
vv     AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  T1A                           0                            1
  T1A1                          0                            1
  T1B                           2                           28
  T1B1                          1                           64
  T1B2                          0                           24
  T2                            0                            4
  T2A                           0                            8
  T2A1                          1                            6
  T2A2                          1                            8
  T2B                           3                           19
  T3                            0                            1
  T3B                           3                            5
  T4                            0                            2
  TIS                           1                            0
  TX                            2                           12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        2         1         1       29
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 14(11P12) MUTATED           3         2        0         1
  AMP PEAK 14(11P12) WILD-TYPE        66        30        3         5
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 14(11P12) MUTATED            0          0         6         0
  AMP PEAK 14(11P12) WILD-TYPE          5          7        21         1
                              vv
clus                           STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 14(11P12) MUTATED            4         0         0
  AMP PEAK 14(11P12) WILD-TYPE         30         3         7
D14V44, multiclass
            clus
vv           AMP PEAK 14(11P12) MUTATED AMP PEAK 14(11P12) WILD-TYPE
  STAGE I                             1                            3
  STAGE IA                            0                            2
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            2                           29
  STAGE IB1                           3                           66
  STAGE IB2                           2                           30
  STAGE II                            0                            3
  STAGE IIA                           1                            5
  STAGE IIA1                          0                            5
  STAGE IIA2                          0                            7
  STAGE IIB                           6                           21
  STAGE III                           0                            1
  STAGE IIIB                          4                           30
  STAGE IVA                           0                            3
  STAGE IVB                           0                            7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(11Q13.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(11Q13.3) MUTATED    23   8
  AMP PEAK 15(11Q13.3) WILD-TYPE 160  42
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            31                            202 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                             8                             42 
$`AMP PEAK 15(11Q13.3) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MF 
       11.44        68.84       144.16         5.46        35.01        53.16 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A8XJ TCGA-DG-A2KJ 
       73.18        73.45       154.32        17.19        75.78        58.88 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-FU-A40J 
        8.28        12.36        26.27         6.64         1.18         1.35 
TCGA-HG-A9SC TCGA-IR-A3LA TCGA-IR-A3LH TCGA-JW-A5VK TCGA-LP-A4AX TCGA-LP-A5U3 
        7.13       137.16        78.71        20.48         0.07         0.82 
TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QF 
        5.49         3.39        14.07        19.96        46.03        49.55 
TCGA-VS-A9U5 
       38.96 

$`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         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        85.55        60.69        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         6.12        20.91         4.47         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18        17.52 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        0.76         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        1.18        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-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        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-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        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        5.13         6.71        21.11       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
       11.28         0.89         0.30         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       13.35        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH 
       20.22        53.52        32.15        23.28        11.51        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       31.27        16.64         4.73        23.24        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       42.08        43.82        39.35        18.05 

  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                        154.32                         195.85 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                         20.48                          15.53 
[1] "0.1 - 154.3 (20.5)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                              T1  T2 T3+T4
  AMP PEAK 15(11Q13.3) MUTATED    14   6     2
  AMP PEAK 15(11Q13.3) WILD-TYPE 107  44     9
D15V3, multiclass
       clus
vv      AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1                              14                            107
  T2                               6                             44
  T3+T4                            2                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED   12  7
  AMP PEAK 15(11Q13.3) WILD-TYPE 99 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     12    7
  AMP PEAK 15(11Q13.3) WILD-TYPE   99   40
   clus
vv  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  0                           12                             99
  1                            7                             40
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 15(11Q13.3) MUTATED   10  2 14
  AMP PEAK 15(11Q13.3) WILD-TYPE 81  6 79
D15V5, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  M0                           10                             81
  M1                            2                              6
  MX                           14                             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"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED               1                               28
  AMP PEAK 15(11Q13.3) WILD-TYPE             4                              169
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 15(11Q13.3) MUTATED                                               0
  AMP PEAK 15(11Q13.3) WILD-TYPE                                             5
                                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                                              0
  AMP PEAK 15(11Q13.3) WILD-TYPE                                            6
D15V6, multiclass
                                               clus
vv                                              AMP PEAK 15(11Q13.3) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              AMP PEAK 15(11Q13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         169
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     7  25
  AMP PEAK 15(11Q13.3) WILD-TYPE  23 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      7   25
  AMP PEAK 15(11Q13.3) WILD-TYPE   23  183
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  NO                             7                             23
  YES                           25                            183
[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                        19
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 15(11Q13.3) MUTATED                                           0
  AMP PEAK 15(11Q13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 15(11Q13.3) MUTATED      24
  AMP PEAK 15(11Q13.3) WILD-TYPE   145
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                            0
  WHITE                                                               24
                                           clus
vv                                          AMP PEAK 15(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             19
  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"
D15V11, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     1  17
  AMP PEAK 15(11Q13.3) WILD-TYPE  15 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      1   17
  AMP PEAK 15(11Q13.3) WILD-TYPE   15  132
                        clus
vv                       AMP PEAK 15(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           17
                        clus
vv                       AMP PEAK 15(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            132
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    9  6
  AMP PEAK 15(11Q13.3) WILD-TYPE 62 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      9    6
  AMP PEAK 15(11Q13.3) WILD-TYPE   62   19
            clus
vv           AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  TUMOR FREE                            9                             62
  WITH TUMOR                            6                             19
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 15(11Q13.3) MUTATED        5      1       0      1       0
  AMP PEAK 15(11Q13.3) WILD-TYPE     18      4       1      9       7
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 15(11Q13.3) MUTATED              23       2
  AMP PEAK 15(11Q13.3) WILD-TYPE           155      12
D15V14, multiclass
               clus
vv              AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  BRAZIL                                   5                             18
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   1                              9
  UKRAINE                                  0                              7
  UNITED STATES                           23                            155
  VIETNAM                                  2                             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 15(11Q13.3) MUTATED    0  9 19  1  2
  AMP PEAK 15(11Q13.3) WILD-TYPE 17 97 78  0 12
D15V15, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  G1                            0                             17
  G2                            9                             97
  G3                           19                             78
  G4                            1                              0
  GX                            2                             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                                          27
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 15(11Q13.3) MUTATED                                        2
  AMP PEAK 15(11Q13.3) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 15(11Q13.3) MUTATED                                                 1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 15(11Q13.3) MUTATED                3                  16
  AMP PEAK 15(11Q13.3) WILD-TYPE             49                  96
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                                                             3
  LIFELONG NON-SMOKER                                                       16
                                                 clus
vv                                                AMP PEAK 15(11Q13.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              49
  LIFELONG NON-SMOKER                                                         96
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V19, continuous
D15V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 15(11Q13.3) MUTATED             4       10             3        1
  AMP PEAK 15(11Q13.3) WILD-TYPE          15       65             9       11
D15V21, multiclass
               clus
vv              AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                10                             65
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     6             1
  AMP PEAK 15(11Q13.3) WILD-TYPE                  22            15
D15V23, multiclass
                     clus
vv                    AMP PEAK 15(11Q13.3) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            6
  REGIONAL SITE                                  1
                     clus
vv                    AMP PEAK 15(11Q13.3) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             22
  REGIONAL SITE                                   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"
D15V24, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    6  1
  AMP PEAK 15(11Q13.3) WILD-TYPE 28  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      6    1
  AMP PEAK 15(11Q13.3) WILD-TYPE   28    2
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  CGY                            6                             28
  GY                             1                              2
[1] 2 2
[1] FALSE
D15V25, continuous
D15V26, continuous
D15V27, continuous
D15V28, continuous
D15V29, continuous
D15V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 15(11Q13.3) MUTATED                         6
  AMP PEAK 15(11Q13.3) WILD-TYPE                      23
                                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                       6
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                              5
  OTHER LOCATION, SPECIFY                                         23
  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 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                                                2
  AMP PEAK 15(11Q13.3) WILD-TYPE                                             14
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 15(11Q13.3) MUTATED                                                                                   6
  AMP PEAK 15(11Q13.3) WILD-TYPE                                                                                62
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 15(11Q13.3) MUTATED                                                                                             17
  AMP PEAK 15(11Q13.3) WILD-TYPE                                                                                           88
D15V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 15(11Q13.3) 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)                                       6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           17
                                                                                              clus
vv                                                                                             AMP PEAK 15(11Q13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D15V33, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    6 10
  AMP PEAK 15(11Q13.3) WILD-TYPE 62 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      6   10
  AMP PEAK 15(11Q13.3) WILD-TYPE   62   60
         clus
vv        AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  ABSENT                             6                             62
  PRESENT                           10                             60
[1] 2 2
[1] FALSE
D15V34, continuous
D15V35, continuous
D15V36, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    4 12
  AMP PEAK 15(11Q13.3) WILD-TYPE 39 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      4   12
  AMP PEAK 15(11Q13.3) WILD-TYPE   39   82
                                          clus
vv                                         AMP PEAK 15(11Q13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           12
                                          clus
vv                                         AMP PEAK 15(11Q13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             82
[1] 2 2
[1] FALSE
D15V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 15(11Q13.3) MUTATED              1           4          9
  AMP PEAK 15(11Q13.3) WILD-TYPE            9          45         48
D15V38, multiclass
              clus
vv             AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  CURRENT USER                            1                              9
  FORMER USER                             4                             45
  NEVER USED                              9                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V39, continuous
D15V40, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED   11  1
  AMP PEAK 15(11Q13.3) WILD-TYPE 78 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     11    1
  AMP PEAK 15(11Q13.3) WILD-TYPE   78   15
         clus
vv        AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  ABSENT                            11                             78
  PRESENT                            1                             15
[1] 2 2
[1] FALSE
D15V41, continuous
[1] "Remove cluster labels:"       "AMP PEAK 15(11Q13.3) MUTATED"
clus
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                             2                             11 
                    TCGA-C5-A1MH                     TCGA-C5-A1ML 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-C5-A1MP 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-GH-A9DA 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MU-A51Y 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-MU-A8JM 
"AMP PEAK 15(11Q13.3) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 15(11Q13.3) MUTATED     1    0   7    3    3  0   0    2    1   3  0
  AMP PEAK 15(11Q13.3) WILD-TYPE   0    1  23   62   21  4   8    5    8  19  1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 15(11Q13.3) MUTATED     2  0   1  3
  AMP PEAK 15(11Q13.3) WILD-TYPE   6  2   0 11
D15V42, multiclass
      clus
vv     AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1A                             1                              0
  T1A1                            0                              1
  T1B                             7                             23
  T1B1                            3                             62
  T1B2                            3                             21
  T2                              0                              4
  T2A                             0                              8
  T2A1                            2                              5
  T2A2                            1                              8
  T2B                             3                             19
  T3                              0                              1
  T3B                             2                              6
  T4                              0                              2
  TIS                             1                              0
  TX                              3                             11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 15(11Q13.3) MUTATED         1        1         0         0        5
  AMP PEAK 15(11Q13.3) WILD-TYPE       3        1         1         1       26
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 15(11Q13.3) MUTATED           5         7        0         1
  AMP PEAK 15(11Q13.3) WILD-TYPE        64        25        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 15(11Q13.3) MUTATED            1          1         7         0
  AMP PEAK 15(11Q13.3) WILD-TYPE          4          6        20         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 15(11Q13.3) MUTATED            3         0         0
  AMP PEAK 15(11Q13.3) WILD-TYPE         31         3         7
D15V44, multiclass
            clus
vv           AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              5                             26
  STAGE IB1                             5                             64
  STAGE IB2                             7                             25
  STAGE II                              0                              3
  STAGE IIA                             1                              5
  STAGE IIA1                            1                              4
  STAGE IIA2                            1                              6
  STAGE IIB                             7                             20
  STAGE III                             0                              1
  STAGE IIIB                            3                             31
  STAGE IVA                             0                              3
  STAGE IVB                             0                              7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(11Q22.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(11Q22.1) MUTATED    31  11
  AMP PEAK 16(11Q22.1) WILD-TYPE 152  39
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                            42                            191 
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                            11                             39 
$`AMP PEAK 16(11Q22.1) MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M9 
       23.67        11.44       144.16       177.04         5.46        35.01 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7X5 
       73.18        73.45        78.35       154.32        17.19        13.61 
TCGA-C5-A7XC TCGA-C5-A8XK TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL 
       50.99        99.91        58.88        87.75        36.76         2.66 
TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EK-A2H1 
        8.28        13.05         1.18         1.81        13.91        26.27 
TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A3L1 TCGA-FU-A40J 
        6.64         1.18         0.07         0.10         6.94         1.35 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MY-A913 
        7.13        21.67        78.71        21.11         0.07         5.49 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A9U5 
        3.88        11.67        10.03        46.03        49.55        38.96 

$`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         0.82        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      182.93       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8XH 
       85.55        60.69        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        75.78        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM 
        4.47         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 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA 
       14.50         1.35         1.35        14.50        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
        0.26        14.89         1.48        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-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         4.04         0.03         0.36        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 
        0.10         0.10         0.03        20.35         7.92        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       25.41        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81       117.40        96.95        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       10.06         5.13         6.71       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       11.28         0.89         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        12.16        61.28        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC 
       14.07        19.96        53.52        32.15        23.28        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        16.64         4.73        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        18.05 

  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                         195.85 
  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE 
                         15.55                          15.88 
[1] "0.1 - 177.0 (15.6)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 16(11Q22.1) MUTATED   23  6     2
  AMP PEAK 16(11Q22.1) WILD-TYPE 98 44     9
D16V3, multiclass
       clus
vv      AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  T1                              23                             98
  T2                               6                             44
  T3+T4                            2                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   21  9
  AMP PEAK 16(11Q22.1) WILD-TYPE 90 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     21    9
  AMP PEAK 16(11Q22.1) WILD-TYPE   90   38
   clus
vv  AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  0                           21                             90
  1                            9                             38
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 16(11Q22.1) MUTATED   19  2 12
  AMP PEAK 16(11Q22.1) WILD-TYPE 72  6 81
D16V5, multiclass
    clus
vv   AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  M0                           19                             72
  M1                            2                              6
  MX                           12                             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(11Q22.1) MUTATED               1                               39
  AMP PEAK 16(11Q22.1) WILD-TYPE             4                              158
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 16(11Q22.1) MUTATED                                               0
  AMP PEAK 16(11Q22.1) WILD-TYPE                                             5
                                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                                              0
  AMP PEAK 16(11Q22.1) WILD-TYPE                                            6
D16V6, multiclass
                                               clus
vv                                              AMP PEAK 16(11Q22.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        39
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              AMP PEAK 16(11Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         158
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q22.1) MUTATED     7  35
  AMP PEAK 16(11Q22.1) WILD-TYPE  23 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED      7   35
  AMP PEAK 16(11Q22.1) WILD-TYPE   23  173
     clus
vv    AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  NO                             7                             23
  YES                           35                            173
[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                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 16(11Q22.1) MUTATED                                           1
  AMP PEAK 16(11Q22.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 16(11Q22.1) MUTATED      28
  AMP PEAK 16(11Q22.1) WILD-TYPE   141
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                            1
  WHITE                                                               28
                                           clus
vv                                          AMP PEAK 16(11Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D16V11, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q22.1) MUTATED     2  25
  AMP PEAK 16(11Q22.1) WILD-TYPE  14 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED      2   25
  AMP PEAK 16(11Q22.1) WILD-TYPE   14  124
                        clus
vv                       AMP PEAK 16(11Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       AMP PEAK 16(11Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            124
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   12  5
  AMP PEAK 16(11Q22.1) WILD-TYPE 59 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     12    5
  AMP PEAK 16(11Q22.1) WILD-TYPE   59   20
            clus
vv           AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  TUMOR FREE                           12                             59
  WITH TUMOR                            5                             20
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 16(11Q22.1) MUTATED        4      1       0      1       2
  AMP PEAK 16(11Q22.1) WILD-TYPE     19      4       1      9       5
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 16(11Q22.1) MUTATED              33       1
  AMP PEAK 16(11Q22.1) WILD-TYPE           145      13
D16V14, multiclass
               clus
vv              AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  BRAZIL                                   4                             19
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   1                              9
  UKRAINE                                  2                              5
  UNITED STATES                           33                            145
  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 14 24  1  2
  AMP PEAK 16(11Q22.1) WILD-TYPE 16 92 73  0 12
D16V15, multiclass
    clus
vv   AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  G1                            1                             16
  G2                           14                             92
  G3                           24                             73
  G4                            1                              0
  GX                            2                             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                                          26
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 16(11Q22.1) MUTATED                                        0
  AMP PEAK 16(11Q22.1) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 16(11Q22.1) MUTATED                                                 1
  AMP PEAK 16(11Q22.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 16(11Q22.1) MUTATED                6                  19
  AMP PEAK 16(11Q22.1) WILD-TYPE             46                  93
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                                                             6
  LIFELONG NON-SMOKER                                                       19
                                                 clus
vv                                                AMP PEAK 16(11Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              46
  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"
D16V19, continuous
D16V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 16(11Q22.1) MUTATED             3       13             5        2
  AMP PEAK 16(11Q22.1) WILD-TYPE          16       62             7       10
D16V21, multiclass
               clus
vv              AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  COMBINATION                              3                             16
  EXTERNAL                                13                             62
  EXTERNAL BEAM                            5                              7
  INTERNAL                                 2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     7             1
  AMP PEAK 16(11Q22.1) WILD-TYPE                  21            15
D16V23, multiclass
                     clus
vv                    AMP PEAK 16(11Q22.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                            7
  REGIONAL SITE                                  1
                     clus
vv                    AMP PEAK 16(11Q22.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             21
  REGIONAL SITE                                   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"
D16V24, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED    7  1
  AMP PEAK 16(11Q22.1) WILD-TYPE 27  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED      7    1
  AMP PEAK 16(11Q22.1) WILD-TYPE   27    2
     clus
vv    AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  CGY                            7                             27
  GY                             1                              2
[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                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 16(11Q22.1) MUTATED                         7
  AMP PEAK 16(11Q22.1) WILD-TYPE                      22
                                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                       5
D16V31, multiclass
                                     clus
vv                                    AMP PEAK 16(11Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        7
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK 16(11Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                         22
  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 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                                                2
  AMP PEAK 16(11Q22.1) WILD-TYPE                                             14
                                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                                                                                64
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 16(11Q22.1) MUTATED                                                                                             26
  AMP PEAK 16(11Q22.1) WILD-TYPE                                                                                           79
D16V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 16(11Q22.1) 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)                                       4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           26
                                                                                              clus
vv                                                                                             AMP PEAK 16(11Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D16V33, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   11 14
  AMP PEAK 16(11Q22.1) WILD-TYPE 57 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     11   14
  AMP PEAK 16(11Q22.1) WILD-TYPE   57   56
         clus
vv        AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  ABSENT                            11                             57
  PRESENT                           14                             56
[1] 2 2
[1] FALSE
D16V34, continuous
D16V35, continuous
D16V36, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   11 17
  AMP PEAK 16(11Q22.1) WILD-TYPE 32 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     11   17
  AMP PEAK 16(11Q22.1) WILD-TYPE   32   77
                                          clus
vv                                         AMP PEAK 16(11Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           17
                                          clus
vv                                         AMP PEAK 16(11Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             77
[1] 2 2
[1] FALSE
D16V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 16(11Q22.1) MUTATED              2           7         12
  AMP PEAK 16(11Q22.1) WILD-TYPE            8          42         45
D16V38, multiclass
              clus
vv             AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  CURRENT USER                            2                              8
  FORMER USER                             7                             42
  NEVER USED                             12                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V39, continuous
D16V40, binary
                                cls
clus                              0  1
  AMP PEAK 16(11Q22.1) MUTATED   17  1
  AMP PEAK 16(11Q22.1) WILD-TYPE 72 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q22.1) MUTATED     17    1
  AMP PEAK 16(11Q22.1) WILD-TYPE   72   15
         clus
vv        AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  ABSENT                            17                             72
  PRESENT                            1                             15
[1] 2 2
[1] FALSE
D16V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 16(11Q22.1) MUTATED     0    0  10   11    2  0   0    3    1   2  0
  AMP PEAK 16(11Q22.1) WILD-TYPE   1    1  20   54   22  4   8    4    8  20  1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 16(11Q22.1) MUTATED     2  0   1  2
  AMP PEAK 16(11Q22.1) WILD-TYPE   6  2   0 12
D16V42, multiclass
      clus
vv     AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                            10                             20
  T1B1                           11                             54
  T1B2                            2                             22
  T2                              0                              4
  T2A                             0                              8
  T2A1                            3                              4
  T2A2                            1                              8
  T2B                             2                             20
  T3                              0                              1
  T3B                             2                              6
  T4                              0                              2
  TIS                             1                              0
  TX                              2                             12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 16(11Q22.1) MUTATED         0        0         0         0       10
  AMP PEAK 16(11Q22.1) WILD-TYPE       4        2         1         1       21
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 16(11Q22.1) MUTATED          10         5        0         1
  AMP PEAK 16(11Q22.1) WILD-TYPE        59        27        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 16(11Q22.1) MUTATED            2          1         7         0
  AMP PEAK 16(11Q22.1) WILD-TYPE          3          6        20         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 16(11Q22.1) MUTATED            4         0         1
  AMP PEAK 16(11Q22.1) WILD-TYPE         30         3         6
D16V44, multiclass
            clus
vv           AMP PEAK 16(11Q22.1) MUTATED AMP PEAK 16(11Q22.1) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             10                             21
  STAGE IB1                            10                             59
  STAGE IB2                             5                             27
  STAGE II                              0                              3
  STAGE IIA                             1                              5
  STAGE IIA1                            2                              3
  STAGE IIA2                            1                              6
  STAGE IIB                             7                             20
  STAGE III                             0                              1
  STAGE IIIB                            4                             30
  STAGE IVA                             0                              3
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(13Q22.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(13Q22.1) MUTATED    39  15
  AMP PEAK 17(13Q22.1) WILD-TYPE 144  35
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                            54                            179 
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                            15                             35 
$`AMP PEAK 17(13Q22.1) MUTATED`
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LZ 
       82.85         5.46        35.01         0.46         3.58       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7X5 
       38.43        52.01        17.85       182.93       154.32        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DS-A0VM TCGA-EA-A3HT 
        2.73        50.99        27.52         1.12       117.99         0.62 
TCGA-EA-A3QD TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
       13.05        12.66         0.26        13.91        14.96         0.36 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GN 
       45.96         1.51         0.36         1.18         2.24         0.03 
TCGA-EX-A8YF TCGA-FU-A3HY TCGA-FU-A40J TCGA-FU-A5XV TCGA-IR-A3L7 TCGA-IR-A3LB 
        4.73         0.66         1.35         1.97       147.39        66.81 
TCGA-IR-A3LK TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW 
       26.56        21.44        21.11       195.85         7.99         0.89 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73R TCGA-VS-A8EC 
        0.07         2.96        13.35         3.39         6.25        34.52 
TCGA-VS-A8Q8 TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A954 TCGA-VS-A959 TCGA-WL-A834 
       32.15        49.55        39.78        42.58        39.35        18.05 

$`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         0.82        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 
       85.55        60.69        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 
       75.78        99.91        23.51         6.12        20.91         4.47 
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         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
        0.82         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
        1.81        12.82        14.89         1.48        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
       13.58        13.48        12.59        26.27         6.64         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-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        4.04         0.03        23.70         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
        6.12         1.22        23.84         0.92         2.17         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-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-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
       14.93         9.44       137.16       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        36.36        27.42         3.29        24.56        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-LP-A4AU 
       15.58        10.06         5.13         6.71        30.31        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 
        5.42        29.72         4.34         5.49        15.58        15.95 
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         5.88        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59         3.88        11.67        93.99        12.16        61.28 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        29.03        20.22        14.07        19.96        53.52 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       46.03        23.28        11.51        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 
       23.24        44.88        42.08        43.82        38.96 

  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 
                        195.85                         177.04 
  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE 
                         13.76                          16.08 
[1] "0.0 - 195.8 (13.8)" "0.0 - 177.0 (16.1)"
[1] "hr=" "1.3"
D17V2, continuous
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 17(13Q22.1) MUTATED   25  9     5
  AMP PEAK 17(13Q22.1) WILD-TYPE 96 41     6
D17V3, multiclass
       clus
vv      AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  T1                              25                             96
  T2                               9                             41
  T3+T4                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   22 12
  AMP PEAK 17(13Q22.1) WILD-TYPE 89 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     22   12
  AMP PEAK 17(13Q22.1) WILD-TYPE   89   35
   clus
vv  AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  0                           22                             89
  1                           12                             35
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 17(13Q22.1) MUTATED   23  0 20
  AMP PEAK 17(13Q22.1) WILD-TYPE 68  8 73
D17V5, multiclass
    clus
vv   AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  M0                           23                             68
  M1                            0                              8
  MX                           20                             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(13Q22.1) MUTATED               1                               44
  AMP PEAK 17(13Q22.1) WILD-TYPE             4                              153
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 17(13Q22.1) MUTATED                                               0
  AMP PEAK 17(13Q22.1) WILD-TYPE                                             5
                                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                                              3
  AMP PEAK 17(13Q22.1) WILD-TYPE                                            3
D17V6, multiclass
                                               clus
vv                                              AMP PEAK 17(13Q22.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             3
                                               clus
vv                                              AMP PEAK 17(13Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(13Q22.1) MUTATED     6  48
  AMP PEAK 17(13Q22.1) WILD-TYPE  24 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED      6   48
  AMP PEAK 17(13Q22.1) WILD-TYPE   24  160
     clus
vv    AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  NO                             6                             24
  YES                           48                            160
[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                        17
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 17(13Q22.1) MUTATED                                           0
  AMP PEAK 17(13Q22.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 17(13Q22.1) MUTATED      40
  AMP PEAK 17(13Q22.1) WILD-TYPE   129
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                            0
  WHITE                                                               40
                                           clus
vv                                          AMP PEAK 17(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D17V11, binary
                                cls
clus                               0   1
  AMP PEAK 17(13Q22.1) MUTATED     1  37
  AMP PEAK 17(13Q22.1) WILD-TYPE  15 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED      1   37
  AMP PEAK 17(13Q22.1) WILD-TYPE   15  112
                        clus
vv                       AMP PEAK 17(13Q22.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       AMP PEAK 17(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            112
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   13  9
  AMP PEAK 17(13Q22.1) WILD-TYPE 58 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     13    9
  AMP PEAK 17(13Q22.1) WILD-TYPE   58   16
            clus
vv           AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  TUMOR FREE                           13                             58
  WITH TUMOR                            9                             16
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 17(13Q22.1) MUTATED        6      1       1      1       3
  AMP PEAK 17(13Q22.1) WILD-TYPE     17      4       0      9       4
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 17(13Q22.1) MUTATED              39       3
  AMP PEAK 17(13Q22.1) WILD-TYPE           139      11
D17V14, multiclass
               clus
vv              AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  BRAZIL                                   6                             17
  CANADA                                   1                              4
  NIGERIA                                  1                              0
  RUSSIA                                   1                              9
  UKRAINE                                  3                              4
  UNITED STATES                           39                            139
  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 24 25  0  3
  AMP PEAK 17(13Q22.1) WILD-TYPE 15 82 72  1 11
D17V15, multiclass
    clus
vv   AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  G1                            2                             15
  G2                           24                             82
  G3                           25                             72
  G4                            0                              1
  GX                            3                             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V16, continuous
D17V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 17(13Q22.1) MUTATED                                             7
  AMP PEAK 17(13Q22.1) WILD-TYPE                                          24
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 17(13Q22.1) MUTATED                                        1
  AMP PEAK 17(13Q22.1) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 17(13Q22.1) MUTATED                                                 0
  AMP PEAK 17(13Q22.1) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 17(13Q22.1) MUTATED                7                  30
  AMP PEAK 17(13Q22.1) WILD-TYPE             45                  82
D17V18, multiclass
                                                 clus
vv                                                AMP PEAK 17(13Q22.1) 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                                                             7
  LIFELONG NON-SMOKER                                                       30
                                                 clus
vv                                                AMP PEAK 17(13Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              45
  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"
D17V19, continuous
D17V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 17(13Q22.1) MUTATED             4       19             2        1
  AMP PEAK 17(13Q22.1) WILD-TYPE          15       56            10       11
D17V21, multiclass
               clus
vv              AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                19                             56
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     4             5
  AMP PEAK 17(13Q22.1) WILD-TYPE                  24            11
D17V23, multiclass
                     clus
vv                    AMP PEAK 17(13Q22.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            4
  REGIONAL SITE                                  5
                     clus
vv                    AMP PEAK 17(13Q22.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             24
  REGIONAL SITE                                   11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V24, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED    7  0
  AMP PEAK 17(13Q22.1) WILD-TYPE 27  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED      7    0
  AMP PEAK 17(13Q22.1) WILD-TYPE   27    3
     clus
vv    AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  CGY                            7                             27
  GY                             0                              3
[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                                     1
  AMP PEAK 17(13Q22.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 17(13Q22.1) MUTATED                         7
  AMP PEAK 17(13Q22.1) WILD-TYPE                      22
                                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                       6
D17V31, multiclass
                                     clus
vv                                    AMP PEAK 17(13Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        7
  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                                         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)
  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                                                3
  AMP PEAK 17(13Q22.1) WILD-TYPE                                             13
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 17(13Q22.1) MUTATED                                                                                  17
  AMP PEAK 17(13Q22.1) WILD-TYPE                                                                                51
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 17(13Q22.1) MUTATED                                                                                             24
  AMP PEAK 17(13Q22.1) WILD-TYPE                                                                                           81
D17V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 17(13Q22.1) 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)                                      17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           24
                                                                                              clus
vv                                                                                             AMP PEAK 17(13Q22.1) 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)                                        51
  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"
D17V33, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   11 20
  AMP PEAK 17(13Q22.1) WILD-TYPE 57 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     11   20
  AMP PEAK 17(13Q22.1) WILD-TYPE   57   50
         clus
vv        AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  ABSENT                            11                             57
  PRESENT                           20                             50
[1] 2 2
[1] FALSE
D17V34, continuous
D17V35, continuous
D17V36, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   10 19
  AMP PEAK 17(13Q22.1) WILD-TYPE 33 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     10   19
  AMP PEAK 17(13Q22.1) WILD-TYPE   33   75
                                          clus
vv                                         AMP PEAK 17(13Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           19
                                          clus
vv                                         AMP PEAK 17(13Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             75
[1] 2 2
[1] FALSE
D17V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 17(13Q22.1) MUTATED              0          14         14
  AMP PEAK 17(13Q22.1) WILD-TYPE           10          35         43
D17V38, multiclass
              clus
vv             AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  CURRENT USER                            0                             10
  FORMER USER                            14                             35
  NEVER USED                             14                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V39, continuous
D17V40, binary
                                cls
clus                              0  1
  AMP PEAK 17(13Q22.1) MUTATED   18  2
  AMP PEAK 17(13Q22.1) WILD-TYPE 71 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q22.1) MUTATED     18    2
  AMP PEAK 17(13Q22.1) WILD-TYPE   71   14
         clus
vv        AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  ABSENT                            18                             71
  PRESENT                            2                             14
[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                             11 
                    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-MU-A51Y                     TCGA-MU-A8JM 
"AMP PEAK 17(13Q22.1) WILD-TYPE" "AMP PEAK 17(13Q22.1) WILD-TYPE" 
                    TCGA-MY-A913 
"AMP PEAK 17(13Q22.1) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 17(13Q22.1) MUTATED     0    0   7   11    7  1   1    2    2   3  1
  AMP PEAK 17(13Q22.1) WILD-TYPE   1    1  23   54   17  3   7    5    7  19  0
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 17(13Q22.1) MUTATED     3  1   0  6
  AMP PEAK 17(13Q22.1) WILD-TYPE   5  1   1  8
D17V42, multiclass
      clus
vv     AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             7                             23
  T1B1                           11                             54
  T1B2                            7                             17
  T2                              1                              3
  T2A                             1                              7
  T2A1                            2                              5
  T2A2                            2                              7
  T2B                             3                             19
  T3                              1                              0
  T3B                             3                              5
  T4                              1                              1
  TIS                             0                              1
  TX                              6                              8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 17(13Q22.1) MUTATED         2        1         0         0        8
  AMP PEAK 17(13Q22.1) WILD-TYPE       2        1         1         1       23
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 17(13Q22.1) MUTATED          13         8        0         1
  AMP PEAK 17(13Q22.1) WILD-TYPE        56        24        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 17(13Q22.1) MUTATED            0          0         7         1
  AMP PEAK 17(13Q22.1) WILD-TYPE          5          7        20         0
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 17(13Q22.1) MUTATED            8         1         1
  AMP PEAK 17(13Q22.1) WILD-TYPE         26         2         6
D17V44, multiclass
            clus
vv           AMP PEAK 17(13Q22.1) MUTATED AMP PEAK 17(13Q22.1) WILD-TYPE
  STAGE I                               2                              2
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              8                             23
  STAGE IB1                            13                             56
  STAGE IB2                             8                             24
  STAGE II                              0                              3
  STAGE IIA                             1                              5
  STAGE IIA1                            0                              5
  STAGE IIA2                            0                              7
  STAGE IIB                             7                             20
  STAGE III                             1                              0
  STAGE IIIB                            8                             26
  STAGE IVA                             1                              2
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(13Q34) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(13Q34) MUTATED    42  16
  AMP PEAK 18(13Q34) WILD-TYPE 141  34
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          58                          175 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          16                           34 
$`AMP PEAK 18(13Q34) MUTATED`
TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CG 
       35.01         0.46         2.43       100.14        17.85       182.93 
TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      154.32        60.69        13.61         2.73        50.99        45.83 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DS-A0VM TCGA-DS-A7WI TCGA-EA-A3HQ 
       23.51        27.52         1.12       117.99         8.28         1.74 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H0 
        0.62        13.05        13.91        14.96         0.36        45.96 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EX-A1H6 
        1.51         0.59         0.36         1.18         2.24         7.92 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A40J TCGA-FU-A5XV 
        6.12         4.73        23.84         1.45         1.35         1.97 
TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VJ 
      147.39        78.71        81.96        26.56        27.42        21.44 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MY-A5BE TCGA-PN-A8MA 
       21.11       195.85        11.28         0.89         0.07         2.96 
TCGA-Q1-A5R2 TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-VS-A8EJ TCGA-VS-A8Q8 
       13.35         5.88         6.25        19.59        19.96        32.15 
TCGA-VS-A8QH TCGA-VS-A954 TCGA-VS-A959 TCGA-WL-A834 
       39.78        42.58        39.35        18.05 

$`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 
        0.82        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        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ 
        9.34         8.35        75.78        99.91         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        4.47        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-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         0.76        12.36         1.32         0.82 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        1.18        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       12.66        12.82         0.26        14.89         1.48        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP 
       14.99        13.58        13.48        12.59        26.27         6.64 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        4.04         0.03        23.70         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-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
        1.22         0.92         2.17         0.66         1.02         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA 
        1.48         0.82         3.52         1.32         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41         7.13        21.67        20.78        14.93         9.44 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LL TCGA-JW-A5VH 
      137.16        66.81       117.40        96.95        36.36         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       30.31         7.99         0.07         0.30         0.82         0.20 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       13.87         0.03         5.42        29.72         4.34         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       15.88        10.39         3.88        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       61.28        10.03        34.52        29.03        20.22        14.07 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       53.52        46.03        23.28        11.51        49.55        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 
       16.64         4.73        23.24        44.88        42.08        43.82 
TCGA-VS-A9U5 
       38.96 

  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      195.85                       177.04 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      14.435                       15.950 
[1] "0.1 - 195.8 (14.4)" "0.0 - 177.0 (15.9)"
[1] "hr=" "1.4"
D18V2, continuous
                              vv
clus                           T1 T2 T3+T4
  AMP PEAK 18(13Q34) MUTATED   25 15     3
  AMP PEAK 18(13Q34) WILD-TYPE 96 35     8
D18V3, multiclass
       clus
vv      AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  T1                            25                           96
  T2                            15                           35
  T3+T4                          3                            8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   26 11
  AMP PEAK 18(13Q34) WILD-TYPE 85 36
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     26   11
  AMP PEAK 18(13Q34) WILD-TYPE   85   36
   clus
vv  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  0                         26                           85
  1                         11                           36
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  AMP PEAK 18(13Q34) MUTATED   23  2 21
  AMP PEAK 18(13Q34) WILD-TYPE 68  6 72
D18V5, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  M0                         23                           68
  M1                          2                            6
  MX                         21                           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"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(13Q34) MUTATED               1                               48
  AMP PEAK 18(13Q34) WILD-TYPE             4                              149
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 18(13Q34) MUTATED                                               0
  AMP PEAK 18(13Q34) WILD-TYPE                                             5
                              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                                              3
  AMP PEAK 18(13Q34) WILD-TYPE                                            3
D18V6, multiclass
                                               clus
vv                                              AMP PEAK 18(13Q34) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      48
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           3
                                               clus
vv                                              AMP PEAK 18(13Q34) WILD-TYPE
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       149
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     4  54
  AMP PEAK 18(13Q34) WILD-TYPE  26 154
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      4   54
  AMP PEAK 18(13Q34) WILD-TYPE   26  154
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  NO                           4                           26
  YES                         54                          154
[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                        18
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 18(13Q34) MUTATED                                           0    44
  AMP PEAK 18(13Q34) WILD-TYPE                                         1   125
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                          0
  WHITE                                                             44
                                           clus
vv                                          AMP PEAK 18(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  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"
D18V11, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     2  36
  AMP PEAK 18(13Q34) WILD-TYPE  14 113
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      2   36
  AMP PEAK 18(13Q34) WILD-TYPE   14  113
                        clus
vv                       AMP PEAK 18(13Q34) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         36
                        clus
vv                       AMP PEAK 18(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               14
  NOT HISPANIC OR LATINO                          113
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   14  8
  AMP PEAK 18(13Q34) WILD-TYPE 57 17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     14    8
  AMP PEAK 18(13Q34) WILD-TYPE   57   17
            clus
vv           AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  TUMOR FREE                         14                           57
  WITH TUMOR                          8                           17
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 18(13Q34) MUTATED        5      1       1      2       2
  AMP PEAK 18(13Q34) WILD-TYPE     18      4       0      8       5
                              vv
clus                           UNITED STATES VIETNAM
  AMP PEAK 18(13Q34) MUTATED              44       3
  AMP PEAK 18(13Q34) WILD-TYPE           134      11
D18V14, multiclass
               clus
vv              AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  BRAZIL                                 5                           18
  CANADA                                 1                            4
  NIGERIA                                1                            0
  RUSSIA                                 2                            8
  UKRAINE                                2                            5
  UNITED STATES                         44                          134
  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 21 29  1  3
  AMP PEAK 18(13Q34) WILD-TYPE 14 85 68  0 11
D18V15, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  G1                          3                           14
  G2                         21                           85
  G3                         29                           68
  G4                          1                            0
  GX                          3                           11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V16, continuous
D18V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 18(13Q34) MUTATED                                             7
  AMP PEAK 18(13Q34) WILD-TYPE                                          24
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 18(13Q34) MUTATED                                        0
  AMP PEAK 18(13Q34) WILD-TYPE                                      8
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 18(13Q34) MUTATED                                                 0
  AMP PEAK 18(13Q34) WILD-TYPE                                               2
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 18(13Q34) MUTATED                8                  35
  AMP PEAK 18(13Q34) WILD-TYPE             44                  77
D18V18, multiclass
                                                 clus
vv                                                AMP PEAK 18(13Q34) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          0
  CURRENT SMOKER                                                           8
  LIFELONG NON-SMOKER                                                     35
                                                 clus
vv                                                AMP PEAK 18(13Q34) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            44
  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"
D18V19, continuous
D18V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 18(13Q34) MUTATED             2       25             2        1
  AMP PEAK 18(13Q34) WILD-TYPE          17       50            10       11
D18V21, multiclass
               clus
vv              AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  COMBINATION                            2                           17
  EXTERNAL                              25                           50
  EXTERNAL BEAM                          2                           10
  INTERNAL                               1                           11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     8             4
  AMP PEAK 18(13Q34) WILD-TYPE                  20            12
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                          8                           20
  REGIONAL SITE                                4                           12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V24, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED    8  1
  AMP PEAK 18(13Q34) WILD-TYPE 26  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      8    1
  AMP PEAK 18(13Q34) WILD-TYPE   26    2
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  CGY                          8                           26
  GY                           1                            2
[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                                     2
  AMP PEAK 18(13Q34) WILD-TYPE                                   4
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 18(13Q34) MUTATED                         6                       0
  AMP PEAK 18(13Q34) WILD-TYPE                      23                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 18(13Q34) MUTATED                         1
  AMP PEAK 18(13Q34) WILD-TYPE                       6
D18V31, multiclass
                                     clus
vv                                    AMP PEAK 18(13Q34) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          2
  OTHER LOCATION, SPECIFY                                      6
  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                                       23
  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 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                                                4
  AMP PEAK 18(13Q34) WILD-TYPE                                             12
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 18(13Q34) MUTATED                                                                                  21
  AMP PEAK 18(13Q34) WILD-TYPE                                                                                47
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 18(13Q34) MUTATED                                                                                             23
  AMP PEAK 18(13Q34) WILD-TYPE                                                                                           82
D18V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 18(13Q34) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         23
                                                                                              clus
vv                                                                                             AMP PEAK 18(13Q34) 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)                                      47
  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"
D18V33, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   11 18
  AMP PEAK 18(13Q34) WILD-TYPE 57 52
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     11   18
  AMP PEAK 18(13Q34) WILD-TYPE   57   52
         clus
vv        AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  ABSENT                          11                           57
  PRESENT                         18                           52
[1] 2 2
[1] FALSE
D18V34, continuous
D18V35, continuous
D18V36, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   14 19
  AMP PEAK 18(13Q34) WILD-TYPE 29 75
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     14   19
  AMP PEAK 18(13Q34) WILD-TYPE   29   75
                                          clus
vv                                         AMP PEAK 18(13Q34) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         19
                                          clus
vv                                         AMP PEAK 18(13Q34) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           75
[1] 2 2
[1] FALSE
D18V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 18(13Q34) MUTATED              1          11         15
  AMP PEAK 18(13Q34) WILD-TYPE            9          38         42
D18V38, multiclass
              clus
vv             AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  CURRENT USER                          1                            9
  FORMER USER                          11                           38
  NEVER USED                           15                           42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V39, continuous
D18V40, binary
                              cls
clus                            0  1
  AMP PEAK 18(13Q34) MUTATED   18  1
  AMP PEAK 18(13Q34) WILD-TYPE 71 15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     18    1
  AMP PEAK 18(13Q34) WILD-TYPE   71   15
         clus
vv        AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  ABSENT                          18                           71
  PRESENT                          1                           15
[1] 2 2
[1] FALSE
D18V41, continuous
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 18(13Q34) MUTATED     0    0   8   11    6  1   3    4    2   5  1
  AMP PEAK 18(13Q34) WILD-TYPE   1    1  22   54   18  3   5    3    7  17  0
                              vv
clus                           T3B T4 TIS TX
  AMP PEAK 18(13Q34) MUTATED     2  0   0  4
  AMP PEAK 18(13Q34) WILD-TYPE   6  2   1 10
D18V42, multiclass
      clus
vv     AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  T1A                           0                            1
  T1A1                          0                            1
  T1B                           8                           22
  T1B1                         11                           54
  T1B2                          6                           18
  T2                            1                            3
  T2A                           3                            5
  T2A1                          4                            3
  T2A2                          2                            7
  T2B                           5                           17
  T3                            1                            0
  T3B                           2                            6
  T4                            0                            2
  TIS                           0                            1
  TX                            4                           10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 18(13Q34) MUTATED         2        1         0         0        8
  AMP PEAK 18(13Q34) WILD-TYPE       2        1         1         1       23
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 18(13Q34) MUTATED          14         6        1         2
  AMP PEAK 18(13Q34) WILD-TYPE        55        26        2         4
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 18(13Q34) MUTATED            2          1         7         1
  AMP PEAK 18(13Q34) WILD-TYPE          3          6        20         0
                              vv
clus                           STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 18(13Q34) MUTATED            8         0         2
  AMP PEAK 18(13Q34) WILD-TYPE         26         3         5
D18V44, multiclass
            clus
vv           AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  STAGE I                             2                            2
  STAGE IA                            1                            1
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            8                           23
  STAGE IB1                          14                           55
  STAGE IB2                           6                           26
  STAGE II                            1                            2
  STAGE IIA                           2                            4
  STAGE IIA1                          2                            3
  STAGE IIA2                          1                            6
  STAGE IIB                           7                           20
  STAGE III                           1                            0
  STAGE IIIB                          8                           26
  STAGE IVA                           0                            3
  STAGE IVB                           2                            5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(15Q26.1) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(15Q26.1) MUTATED    46  13
  AMP PEAK 19(15Q26.1) WILD-TYPE 137  37
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                            59                            174 
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                            13                             37 
$`AMP PEAK 19(15Q26.1) MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1ME 
       49.48        18.74       177.04        31.40        30.21        57.73 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A2M2 
       35.61         2.43         3.58        73.18       100.14         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UI TCGA-C5-A7X3 
       52.01        18.02       101.82        20.35        94.95         9.34 
TCGA-C5-A7X8 TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DR-A0ZL 
        2.73        20.91         4.47         1.12        44.94        87.75 
TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 
        2.66         8.28         1.74         0.26        14.89        13.91 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF 
        4.04         0.03         2.24         6.94        19.79         4.73 
TCGA-FU-A23L TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-IR-A3LA 
       23.84         1.97         9.01         7.13        20.78       137.16 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 
       27.42        21.44        15.58         7.99        11.28         0.30 
TCGA-MY-A5BE TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EH 
        0.07        10.39        19.59        12.16        34.52        20.22 
TCGA-VS-A8EI TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A959 
       14.07        46.03        11.51        49.55        39.35 

$`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       182.93       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        85.55        60.69        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35        75.78        99.91        23.51        27.52         6.12 
TCGA-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         0.76 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.82         1.48        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        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       14.70         6.12         1.22         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-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        26.56        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 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.89         0.07         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         4.34         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       13.35        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       15.88         5.88         6.25         3.88        11.67        93.99 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       61.28        10.03        29.03        19.96        53.52        32.15 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       23.28        39.78        31.27        16.64         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       44.88        42.58        42.08        43.82        38.96        18.05 

  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                         195.85 
  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE 
                        15.580                         15.915 
[1] "0.0 - 177.0 (15.6)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.1"
D19V2, continuous
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 19(15Q26.1) MUTATED   23 16     5
  AMP PEAK 19(15Q26.1) WILD-TYPE 98 34     6
D19V3, multiclass
       clus
vv      AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  T1                              23                             98
  T2                              16                             34
  T3+T4                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   25 13
  AMP PEAK 19(15Q26.1) WILD-TYPE 86 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     25   13
  AMP PEAK 19(15Q26.1) WILD-TYPE   86   34
   clus
vv  AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  0                           25                             86
  1                           13                             34
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 19(15Q26.1) MUTATED   24  0 24
  AMP PEAK 19(15Q26.1) WILD-TYPE 67  8 69
D19V5, multiclass
    clus
vv   AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  M0                           24                             67
  M1                            0                              8
  MX                           24                             69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(15Q26.1) MUTATED               3                               50
  AMP PEAK 19(15Q26.1) WILD-TYPE             2                              147
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 19(15Q26.1) MUTATED                                               2
  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                                              1
  AMP PEAK 19(15Q26.1) WILD-TYPE                                            5
D19V6, multiclass
                                               clus
vv                                              AMP PEAK 19(15Q26.1) MUTATED
  ADENOSQUAMOUS                                                            3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 19(15Q26.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         147
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  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"
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(15Q26.1) MUTATED     8  53
  AMP PEAK 19(15Q26.1) WILD-TYPE  22 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED      8   53
  AMP PEAK 19(15Q26.1) WILD-TYPE   22  155
     clus
vv    AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  NO                             8                             22
  YES                           53                            155
[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                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 19(15Q26.1) MUTATED                                           0
  AMP PEAK 19(15Q26.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 19(15Q26.1) MUTATED      43
  AMP PEAK 19(15Q26.1) WILD-TYPE   126
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                            0
  WHITE                                                               43
                                           clus
vv                                          AMP PEAK 19(15Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             20
  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"
D19V11, binary
                                cls
clus                               0   1
  AMP PEAK 19(15Q26.1) MUTATED     5  38
  AMP PEAK 19(15Q26.1) WILD-TYPE  11 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED      5   38
  AMP PEAK 19(15Q26.1) WILD-TYPE   11  111
                        clus
vv                       AMP PEAK 19(15Q26.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           38
                        clus
vv                       AMP PEAK 19(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            111
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   19  8
  AMP PEAK 19(15Q26.1) WILD-TYPE 52 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     19    8
  AMP PEAK 19(15Q26.1) WILD-TYPE   52   17
            clus
vv           AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  TUMOR FREE                           19                             52
  WITH TUMOR                            8                             17
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 19(15Q26.1) MUTATED        7      2       0      2       1
  AMP PEAK 19(15Q26.1) WILD-TYPE     16      3       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 19(15Q26.1) MUTATED              46       3
  AMP PEAK 19(15Q26.1) WILD-TYPE           132      11
D19V14, multiclass
               clus
vv              AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  BRAZIL                                   7                             16
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  1                              6
  UNITED STATES                           46                            132
  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    5 26 28  0  2
  AMP PEAK 19(15Q26.1) WILD-TYPE 12 80 69  1 12
D19V15, multiclass
    clus
vv   AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  G1                            5                             12
  G2                           26                             80
  G3                           28                             69
  G4                            0                              1
  GX                            2                             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V16, continuous
D19V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 19(15Q26.1) MUTATED                                            10
  AMP PEAK 19(15Q26.1) WILD-TYPE                                          21
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 19(15Q26.1) MUTATED                                        0
  AMP PEAK 19(15Q26.1) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 19(15Q26.1) MUTATED                                                 0
  AMP PEAK 19(15Q26.1) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 19(15Q26.1) MUTATED               15                  31
  AMP PEAK 19(15Q26.1) WILD-TYPE             37                  81
D19V18, multiclass
                                                 clus
vv                                                AMP PEAK 19(15Q26.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            15
  LIFELONG NON-SMOKER                                                       31
                                                 clus
vv                                                AMP PEAK 19(15Q26.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              37
  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"
D19V19, continuous
D19V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 19(15Q26.1) MUTATED             5       25             3        2
  AMP PEAK 19(15Q26.1) WILD-TYPE          14       50             9       10
D19V21, multiclass
               clus
vv              AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  COMBINATION                              5                             14
  EXTERNAL                                25                             50
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    13             6
  AMP PEAK 19(15Q26.1) WILD-TYPE                  15            10
D19V23, multiclass
                     clus
vv                    AMP PEAK 19(15Q26.1) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                           13
  REGIONAL SITE                                  6
                     clus
vv                    AMP PEAK 19(15Q26.1) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             15
  REGIONAL SITE                                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V24, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   15  1
  AMP PEAK 19(15Q26.1) WILD-TYPE 19  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     15    1
  AMP PEAK 19(15Q26.1) WILD-TYPE   19    2
     clus
vv    AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  CGY                           15                             19
  GY                             1                              2
[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                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 19(15Q26.1) MUTATED                         8
  AMP PEAK 19(15Q26.1) WILD-TYPE                      21
                                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                       6
D19V31, multiclass
                                     clus
vv                                    AMP PEAK 19(15Q26.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  OTHER LOCATION, SPECIFY                                        8
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 19(15Q26.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         21
  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 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                                                5
  AMP PEAK 19(15Q26.1) WILD-TYPE                                             11
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 19(15Q26.1) MUTATED                                                                                  17
  AMP PEAK 19(15Q26.1) WILD-TYPE                                                                                51
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 19(15Q26.1) MUTATED                                                                                             25
  AMP PEAK 19(15Q26.1) WILD-TYPE                                                                                           80
D19V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 19(15Q26.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           25
                                                                                              clus
vv                                                                                             AMP PEAK 19(15Q26.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D19V33, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   16 18
  AMP PEAK 19(15Q26.1) WILD-TYPE 52 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     16   18
  AMP PEAK 19(15Q26.1) WILD-TYPE   52   52
         clus
vv        AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  ABSENT                            16                             52
  PRESENT                           18                             52
[1] 2 2
[1] FALSE
D19V34, continuous
D19V35, continuous
D19V36, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED    9 22
  AMP PEAK 19(15Q26.1) WILD-TYPE 34 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED      9   22
  AMP PEAK 19(15Q26.1) WILD-TYPE   34   72
                                          clus
vv                                         AMP PEAK 19(15Q26.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           22
                                          clus
vv                                         AMP PEAK 19(15Q26.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             72
[1] 2 2
[1] FALSE
D19V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 19(15Q26.1) MUTATED              2           8         18
  AMP PEAK 19(15Q26.1) WILD-TYPE            8          41         39
D19V38, multiclass
              clus
vv             AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  CURRENT USER                            2                              8
  FORMER USER                             8                             41
  NEVER USED                             18                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V39, continuous
D19V40, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.1) MUTATED   19  4
  AMP PEAK 19(15Q26.1) WILD-TYPE 70 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.1) MUTATED     19    4
  AMP PEAK 19(15Q26.1) WILD-TYPE   70   12
         clus
vv        AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  ABSENT                            19                             70
  PRESENT                            4                             12
[1] 2 2
[1] FALSE
D19V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 19(15Q26.1) MUTATED     0    0   5   13    5  1   6    3    1   5  0
  AMP PEAK 19(15Q26.1) WILD-TYPE   1    1  25   52   19  3   2    4    8  17  1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 19(15Q26.1) MUTATED     4  1   0  4
  AMP PEAK 19(15Q26.1) WILD-TYPE   4  1   1 10
D19V42, multiclass
      clus
vv     AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             5                             25
  T1B1                           13                             52
  T1B2                            5                             19
  T2                              1                              3
  T2A                             6                              2
  T2A1                            3                              4
  T2A2                            1                              8
  T2B                             5                             17
  T3                              0                              1
  T3B                             4                              4
  T4                              1                              1
  TIS                             0                              1
  TX                              4                             10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 19(15Q26.1) MUTATED         0        0         0         0        7
  AMP PEAK 19(15Q26.1) WILD-TYPE       4        2         1         1       24
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 19(15Q26.1) MUTATED          17         7        1         4
  AMP PEAK 19(15Q26.1) WILD-TYPE        52        25        2         2
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 19(15Q26.1) MUTATED            2          2         8         0
  AMP PEAK 19(15Q26.1) WILD-TYPE          3          5        19         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 19(15Q26.1) MUTATED           11         2         0
  AMP PEAK 19(15Q26.1) WILD-TYPE         23         1         7
D19V44, multiclass
            clus
vv           AMP PEAK 19(15Q26.1) MUTATED AMP PEAK 19(15Q26.1) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              7                             24
  STAGE IB1                            17                             52
  STAGE IB2                             7                             25
  STAGE II                              1                              2
  STAGE IIA                             4                              2
  STAGE IIA1                            2                              3
  STAGE IIA2                            2                              5
  STAGE IIB                             8                             19
  STAGE III                             0                              1
  STAGE IIIB                           11                             23
  STAGE IVA                             2                              1
  STAGE IVB                             0                              7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(16P13.13) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(16P13.13) MUTATED    37  11
  AMP PEAK 20(16P13.13) WILD-TYPE 146  39
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                             48                             185 
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                             11                              39 
$`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         1.74        13.05 
TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2RC 
       14.50        13.91        14.96         0.36        26.27         4.04 
TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-FU-A23L TCGA-FU-A3EO 
        0.03        23.70         0.10         0.03        23.84         2.17 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LI 
        1.45         1.58         1.48         1.35        20.78        81.96 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-PN-A8MA TCGA-UC-A7PF 
       21.44        15.58       195.85         7.99         2.96        93.99 
TCGA-UC-A7PG TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A952 TCGA-VS-A9U5 
       12.16        19.96        32.15        23.28        44.88        38.96 

$`AMP PEAK 20(16P13.13) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK 
       67.46        30.21        35.01        57.73        53.16         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93         3.58        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43         0.82        52.01        18.02 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19        85.55        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KM 
       23.51         6.12        20.91         4.47        50.76        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR 
       16.83        16.18        17.52         0.76        12.36         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.82         0.62         1.18        14.50         1.35         1.35 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       15.02        14.99        13.58        13.48        12.59        45.96 
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-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM 
        0.13        16.08         0.07         0.36         1.18         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK 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-A23K TCGA-FU-A2QG 
       14.70        19.79         6.12         4.73         1.22         0.92 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        0.66         1.02         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 
        1.12         9.01        25.41         7.13        21.67        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 
       20.48        10.06         5.13         6.71        21.11        30.31 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89         0.07         0.30         0.82         0.20 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        5.49        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59         3.88        11.67        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QC 
       29.03        20.22        14.07        53.52        46.03        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       49.55        39.78        31.27        16.64         4.73        23.24 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        18.05 

  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                           0.03                            0.03 
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                         195.85                          182.93 
  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE 
                         18.905                          15.580 
[1] "0.0 - 195.8 (18.9)" "0.0 - 182.9 (15.6)"
[1] "hr=" "1.1"
D20V2, continuous
                                 vv
clus                              T1 T2 T3+T4
  AMP PEAK 20(16P13.13) MUTATED   23 15     3
  AMP PEAK 20(16P13.13) WILD-TYPE 98 35     8
D20V3, multiclass
       clus
vv      AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  T1                               23                              98
  T2                               15                              35
  T3+T4                             3                               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   22 14
  AMP PEAK 20(16P13.13) WILD-TYPE 89 33
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     22   14
  AMP PEAK 20(16P13.13) WILD-TYPE   89   33
   clus
vv  AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  0                            22                              89
  1                            14                              33
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 20(16P13.13) MUTATED   20  2 18
  AMP PEAK 20(16P13.13) WILD-TYPE 71  6 75
D20V5, multiclass
    clus
vv   AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  M0                            20                              71
  M1                             2                               6
  MX                            18                              75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  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                                 39
  AMP PEAK 20(16P13.13) WILD-TYPE                              158
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 20(16P13.13) MUTATED                                               1
  AMP PEAK 20(16P13.13) WILD-TYPE                                             4
                                 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                                              3
  AMP PEAK 20(16P13.13) WILD-TYPE                                            3
D20V6, multiclass
                                               clus
vv                                              AMP PEAK 20(16P13.13) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         39
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
                                               clus
vv                                              AMP PEAK 20(16P13.13) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          158
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(16P13.13) MUTATED     6  43
  AMP PEAK 20(16P13.13) WILD-TYPE  24 165
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED      6   43
  AMP PEAK 20(16P13.13) WILD-TYPE   24  165
     clus
vv    AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  NO                              6                              24
  YES                            43                             165
[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                           3
  AMP PEAK 20(16P13.13) WILD-TYPE                        21
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 20(16P13.13) MUTATED                                           1
  AMP PEAK 20(16P13.13) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 20(16P13.13) MUTATED      32
  AMP PEAK 20(16P13.13) WILD-TYPE   137
D20V10, multiclass
                                           clus
vv                                          AMP PEAK 20(16P13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 2
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                32
                                           clus
vv                                          AMP PEAK 20(16P13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        5
  ASIAN                                                                  16
  BLACK OR AFRICAN AMERICAN                                              21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  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"
D20V11, binary
                                 cls
clus                                0   1
  AMP PEAK 20(16P13.13) MUTATED     2  27
  AMP PEAK 20(16P13.13) WILD-TYPE  14 122
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED      2   27
  AMP PEAK 20(16P13.13) WILD-TYPE   14  122
                        clus
vv                       AMP PEAK 20(16P13.13) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            27
                        clus
vv                       AMP PEAK 20(16P13.13) WILD-TYPE
  HISPANIC OR LATINO                                  14
  NOT HISPANIC OR LATINO                             122
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   14  8
  AMP PEAK 20(16P13.13) WILD-TYPE 57 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     14    8
  AMP PEAK 20(16P13.13) WILD-TYPE   57   17
            clus
vv           AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  TUMOR FREE                            14                              57
  WITH TUMOR                             8                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 20(16P13.13) MUTATED        5      3       1      1       2
  AMP PEAK 20(16P13.13) WILD-TYPE     18      2       0      9       5
                                 vv
clus                              UNITED STATES VIETNAM
  AMP PEAK 20(16P13.13) MUTATED              35       2
  AMP PEAK 20(16P13.13) WILD-TYPE           143      12
D20V14, multiclass
               clus
vv              AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  BRAZIL                                    5                              18
  CANADA                                    3                               2
  NIGERIA                                   1                               0
  RUSSIA                                    1                               9
  UKRAINE                                   2                               5
  UNITED STATES                            35                             143
  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    4 22 21  0  2
  AMP PEAK 20(16P13.13) WILD-TYPE 13 84 76  1 12
D20V15, multiclass
    clus
vv   AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  G1                             4                              13
  G2                            22                              84
  G3                            21                              76
  G4                             0                               1
  GX                             2                              12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V16, continuous
D20V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 20(16P13.13) MUTATED                                             4
  AMP PEAK 20(16P13.13) WILD-TYPE                                          27
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 20(16P13.13) MUTATED                                        2
  AMP PEAK 20(16P13.13) WILD-TYPE                                      6
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 20(16P13.13) MUTATED                                                 0
  AMP PEAK 20(16P13.13) WILD-TYPE                                               2
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 20(16P13.13) MUTATED               12                  22
  AMP PEAK 20(16P13.13) WILD-TYPE             40                  90
D20V18, multiclass
                                                 clus
vv                                                AMP PEAK 20(16P13.13) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             12
  LIFELONG NON-SMOKER                                                        22
                                                 clus
vv                                                AMP PEAK 20(16P13.13) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               2
  CURRENT SMOKER                                                               40
  LIFELONG NON-SMOKER                                                          90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V19, continuous
D20V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 20(16P13.13) MUTATED             4       14             2        1
  AMP PEAK 20(16P13.13) WILD-TYPE          15       61            10       11
D20V21, multiclass
               clus
vv              AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  COMBINATION                               4                              15
  EXTERNAL                                 14                              61
  EXTERNAL BEAM                             2                              10
  INTERNAL                                  1                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     5             1
  AMP PEAK 20(16P13.13) WILD-TYPE                  23            15
D20V23, multiclass
                     clus
vv                    AMP PEAK 20(16P13.13) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                0
  PRIMARY TUMOR FIELD                             5
  REGIONAL SITE                                   1
                     clus
vv                    AMP PEAK 20(16P13.13) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  2
  PRIMARY TUMOR FIELD                              23
  REGIONAL SITE                                    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"
D20V24, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED    6  0
  AMP PEAK 20(16P13.13) WILD-TYPE 28  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED      6    0
  AMP PEAK 20(16P13.13) WILD-TYPE   28    3
     clus
vv    AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  CGY                             6                              28
  GY                              0                               3
[1] 2 2
[1] FALSE
D20V25, continuous
D20V26, continuous
D20V27, continuous
D20V28, continuous
D20V29, continuous
D20V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 20(16P13.13) MUTATED                         5
  AMP PEAK 20(16P13.13) WILD-TYPE                      24
                                 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                       4
D20V31, multiclass
                                     clus
vv                                    AMP PEAK 20(16P13.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         5
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         3
                                     clus
vv                                    AMP PEAK 20(16P13.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                          24
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 20(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                                                5
  AMP PEAK 20(16P13.13) WILD-TYPE                                             11
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 20(16P13.13) MUTATED                                                                                  16
  AMP PEAK 20(16P13.13) WILD-TYPE                                                                                52
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 20(16P13.13) MUTATED                                                                                             18
  AMP PEAK 20(16P13.13) WILD-TYPE                                                                                           87
D20V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 20(16P13.13) 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)                                       16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            18
                                                                                              clus
vv                                                                                             AMP PEAK 20(16P13.13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         52
  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"
D20V33, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   19 15
  AMP PEAK 20(16P13.13) WILD-TYPE 49 55
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     19   15
  AMP PEAK 20(16P13.13) WILD-TYPE   49   55
         clus
vv        AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  ABSENT                             19                              49
  PRESENT                            15                              55
[1] 2 2
[1] FALSE
D20V34, continuous
D20V35, continuous
D20V36, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED    8 19
  AMP PEAK 20(16P13.13) WILD-TYPE 35 75
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED      8   19
  AMP PEAK 20(16P13.13) WILD-TYPE   35   75
                                          clus
vv                                         AMP PEAK 20(16P13.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            19
                                          clus
vv                                         AMP PEAK 20(16P13.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              75
[1] 2 2
[1] FALSE
D20V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 20(16P13.13) MUTATED              0           7         12
  AMP PEAK 20(16P13.13) WILD-TYPE           10          42         45
D20V38, multiclass
              clus
vv             AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  CURRENT USER                             0                              10
  FORMER USER                              7                              42
  NEVER USED                              12                              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V39, continuous
D20V40, binary
                                 cls
clus                               0  1
  AMP PEAK 20(16P13.13) MUTATED   16  5
  AMP PEAK 20(16P13.13) WILD-TYPE 73 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(16P13.13) MUTATED     16    5
  AMP PEAK 20(16P13.13) WILD-TYPE   73   11
         clus
vv        AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  ABSENT                             16                              73
  PRESENT                             5                              11
[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                              11 
                     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-MU-A51Y                      TCGA-MU-A8JM 
"AMP PEAK 20(16P13.13) WILD-TYPE" "AMP PEAK 20(16P13.13) WILD-TYPE" 
                     TCGA-MY-A913 
"AMP PEAK 20(16P13.13) WILD-TYPE" 
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 20(16P13.13) MUTATED     0    0   5   13    5  0   3    3    1   8
  AMP PEAK 20(16P13.13) WILD-TYPE   1    1  25   52   19  4   5    4    8  14
                                 vv
clus                              T3 T3B T4 TIS TX
  AMP PEAK 20(16P13.13) MUTATED    1   2  0   0  1
  AMP PEAK 20(16P13.13) WILD-TYPE  0   6  2   1 13
D20V42, multiclass
      clus
vv     AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  T1A                              0                               1
  T1A1                             0                               1
  T1B                              5                              25
  T1B1                            13                              52
  T1B2                             5                              19
  T2                               0                               4
  T2A                              3                               5
  T2A1                             3                               4
  T2A2                             1                               8
  T2B                              8                              14
  T3                               1                               0
  T3B                              2                               6
  T4                               0                               2
  TIS                              0                               1
  TX                               1                              13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        2         1         1       26
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 20(16P13.13) MUTATED          13         7        1         1
  AMP PEAK 20(16P13.13) WILD-TYPE        56        25        2         5
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 20(16P13.13) MUTATED            2          2         7         1
  AMP PEAK 20(16P13.13) WILD-TYPE          3          5        20         0
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 20(16P13.13) MUTATED            9         0         1
  AMP PEAK 20(16P13.13) WILD-TYPE         25         3         6
D20V44, multiclass
            clus
vv           AMP PEAK 20(16P13.13) MUTATED AMP PEAK 20(16P13.13) WILD-TYPE
  STAGE I                                0                               4
  STAGE IA                               0                               2
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               5                              26
  STAGE IB1                             13                              56
  STAGE IB2                              7                              25
  STAGE II                               1                               2
  STAGE IIA                              1                               5
  STAGE IIA1                             2                               3
  STAGE IIA2                             2                               5
  STAGE IIB                              7                              20
  STAGE III                              1                               0
  STAGE IIIB                             9                              25
  STAGE IVA                              0                               3
  STAGE IVB                              1                               6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(17Q12) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(17Q12) MUTATED    38   8
  AMP PEAK 21(17Q12) WILD-TYPE 145  42
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                          46                          187 
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                           8                           42 
$`AMP PEAK 21(17Q12) MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MP TCGA-C5-A2LZ 
       23.67        31.40        35.01        35.61         3.58       100.14 
TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-C5-A8YT 
      154.32       147.35        85.55         2.73        75.78         6.12 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH 
        1.12        58.88       117.99        22.98        16.18        17.52 
TCGA-EA-A3HR TCGA-EA-A5ZF TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RM 
        1.32        14.96         0.13        16.08         0.03         2.24 
TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A40J TCGA-JW-A69B TCGA-JX-A3Q8 
        0.10         6.94         6.12         1.35        10.06        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MY-A913 TCGA-Q1-A5R2 
        7.99        11.28         0.82        13.87         5.49        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A73R TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EI 
       15.95         6.25        93.99        61.28        34.52        14.07 
TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A959 TCGA-VS-A9U5 
       19.96        16.64        39.35        38.96 

$`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         0.82        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       15.48        20.35        17.19        60.69        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         4.47        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         0.76        12.36         1.74         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       13.91        15.02        14.99        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       12.59        45.96        26.27         6.64         1.51         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
        0.59         0.59         1.45         0.07         4.04         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
        1.18        23.70         0.10         0.07         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
       20.35         7.92        14.70        19.79         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        26.56        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
        3.29        24.56        21.44        20.48        15.58         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
        6.71        21.11       195.85         0.89         0.07         0.30 
TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.20         0.03         5.42        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        2.96        15.58         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       15.88         5.88        10.39        19.59         3.88        11.67 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 
       12.16        10.03        29.03        20.22        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       46.03        23.28        11.51        49.55        39.78        31.27 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-WL-A834 
       18.05 

  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 
                      154.32                       195.85 
  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE 
                      16.015                       15.580 
[1] "0.0 - 154.3 (16.0)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.3"
D21V2, continuous
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 21(17Q12) MUTATED    19  11     4
  AMP PEAK 21(17Q12) WILD-TYPE 102  39     7
D21V3, multiclass
       clus
vv      AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  T1                            19                          102
  T2                            11                           39
  T3+T4                          4                            7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   17 10
  AMP PEAK 21(17Q12) WILD-TYPE 94 37
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     17   10
  AMP PEAK 21(17Q12) WILD-TYPE   94   37
   clus
vv  AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  0                         17                           94
  1                         10                           37
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  AMP PEAK 21(17Q12) MUTATED   18  2 17
  AMP PEAK 21(17Q12) WILD-TYPE 73  6 76
D21V5, multiclass
    clus
vv   AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  M0                         18                           73
  M1                          2                            6
  MX                         17                           76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(17Q12) MUTATED               2                               35
  AMP PEAK 21(17Q12) WILD-TYPE             3                              162
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 21(17Q12) MUTATED                                               0
  AMP PEAK 21(17Q12) WILD-TYPE                                             5
                              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                                              1
  AMP PEAK 21(17Q12) WILD-TYPE                                            5
D21V6, multiclass
                                               clus
vv                                              AMP PEAK 21(17Q12) MUTATED
  ADENOSQUAMOUS                                                          2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      35
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           1
                                               clus
vv                                              AMP PEAK 21(17Q12) WILD-TYPE
  ADENOSQUAMOUS                                                            3
  CERVICAL SQUAMOUS CELL CARCINOMA                                       162
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(17Q12) MUTATED     4  43
  AMP PEAK 21(17Q12) WILD-TYPE  26 165
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED      4   43
  AMP PEAK 21(17Q12) WILD-TYPE   26  165
     clus
vv    AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  NO                           4                           26
  YES                         43                          165
[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                        21
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 21(17Q12) MUTATED                                           0    32
  AMP PEAK 21(17Q12) WILD-TYPE                                         1   137
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                                                             32
                                           clus
vv                                          AMP PEAK 21(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     7
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                           21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  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"
D21V11, binary
                              cls
clus                             0   1
  AMP PEAK 21(17Q12) MUTATED     5  27
  AMP PEAK 21(17Q12) WILD-TYPE  11 122
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED      5   27
  AMP PEAK 21(17Q12) WILD-TYPE   11  122
                        clus
vv                       AMP PEAK 21(17Q12) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         27
                        clus
vv                       AMP PEAK 21(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          122
[1] 2 2
[1] FALSE
D21V12, continuous
D21V13, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   13  7
  AMP PEAK 21(17Q12) WILD-TYPE 58 18
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     13    7
  AMP PEAK 21(17Q12) WILD-TYPE   58   18
            clus
vv           AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  TUMOR FREE                         13                           58
  WITH TUMOR                          7                           18
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 21(17Q12) MUTATED        6      2       0      1       0
  AMP PEAK 21(17Q12) WILD-TYPE     17      3       1      9       7
                              vv
clus                           UNITED STATES VIETNAM
  AMP PEAK 21(17Q12) MUTATED              35       3
  AMP PEAK 21(17Q12) WILD-TYPE           143      11
D21V14, multiclass
               clus
vv              AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  BRAZIL                                 6                           17
  CANADA                                 2                            3
  NIGERIA                                0                            1
  RUSSIA                                 1                            9
  UKRAINE                                0                            7
  UNITED STATES                         35                          143
  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 16 25  0  4
  AMP PEAK 21(17Q12) WILD-TYPE 16 90 72  1 10
D21V15, multiclass
    clus
vv   AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  G1                          1                           16
  G2                         16                           90
  G3                         25                           72
  G4                          0                            1
  GX                          4                           10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V16, continuous
D21V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 21(17Q12) MUTATED                                             3
  AMP PEAK 21(17Q12) WILD-TYPE                                          28
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 21(17Q12) MUTATED                                        2
  AMP PEAK 21(17Q12) WILD-TYPE                                      6
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 21(17Q12) MUTATED                                                 1
  AMP PEAK 21(17Q12) WILD-TYPE                                               1
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 21(17Q12) MUTATED                7                  27
  AMP PEAK 21(17Q12) WILD-TYPE             45                  85
D21V18, multiclass
                                                 clus
vv                                                AMP PEAK 21(17Q12) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          1
  CURRENT SMOKER                                                           7
  LIFELONG NON-SMOKER                                                     27
                                                 clus
vv                                                AMP PEAK 21(17Q12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            45
  LIFELONG NON-SMOKER                                                       85
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V19, continuous
D21V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 21(17Q12) MUTATED             2       16             2        5
  AMP PEAK 21(17Q12) WILD-TYPE          17       59            10        7
D21V21, multiclass
               clus
vv              AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  COMBINATION                            2                           17
  EXTERNAL                              16                           59
  EXTERNAL BEAM                          2                           10
  INTERNAL                               5                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     8             5
  AMP PEAK 21(17Q12) WILD-TYPE                  20            11
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                          8                           20
  REGIONAL SITE                                5                           11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V24, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   10  1
  AMP PEAK 21(17Q12) WILD-TYPE 24  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     10    1
  AMP PEAK 21(17Q12) WILD-TYPE   24    2
     clus
vv    AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  CGY                         10                           24
  GY                           1                            2
[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                                   5
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 21(17Q12) MUTATED                         5                       0
  AMP PEAK 21(17Q12) WILD-TYPE                      24                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 21(17Q12) MUTATED                         0
  AMP PEAK 21(17Q12) WILD-TYPE                       7
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                            5
  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)
  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                                                4
  AMP PEAK 21(17Q12) WILD-TYPE                                             12
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 21(17Q12) MUTATED                                                                                  12
  AMP PEAK 21(17Q12) WILD-TYPE                                                                                56
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 21(17Q12) MUTATED                                                                                             19
  AMP PEAK 21(17Q12) WILD-TYPE                                                                                           86
D21V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 21(17Q12) 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)                                    12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         19
                                                                                              clus
vv                                                                                             AMP PEAK 21(17Q12) 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)                                      56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V33, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   11 13
  AMP PEAK 21(17Q12) WILD-TYPE 57 57
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     11   13
  AMP PEAK 21(17Q12) WILD-TYPE   57   57
         clus
vv        AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  ABSENT                          11                           57
  PRESENT                         13                           57
[1] 2 2
[1] FALSE
D21V34, continuous
D21V35, continuous
D21V36, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED    3 16
  AMP PEAK 21(17Q12) WILD-TYPE 40 78
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED      3   16
  AMP PEAK 21(17Q12) WILD-TYPE   40   78
                                          clus
vv                                         AMP PEAK 21(17Q12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              3
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         16
                                          clus
vv                                         AMP PEAK 21(17Q12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           78
[1] 2 2
[1] FALSE
D21V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 21(17Q12) MUTATED              2          11         10
  AMP PEAK 21(17Q12) WILD-TYPE            8          38         47
D21V38, multiclass
              clus
vv             AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  CURRENT USER                          2                            8
  FORMER USER                          11                           38
  NEVER USED                           10                           47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V39, continuous
D21V40, binary
                              cls
clus                            0  1
  AMP PEAK 21(17Q12) MUTATED   16  3
  AMP PEAK 21(17Q12) WILD-TYPE 73 13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(17Q12) MUTATED     16    3
  AMP PEAK 21(17Q12) WILD-TYPE   73   13
         clus
vv        AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  ABSENT                          16                           73
  PRESENT                          3                           13
[1] 2 2
[1] FALSE
D21V41, continuous
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 21(17Q12) MUTATED     1    0   1   13    4  1   2    3    1   4  0
  AMP PEAK 21(17Q12) WILD-TYPE   0    1  29   52   20  3   6    4    8  18  1
                              vv
clus                           T3B T4 TIS TX
  AMP PEAK 21(17Q12) MUTATED     4  0   1  3
  AMP PEAK 21(17Q12) WILD-TYPE   4  2   0 11
D21V42, multiclass
      clus
vv     AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  T1A                           1                            0
  T1A1                          0                            1
  T1B                           1                           29
  T1B1                         13                           52
  T1B2                          4                           20
  T2                            1                            3
  T2A                           2                            6
  T2A1                          3                            4
  T2A2                          1                            8
  T2B                           4                           18
  T3                            0                            1
  T3B                           4                            4
  T4                            0                            2
  TIS                           1                            0
  TX                            3                           11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 21(17Q12) MUTATED         1        1         0         0        3
  AMP PEAK 21(17Q12) WILD-TYPE       3        1         1         1       28
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 21(17Q12) MUTATED          16         5        1         2
  AMP PEAK 21(17Q12) WILD-TYPE        53        27        2         4
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 21(17Q12) MUTATED            2          1         7         0
  AMP PEAK 21(17Q12) WILD-TYPE          3          6        20         1
                              vv
clus                           STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 21(17Q12) MUTATED            6         0         0
  AMP PEAK 21(17Q12) WILD-TYPE         28         3         7
D21V44, multiclass
            clus
vv           AMP PEAK 21(17Q12) MUTATED AMP PEAK 21(17Q12) WILD-TYPE
  STAGE I                             1                            3
  STAGE IA                            1                            1
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            3                           28
  STAGE IB1                          16                           53
  STAGE IB2                           5                           27
  STAGE II                            1                            2
  STAGE IIA                           2                            4
  STAGE IIA1                          2                            3
  STAGE IIA2                          1                            6
  STAGE IIB                           7                           20
  STAGE III                           0                            1
  STAGE IIIB                          6                           28
  STAGE IVA                           0                            3
  STAGE IVB                           0                            7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(17Q25.1) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(17Q25.1) MUTATED    50  13
  AMP PEAK 22(17Q25.1) WILD-TYPE 133  37
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            63                            170 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            13                             37 
$`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        85.55 
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         1.74         1.32        13.05        14.50        14.89 
TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA 
       13.91        14.96         6.64         0.59         0.13        16.08 
TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A3HY 
        0.03         2.24         0.10         6.94         6.12         0.66 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-IR-A3L7 
        1.45         1.58         1.35         7.13        14.93       147.39 
TCGA-IR-A3LC TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
      117.40        24.56        10.06        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MU-A51Y TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.89         0.30        13.87         5.49        13.35        15.95 
TCGA-Q1-A73Q TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EI 
        5.88        93.99        61.28        10.03        34.52        14.07 
TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A9U5 
       19.96        16.64        38.96 

$`AMP PEAK 22(17Q25.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MJ 
       67.46        46.32        30.21        57.73        38.99         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        2.43        20.91        40.93        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35        38.43         0.82        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7UC 
       17.85        20.42       182.93       101.82        15.48        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI 
       60.69        94.95         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 
       75.78        99.91        27.52         6.12        20.91         4.47 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       50.76        44.94        40.04        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99       118.65        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 
        0.76        12.36         0.82         0.62         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
        1.48        15.02        14.99        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 
       12.59        45.96        26.27         1.51         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        1.45         0.07         4.04         0.36         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.07         0.10         0.03        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70        19.79         4.73         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        2.17         1.02         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.97         1.12         9.01        25.41        21.67        20.78 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
        9.44       137.16        66.81        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        27.42         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AX 
       15.58         5.13         6.71        21.11       195.85         0.07 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82         0.20         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         2.96        15.58         3.39        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         6.25        10.39        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        29.03        20.22        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       46.03        23.28        11.51        49.55        39.78        31.27 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-WL-A834 
       39.35        18.05 

  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 
                        154.32                         195.85 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                         14.50                          17.01 
[1] "0.0 - 154.3 (14.5)" "0.0 - 195.8 (17.0)"
[1] "hr=" "1"  
D22V2, continuous
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 22(17Q25.1) MUTATED   28 15     5
  AMP PEAK 22(17Q25.1) WILD-TYPE 93 35     6
D22V3, multiclass
       clus
vv      AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  T1                              28                             93
  T2                              15                             35
  T3+T4                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   25 15
  AMP PEAK 22(17Q25.1) WILD-TYPE 86 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     25   15
  AMP PEAK 22(17Q25.1) WILD-TYPE   86   32
   clus
vv  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  0                           25                             86
  1                           15                             32
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 22(17Q25.1) MUTATED   24  3 24
  AMP PEAK 22(17Q25.1) WILD-TYPE 67  5 69
D22V5, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  M0                           24                             67
  M1                            3                              5
  MX                           24                             69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(17Q25.1) MUTATED               2                               53
  AMP PEAK 22(17Q25.1) WILD-TYPE             3                              144
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 22(17Q25.1) MUTATED                                               2
  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                                              0
  AMP PEAK 22(17Q25.1) WILD-TYPE                                            6
D22V6, multiclass
                                               clus
vv                                              AMP PEAK 22(17Q25.1) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        53
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              AMP PEAK 22(17Q25.1) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         144
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  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"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED     5  60
  AMP PEAK 22(17Q25.1) WILD-TYPE  25 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      5   60
  AMP PEAK 22(17Q25.1) WILD-TYPE   25  148
     clus
vv    AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  NO                             5                             25
  YES                           60                            148
[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                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 22(17Q25.1) MUTATED                                           0
  AMP PEAK 22(17Q25.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 22(17Q25.1) MUTATED      48
  AMP PEAK 22(17Q25.1) WILD-TYPE   121
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                                                               48
                                           clus
vv                                          AMP PEAK 22(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                121
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED     6  39
  AMP PEAK 22(17Q25.1) WILD-TYPE  10 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      6   39
  AMP PEAK 22(17Q25.1) WILD-TYPE   10  110
                        clus
vv                       AMP PEAK 22(17Q25.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           39
                        clus
vv                       AMP PEAK 22(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            110
[1] 2 2
[1] FALSE
D22V12, continuous
D22V13, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   20  7
  AMP PEAK 22(17Q25.1) WILD-TYPE 51 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     20    7
  AMP PEAK 22(17Q25.1) WILD-TYPE   51   18
            clus
vv           AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  TUMOR FREE                           20                             51
  WITH TUMOR                            7                             18
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 22(17Q25.1) MUTATED        6      2       0      3       1
  AMP PEAK 22(17Q25.1) WILD-TYPE     17      3       1      7       6
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 22(17Q25.1) MUTATED              48       5
  AMP PEAK 22(17Q25.1) WILD-TYPE           130       9
D22V14, multiclass
               clus
vv              AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  BRAZIL                                   6                             17
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   3                              7
  UKRAINE                                  1                              6
  UNITED STATES                           48                            130
  VIETNAM                                  5                              9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 22(17Q25.1) MUTATED    2 24 33  0  5
  AMP PEAK 22(17Q25.1) WILD-TYPE 15 82 64  1  9
D22V15, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  G1                            2                             15
  G2                           24                             82
  G3                           33                             64
  G4                            0                              1
  GX                            5                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V16, continuous
D22V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 22(17Q25.1) MUTATED                                             8
  AMP PEAK 22(17Q25.1) WILD-TYPE                                          23
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 22(17Q25.1) MUTATED                                        3
  AMP PEAK 22(17Q25.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 22(17Q25.1) MUTATED                                                 2
  AMP PEAK 22(17Q25.1) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 22(17Q25.1) MUTATED               12                  29
  AMP PEAK 22(17Q25.1) WILD-TYPE             40                  83
D22V18, multiclass
                                                 clus
vv                                                AMP PEAK 22(17Q25.1) 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                                                            12
  LIFELONG NON-SMOKER                                                       29
                                                 clus
vv                                                AMP PEAK 22(17Q25.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                              40
  LIFELONG NON-SMOKER                                                         83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V19, continuous
D22V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 22(17Q25.1) MUTATED             3       24             3        4
  AMP PEAK 22(17Q25.1) WILD-TYPE          16       51             9        8
D22V21, multiclass
               clus
vv              AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  COMBINATION                              3                             16
  EXTERNAL                                24                             51
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 4                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    12             3
  AMP PEAK 22(17Q25.1) WILD-TYPE                  16            13
D22V23, multiclass
                     clus
vv                    AMP PEAK 22(17Q25.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                           12
  REGIONAL SITE                                  3
                     clus
vv                    AMP PEAK 22(17Q25.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             16
  REGIONAL SITE                                   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"
D22V24, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   10  1
  AMP PEAK 22(17Q25.1) WILD-TYPE 24  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     10    1
  AMP PEAK 22(17Q25.1) WILD-TYPE   24    2
     clus
vv    AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  CGY                           10                             24
  GY                             1                              2
[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                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 22(17Q25.1) MUTATED                         6
  AMP PEAK 22(17Q25.1) WILD-TYPE                      23
                                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                       6
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                              5
  OTHER LOCATION, SPECIFY                                         23
  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 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                                                5
  AMP PEAK 22(17Q25.1) WILD-TYPE                                             11
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 22(17Q25.1) MUTATED                                                                                  15
  AMP PEAK 22(17Q25.1) WILD-TYPE                                                                                53
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 22(17Q25.1) MUTATED                                                                                             30
  AMP PEAK 22(17Q25.1) WILD-TYPE                                                                                           75
D22V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 22(17Q25.1) 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)                                      15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           30
                                                                                              clus
vv                                                                                             AMP PEAK 22(17Q25.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V33, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   12 22
  AMP PEAK 22(17Q25.1) WILD-TYPE 56 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     12   22
  AMP PEAK 22(17Q25.1) WILD-TYPE   56   48
         clus
vv        AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  ABSENT                            12                             56
  PRESENT                           22                             48
[1] 2 2
[1] FALSE
D22V34, continuous
D22V35, continuous
D22V36, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   12 20
  AMP PEAK 22(17Q25.1) WILD-TYPE 31 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     12   20
  AMP PEAK 22(17Q25.1) WILD-TYPE   31   74
                                          clus
vv                                         AMP PEAK 22(17Q25.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           20
                                          clus
vv                                         AMP PEAK 22(17Q25.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             74
[1] 2 2
[1] FALSE
D22V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 22(17Q25.1) MUTATED              3          16         12
  AMP PEAK 22(17Q25.1) WILD-TYPE            7          33         45
D22V38, multiclass
              clus
vv             AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  CURRENT USER                            3                              7
  FORMER USER                            16                             33
  NEVER USED                             12                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V39, continuous
D22V40, binary
                                cls
clus                              0  1
  AMP PEAK 22(17Q25.1) MUTATED   23  5
  AMP PEAK 22(17Q25.1) WILD-TYPE 66 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     23    5
  AMP PEAK 22(17Q25.1) WILD-TYPE   66   11
         clus
vv        AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  ABSENT                            23                             66
  PRESENT                            5                             11
[1] 2 2
[1] FALSE
D22V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 22(17Q25.1) MUTATED     0    0   2   19    7  1   3    4    1   6  0
  AMP PEAK 22(17Q25.1) WILD-TYPE   1    1  28   46   17  3   5    3    8  16  1
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 22(17Q25.1) MUTATED     5  0   1  3
  AMP PEAK 22(17Q25.1) WILD-TYPE   3  2   0 11
D22V42, multiclass
      clus
vv     AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             2                             28
  T1B1                           19                             46
  T1B2                            7                             17
  T2                              1                              3
  T2A                             3                              5
  T2A1                            4                              3
  T2A2                            1                              8
  T2B                             6                             16
  T3                              0                              1
  T3B                             5                              3
  T4                              0                              2
  TIS                             1                              0
  TX                              3                             11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 22(17Q25.1) MUTATED         1        1         0         0        2
  AMP PEAK 22(17Q25.1) WILD-TYPE       3        1         1         1       29
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 22(17Q25.1) MUTATED          20         8        2         2
  AMP PEAK 22(17Q25.1) WILD-TYPE        49        24        1         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 22(17Q25.1) MUTATED            3          1         9         0
  AMP PEAK 22(17Q25.1) WILD-TYPE          2          6        18         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 22(17Q25.1) MUTATED           12         1         1
  AMP PEAK 22(17Q25.1) WILD-TYPE         22         2         6
D22V44, multiclass
            clus
vv           AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              2                             29
  STAGE IB1                            20                             49
  STAGE IB2                             8                             24
  STAGE II                              2                              1
  STAGE IIA                             2                              4
  STAGE IIA1                            3                              2
  STAGE IIA2                            1                              6
  STAGE IIB                             9                             18
  STAGE III                             0                              1
  STAGE IIIB                           12                             22
  STAGE IVA                             1                              2
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(19P13.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(19P13.3) MUTATED    28   2
  AMP PEAK 23(19P13.3) WILD-TYPE 155  48
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                            30                            203 
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                             2                             48 
$`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       182.93       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         5.13 
TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BE TCGA-Q1-A5R2 
      195.85        11.28         0.30         0.20         0.07        13.35 
TCGA-Q1-A73R TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A954 TCGA-VS-A9U5 TCGA-WL-A834 
        6.25        93.99        14.07        42.58        38.96        18.05 

$`AMP PEAK 23(19P13.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       31.40        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43         0.82        52.01        18.02        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       85.55        60.69        94.95         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       50.99        45.83         8.35        75.78        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52         6.12        20.91         4.47         1.12        50.76 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       40.04        87.75        58.88        36.76       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       12.36         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        1.18        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 
       12.59        45.96        26.27         1.51         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        3.52         1.32         1.97         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
        7.13        21.67        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
       66.81        96.95        78.71        81.96        26.56        27.42 
TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-AAVH 
        3.29        21.44        20.48        15.58        10.06         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       21.11        30.31         7.99         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       13.87         0.03         5.42        29.72         4.34         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        15.58        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88         5.88        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       20.22        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.08        43.82        39.35 

  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                        195.85                         173.29 
  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE 
                        19.415                         15.580 
[1] "0.1 - 195.8 (19.4)" "0.0 - 173.3 (15.6)"
[1] "hr=" "5.1"
D23V2, continuous
                                vv
clus                              T1  T2 T3+T4
  AMP PEAK 23(19P13.3) MUTATED    13   9     3
  AMP PEAK 23(19P13.3) WILD-TYPE 108  41     8
D23V3, multiclass
       clus
vv      AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  T1                              13                            108
  T2                               9                             41
  T3+T4                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.3) MUTATED    11  10
  AMP PEAK 23(19P13.3) WILD-TYPE 100  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED     11   10
  AMP PEAK 23(19P13.3) WILD-TYPE  100   37
   clus
vv  AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  0                           11                            100
  1                           10                             37
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 23(19P13.3) MUTATED   10  0 15
  AMP PEAK 23(19P13.3) WILD-TYPE 81  8 78
D23V5, multiclass
    clus
vv   AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  M0                           10                             81
  M1                            0                              8
  MX                           15                             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(19P13.3) MUTATED               0                               26
  AMP PEAK 23(19P13.3) WILD-TYPE             5                              171
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 23(19P13.3) MUTATED                                               1
  AMP PEAK 23(19P13.3) WILD-TYPE                                             4
                                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                                              0
  AMP PEAK 23(19P13.3) WILD-TYPE                                            6
D23V6, multiclass
                                               clus
vv                                              AMP PEAK 23(19P13.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        26
  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 23(19P13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         171
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.3) MUTATED     3  27
  AMP PEAK 23(19P13.3) WILD-TYPE  27 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      3   27
  AMP PEAK 23(19P13.3) WILD-TYPE   27  181
     clus
vv    AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  NO                             3                             27
  YES                           27                            181
[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                        21
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 23(19P13.3) MUTATED                                           0
  AMP PEAK 23(19P13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 23(19P13.3) MUTATED      19
  AMP PEAK 23(19P13.3) WILD-TYPE   150
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                                                               19
                                           clus
vv                                          AMP PEAK 23(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             21
  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"
D23V11, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.3) MUTATED     2  15
  AMP PEAK 23(19P13.3) WILD-TYPE  14 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      2   15
  AMP PEAK 23(19P13.3) WILD-TYPE   14  134
                        clus
vv                       AMP PEAK 23(19P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       AMP PEAK 23(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            134
[1] 2 2
[1] FALSE
D23V12, continuous
D23V13, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED    9  3
  AMP PEAK 23(19P13.3) WILD-TYPE 62 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      9    3
  AMP PEAK 23(19P13.3) WILD-TYPE   62   22
            clus
vv           AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  TUMOR FREE                            9                             62
  WITH TUMOR                            3                             22
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 23(19P13.3) MUTATED        3      2       0      0       0
  AMP PEAK 23(19P13.3) WILD-TYPE     20      3       1     10       7
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 23(19P13.3) MUTATED              22       3
  AMP PEAK 23(19P13.3) WILD-TYPE           156      11
D23V14, multiclass
               clus
vv              AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  BRAZIL                                   3                             20
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   0                             10
  UKRAINE                                  0                              7
  UNITED STATES                           22                            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 23(19P13.3) MUTATED    1 11 16  0  2
  AMP PEAK 23(19P13.3) WILD-TYPE 16 95 81  1 12
D23V15, multiclass
    clus
vv   AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  G1                            1                             16
  G2                           11                             95
  G3                           16                             81
  G4                            0                              1
  GX                            2                             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V16, continuous
D23V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 23(19P13.3) MUTATED                                             3
  AMP PEAK 23(19P13.3) WILD-TYPE                                          28
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 23(19P13.3) MUTATED                                        2
  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                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 23(19P13.3) MUTATED                4                  17
  AMP PEAK 23(19P13.3) WILD-TYPE             48                  95
D23V18, multiclass
                                                 clus
vv                                                AMP PEAK 23(19P13.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             4
  LIFELONG NON-SMOKER                                                       17
                                                 clus
vv                                                AMP PEAK 23(19P13.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              48
  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"
D23V19, continuous
D23V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 23(19P13.3) MUTATED             2       11             1        0
  AMP PEAK 23(19P13.3) WILD-TYPE          17       64            11       12
D23V21, multiclass
               clus
vv              AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  COMBINATION                              2                             17
  EXTERNAL                                11                             64
  EXTERNAL BEAM                            1                             11
  INTERNAL                                 0                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     3             1
  AMP PEAK 23(19P13.3) WILD-TYPE                  25            15
D23V23, multiclass
                     clus
vv                    AMP PEAK 23(19P13.3) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            3
  REGIONAL SITE                                  1
                     clus
vv                    AMP PEAK 23(19P13.3) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             25
  REGIONAL SITE                                   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"
D23V24, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED    4  0
  AMP PEAK 23(19P13.3) WILD-TYPE 30  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      4    0
  AMP PEAK 23(19P13.3) WILD-TYPE   30    3
     clus
vv    AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  CGY                            4                             30
  GY                             0                              3
[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                                     0
  AMP PEAK 23(19P13.3) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 23(19P13.3) MUTATED                         2
  AMP PEAK 23(19P13.3) WILD-TYPE                      27
                                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                       6
D23V31, multiclass
                                     clus
vv                                    AMP PEAK 23(19P13.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  OTHER LOCATION, SPECIFY                                        2
  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                                         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 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                                                1
  AMP PEAK 23(19P13.3) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 23(19P13.3) MUTATED                                                                                  11
  AMP PEAK 23(19P13.3) WILD-TYPE                                                                                57
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 23(19P13.3) MUTATED                                                                                             13
  AMP PEAK 23(19P13.3) WILD-TYPE                                                                                           92
D23V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 23(19P13.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           13
                                                                                              clus
vv                                                                                             AMP PEAK 23(19P13.3) 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)                                        57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V33, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED    4 11
  AMP PEAK 23(19P13.3) WILD-TYPE 64 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      4   11
  AMP PEAK 23(19P13.3) WILD-TYPE   64   59
         clus
vv        AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  ABSENT                             4                             64
  PRESENT                           11                             59
[1] 2 2
[1] FALSE
D23V34, continuous
D23V35, continuous
D23V36, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED    8  8
  AMP PEAK 23(19P13.3) WILD-TYPE 35 86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED      8    8
  AMP PEAK 23(19P13.3) WILD-TYPE   35   86
                                          clus
vv                                         AMP PEAK 23(19P13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            8
                                          clus
vv                                         AMP PEAK 23(19P13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             86
[1] 2 2
[1] FALSE
D23V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 23(19P13.3) MUTATED              1           3          9
  AMP PEAK 23(19P13.3) WILD-TYPE            9          46         48
D23V38, multiclass
              clus
vv             AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  CURRENT USER                            1                              9
  FORMER USER                             3                             46
  NEVER USED                              9                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V39, continuous
D23V40, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.3) MUTATED   10  2
  AMP PEAK 23(19P13.3) WILD-TYPE 79 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.3) MUTATED     10    2
  AMP PEAK 23(19P13.3) WILD-TYPE   79   14
         clus
vv        AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  ABSENT                            10                             79
  PRESENT                            2                             14
[1] 2 2
[1] FALSE
D23V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 23(19P13.3) MUTATED     0    0   4    9    0  2   2    1    0   4  1
  AMP PEAK 23(19P13.3) WILD-TYPE   1    1  26   56   24  2   6    6    9  18  0
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 23(19P13.3) MUTATED     2  0   0  2
  AMP PEAK 23(19P13.3) WILD-TYPE   6  2   1 12
D23V42, multiclass
      clus
vv     AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             4                             26
  T1B1                            9                             56
  T1B2                            0                             24
  T2                              2                              2
  T2A                             2                              6
  T2A1                            1                              6
  T2A2                            0                              9
  T2B                             4                             18
  T3                              1                              0
  T3B                             2                              6
  T4                              0                              2
  TIS                             0                              1
  TX                              2                             12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 23(19P13.3) MUTATED         1        0         0         0        3
  AMP PEAK 23(19P13.3) WILD-TYPE       3        2         1         1       28
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 23(19P13.3) MUTATED           7         1        1         1
  AMP PEAK 23(19P13.3) WILD-TYPE        62        31        2         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 23(19P13.3) MUTATED            0          1         6         1
  AMP PEAK 23(19P13.3) WILD-TYPE          5          6        21         0
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 23(19P13.3) MUTATED            6         0         0
  AMP PEAK 23(19P13.3) WILD-TYPE         28         3         7
D23V44, multiclass
            clus
vv           AMP PEAK 23(19P13.3) MUTATED AMP PEAK 23(19P13.3) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              3                             28
  STAGE IB1                             7                             62
  STAGE IB2                             1                             31
  STAGE II                              1                              2
  STAGE IIA                             1                              5
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             6                             21
  STAGE III                             1                              0
  STAGE IIIB                            6                             28
  STAGE IVA                             0                              3
  STAGE IVB                             0                              7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(19P13.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(19P13.2) MUTATED    33   4
  AMP PEAK 24(19P13.2) WILD-TYPE 150  46
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                            37                            196 
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                             4                             46 
$`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       182.93 
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         0.07         0.30         0.20         0.07         5.49 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A9U5 
       14.07        32.15        46.03        44.88        42.58        38.96 
TCGA-WL-A834 
       18.05 

$`AMP PEAK 24(19P13.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI 
       31.40        46.32        30.21        35.01        57.73        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-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.18        73.45        83.05       100.14        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        18.02        17.85        20.42       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95         9.34         2.73        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        50.76        40.04        87.75        58.88        36.76 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
      117.99       118.65        16.18        17.52         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       12.36         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        1.18        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       12.66        12.82         0.26        14.89         1.48        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         6.64         1.51         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.18        23.70         2.24         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        6.12         4.73         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.66         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        3.52         1.32         1.97         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
        7.13        21.67        14.93         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        26.56        27.42 
TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U3 
        6.71        21.11        30.31         7.99         0.89         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA 
       13.87         0.03         5.42        29.72         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
        3.88        11.67        93.99        12.16        61.28        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA 
       34.52        29.03        20.22        19.96        53.52        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        42.08        43.82        39.35 

  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                        195.85                         173.29 
  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE 
                        22.980                         15.005 
[1] "0.1 - 195.8 (23.0)" "0.0 - 173.3 (15.0)"
[1] "hr=" "3.1"
D24V2, continuous
                                vv
clus                              T1  T2 T3+T4
  AMP PEAK 24(19P13.2) MUTATED    17   9     4
  AMP PEAK 24(19P13.2) WILD-TYPE 104  41     7
D24V3, multiclass
       clus
vv      AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  T1                              17                            104
  T2                               9                             41
  T3+T4                            4                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED   20  8
  AMP PEAK 24(19P13.2) WILD-TYPE 91 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     20    8
  AMP PEAK 24(19P13.2) WILD-TYPE   91   39
   clus
vv  AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  0                           20                             91
  1                            8                             39
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 24(19P13.2) MUTATED   15  1 16
  AMP PEAK 24(19P13.2) WILD-TYPE 76  7 77
D24V5, multiclass
    clus
vv   AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  M0                           15                             76
  M1                            1                              7
  MX                           16                             77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(19P13.2) MUTATED               0                               32
  AMP PEAK 24(19P13.2) WILD-TYPE             5                              165
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 24(19P13.2) MUTATED                                               1
  AMP PEAK 24(19P13.2) WILD-TYPE                                             4
                                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                                            5
D24V6, multiclass
                                               clus
vv                                              AMP PEAK 24(19P13.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        32
  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                                         165
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(19P13.2) MUTATED     6  31
  AMP PEAK 24(19P13.2) WILD-TYPE  24 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      6   31
  AMP PEAK 24(19P13.2) WILD-TYPE   24  177
     clus
vv    AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  NO                             6                             24
  YES                           31                            177
[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                        19
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 24(19P13.2) MUTATED                                           0
  AMP PEAK 24(19P13.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 24(19P13.2) MUTATED      23
  AMP PEAK 24(19P13.2) WILD-TYPE   146
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                                                               23
                                           clus
vv                                          AMP PEAK 24(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                146
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                                cls
clus                               0   1
  AMP PEAK 24(19P13.2) MUTATED     2  20
  AMP PEAK 24(19P13.2) WILD-TYPE  14 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      2   20
  AMP PEAK 24(19P13.2) WILD-TYPE   14  129
                        clus
vv                       AMP PEAK 24(19P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       AMP PEAK 24(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            129
[1] 2 2
[1] FALSE
D24V12, continuous
D24V13, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED   12  3
  AMP PEAK 24(19P13.2) WILD-TYPE 59 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     12    3
  AMP PEAK 24(19P13.2) WILD-TYPE   59   22
            clus
vv           AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  TUMOR FREE                           12                             59
  WITH TUMOR                            3                             22
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 24(19P13.2) MUTATED        6      2       0      0       2
  AMP PEAK 24(19P13.2) WILD-TYPE     17      3       1     10       5
                                vv
clus                             UNITED STATES VIETNAM
  AMP PEAK 24(19P13.2) MUTATED              23       4
  AMP PEAK 24(19P13.2) WILD-TYPE           155      10
D24V14, multiclass
               clus
vv              AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  BRAZIL                                   6                             17
  CANADA                                   2                              3
  NIGERIA                                  0                              1
  RUSSIA                                   0                             10
  UKRAINE                                  2                              5
  UNITED STATES                           23                            155
  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    2 17 17  0  1
  AMP PEAK 24(19P13.2) WILD-TYPE 15 89 80  1 13
D24V15, multiclass
    clus
vv   AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  G1                            2                             15
  G2                           17                             89
  G3                           17                             80
  G4                            0                              1
  GX                            1                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                                          27
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 24(19P13.2) MUTATED                                        2
  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                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 24(19P13.2) MUTATED                5                  21
  AMP PEAK 24(19P13.2) WILD-TYPE             47                  91
D24V18, multiclass
                                                 clus
vv                                                AMP PEAK 24(19P13.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             5
  LIFELONG NON-SMOKER                                                       21
                                                 clus
vv                                                AMP PEAK 24(19P13.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              47
  LIFELONG NON-SMOKER                                                         91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V19, continuous
D24V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 24(19P13.2) MUTATED             4       15             2        1
  AMP PEAK 24(19P13.2) WILD-TYPE          15       60            10       11
D24V21, multiclass
               clus
vv              AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                15                             60
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     6             2
  AMP PEAK 24(19P13.2) WILD-TYPE                  22            14
D24V23, multiclass
                     clus
vv                    AMP PEAK 24(19P13.2) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            6
  REGIONAL SITE                                  2
                     clus
vv                    AMP PEAK 24(19P13.2) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             22
  REGIONAL SITE                                   14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V24, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED    6  1
  AMP PEAK 24(19P13.2) WILD-TYPE 28  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      6    1
  AMP PEAK 24(19P13.2) WILD-TYPE   28    2
     clus
vv    AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  CGY                            6                             28
  GY                             1                              2
[1] 2 2
[1] FALSE
D24V25, continuous
D24V26, continuous
D24V27, continuous
D24V28, continuous
D24V29, continuous
D24V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                     0
  AMP PEAK 24(19P13.2) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 24(19P13.2) MUTATED                         5
  AMP PEAK 24(19P13.2) WILD-TYPE                      24
                                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                       6
D24V31, multiclass
                                     clus
vv                                    AMP PEAK 24(19P13.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  OTHER LOCATION, SPECIFY                                        5
  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                                         24
  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 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                                             14
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 24(19P13.2) MUTATED                                                                                  14
  AMP PEAK 24(19P13.2) WILD-TYPE                                                                                54
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 24(19P13.2) MUTATED                                                                                             15
  AMP PEAK 24(19P13.2) WILD-TYPE                                                                                           90
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)                                      14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           15
                                                                                              clus
vv                                                                                             AMP PEAK 24(19P13.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        54
  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"
D24V33, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED    9 11
  AMP PEAK 24(19P13.2) WILD-TYPE 59 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED      9   11
  AMP PEAK 24(19P13.2) WILD-TYPE   59   59
         clus
vv        AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  ABSENT                             9                             59
  PRESENT                           11                             59
[1] 2 2
[1] FALSE
D24V34, continuous
D24V35, continuous
D24V36, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED   12  8
  AMP PEAK 24(19P13.2) WILD-TYPE 31 86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     12    8
  AMP PEAK 24(19P13.2) WILD-TYPE   31   86
                                          clus
vv                                         AMP PEAK 24(19P13.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            8
                                          clus
vv                                         AMP PEAK 24(19P13.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             86
[1] 2 2
[1] FALSE
D24V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 24(19P13.2) MUTATED              0           6         13
  AMP PEAK 24(19P13.2) WILD-TYPE           10          43         44
D24V38, multiclass
              clus
vv             AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  CURRENT USER                            0                             10
  FORMER USER                             6                             43
  NEVER USED                             13                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V39, continuous
D24V40, binary
                                cls
clus                              0  1
  AMP PEAK 24(19P13.2) MUTATED   14  0
  AMP PEAK 24(19P13.2) WILD-TYPE 75 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(19P13.2) MUTATED     14    0
  AMP PEAK 24(19P13.2) WILD-TYPE   75   16
         clus
vv        AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  ABSENT                            14                             75
  PRESENT                            0                             16
[1] 2 2
[1] FALSE
D24V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 24(19P13.2) MUTATED     0    0   6    8    3  2   2    1    0   4  1
  AMP PEAK 24(19P13.2) WILD-TYPE   1    1  24   57   21  2   6    6    9  18  0
                                vv
clus                             T3B T4 TIS TX
  AMP PEAK 24(19P13.2) MUTATED     3  0   1  2
  AMP PEAK 24(19P13.2) WILD-TYPE   5  2   0 12
D24V42, multiclass
      clus
vv     AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             6                             24
  T1B1                            8                             57
  T1B2                            3                             21
  T2                              2                              2
  T2A                             2                              6
  T2A1                            1                              6
  T2A2                            0                              9
  T2B                             4                             18
  T3                              1                              0
  T3B                             3                              5
  T4                              0                              2
  TIS                             1                              0
  TX                              2                             12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        2         1         1       26
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 24(19P13.2) MUTATED          10         3        1         2
  AMP PEAK 24(19P13.2) WILD-TYPE        59        29        2         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 24(19P13.2) MUTATED            0          1         5         1
  AMP PEAK 24(19P13.2) WILD-TYPE          5          6        22         0
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 24(19P13.2) MUTATED            7         0         1
  AMP PEAK 24(19P13.2) WILD-TYPE         27         3         6
D24V44, multiclass
            clus
vv           AMP PEAK 24(19P13.2) MUTATED AMP PEAK 24(19P13.2) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              5                             26
  STAGE IB1                            10                             59
  STAGE IB2                             3                             29
  STAGE II                              1                              2
  STAGE IIA                             2                              4
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             5                             22
  STAGE III                             1                              0
  STAGE IIIB                            7                             27
  STAGE IVA                             0                              3
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(19Q13.13) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(19Q13.13) MUTATED    55  19
  AMP PEAK 25(19Q13.13) WILD-TYPE 128  31
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                             74                             159 
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                             19                              31 
$`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       182.93       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         4.47        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         1.32 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 
       14.50         1.35        14.50         1.81         0.26        13.91 
TCGA-EA-A5ZF TCGA-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 
        7.13        21.67        20.78        26.56        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         0.20        29.72         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73S TCGA-UC-A7PG TCGA-VS-A8EB 
        2.96        15.95         3.39        10.39        12.16        10.03 
TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 
       14.07        49.55        16.64        42.58        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

$`AMP PEAK 25(19Q13.13) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK 
       49.48        57.04        68.84        18.74        36.56       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85        19.86        67.46        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       35.01         0.46        20.91        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       73.45        83.05       100.14         0.82        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UE 
       17.85        20.42       101.82        15.48        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
       60.69        94.95         2.73        50.99         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KK 
       99.91        23.51         6.12        20.91         1.12        50.76 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       87.75        58.88        36.76       117.99       118.65        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
       16.18        17.52         0.76        12.36         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA 
        0.62        13.05         1.18         1.35        12.66        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       14.89         1.48        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-A2R8 
       12.59        45.96        26.27         6.64         1.51         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        0.13         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         6.12         4.73         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17         0.66         1.02         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-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-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       25.41        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        96.95        78.71        81.96        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        15.58        10.06         5.13         6.71        21.11 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       30.31         7.99        11.28         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
       13.87         0.03         5.42         4.34         5.49        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       13.35        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
        6.25        19.59         3.88        11.67        93.99        61.28 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       34.52        29.03        20.22        19.96        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y 
       46.03        23.28        11.51        39.78        31.27         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 
       23.24        44.88        42.08 

  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                           0.07                            0.03 
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                         195.85                          177.04 
  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE 
                          16.36                           15.58 
[1] "0.1 - 195.8 (16.4)" "0.0 - 177.0 (15.6)"
[1] "hr=" "1.2"
D25V2, continuous
                                 vv
clus                              T1 T2 T3+T4
  AMP PEAK 25(19Q13.13) MUTATED   30 19     7
  AMP PEAK 25(19Q13.13) WILD-TYPE 91 31     4
D25V3, multiclass
       clus
vv      AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  T1                               30                              91
  T2                               19                              31
  T3+T4                             7                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   29 17
  AMP PEAK 25(19Q13.13) WILD-TYPE 82 30
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     29   17
  AMP PEAK 25(19Q13.13) WILD-TYPE   82   30
   clus
vv  AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  0                            29                              82
  1                            17                              30
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 25(19Q13.13) MUTATED   28  1 29
  AMP PEAK 25(19Q13.13) WILD-TYPE 63  7 64
D25V5, multiclass
    clus
vv   AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  M0                            28                              63
  M1                             1                               7
  MX                            29                              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  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                                 67
  AMP PEAK 25(19Q13.13) WILD-TYPE                              130
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 25(19Q13.13) MUTATED                                               2
  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                                              0
  AMP PEAK 25(19Q13.13) WILD-TYPE                                            6
D25V6, multiclass
                                               clus
vv                                              AMP PEAK 25(19Q13.13) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         67
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              0
                                               clus
vv                                              AMP PEAK 25(19Q13.13) WILD-TYPE
  ADENOSQUAMOUS                                                               3
  CERVICAL SQUAMOUS CELL CARCINOMA                                          130
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19Q13.13) MUTATED    13  63
  AMP PEAK 25(19Q13.13) WILD-TYPE  17 145
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     13   63
  AMP PEAK 25(19Q13.13) WILD-TYPE   17  145
     clus
vv    AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  NO                             13                              17
  YES                            63                             145
[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                        16
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 25(19Q13.13) MUTATED                                           0
  AMP PEAK 25(19Q13.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 25(19Q13.13) MUTATED      55
  AMP PEAK 25(19Q13.13) WILD-TYPE   114
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                                                                55
                                           clus
vv                                          AMP PEAK 25(19Q13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              16
  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"
D25V11, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19Q13.13) MUTATED     5  48
  AMP PEAK 25(19Q13.13) WILD-TYPE  11 101
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED      5   48
  AMP PEAK 25(19Q13.13) WILD-TYPE   11  101
                        clus
vv                       AMP PEAK 25(19Q13.13) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            48
                        clus
vv                       AMP PEAK 25(19Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             101
[1] 2 2
[1] FALSE
D25V12, continuous
D25V13, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   20 14
  AMP PEAK 25(19Q13.13) WILD-TYPE 51 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     20   14
  AMP PEAK 25(19Q13.13) WILD-TYPE   51   11
            clus
vv           AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  TUMOR FREE                            20                              51
  WITH TUMOR                            14                              11
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 25(19Q13.13) MUTATED        8      3       1      2       4
  AMP PEAK 25(19Q13.13) WILD-TYPE     15      2       0      8       3
                                 vv
clus                              UNITED STATES VIETNAM
  AMP PEAK 25(19Q13.13) MUTATED              53       5
  AMP PEAK 25(19Q13.13) WILD-TYPE           125       9
D25V14, multiclass
               clus
vv              AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  BRAZIL                                    8                              15
  CANADA                                    3                               2
  NIGERIA                                   1                               0
  RUSSIA                                    2                               8
  UKRAINE                                   4                               3
  UNITED STATES                            53                             125
  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    4 33 34  0  3
  AMP PEAK 25(19Q13.13) WILD-TYPE 13 73 63  1 11
D25V15, multiclass
    clus
vv   AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  G1                             4                              13
  G2                            33                              73
  G3                            34                              63
  G4                             0                               1
  GX                             3                              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V16, continuous
D25V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 25(19Q13.13) MUTATED                                            12
  AMP PEAK 25(19Q13.13) WILD-TYPE                                          19
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 25(19Q13.13) MUTATED                                        4
  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                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 25(19Q13.13) MUTATED                8                  39
  AMP PEAK 25(19Q13.13) WILD-TYPE             44                  73
D25V18, multiclass
                                                 clus
vv                                                AMP PEAK 25(19Q13.13) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                              8
  LIFELONG NON-SMOKER                                                        39
                                                 clus
vv                                                AMP PEAK 25(19Q13.13) 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                                                               44
  LIFELONG NON-SMOKER                                                          73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V19, continuous
D25V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 25(19Q13.13) MUTATED             8       26             5        3
  AMP PEAK 25(19Q13.13) WILD-TYPE          11       49             7        9
D25V21, multiclass
               clus
vv              AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  COMBINATION                               8                              11
  EXTERNAL                                 26                              49
  EXTERNAL BEAM                             5                               7
  INTERNAL                                  3                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    10             6
  AMP PEAK 25(19Q13.13) WILD-TYPE                  18            10
D25V23, multiclass
                     clus
vv                    AMP PEAK 25(19Q13.13) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                2
  PRIMARY TUMOR FIELD                            10
  REGIONAL SITE                                   6
                     clus
vv                    AMP PEAK 25(19Q13.13) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  0
  PRIMARY TUMOR FIELD                              18
  REGIONAL SITE                                    10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V24, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   15  0
  AMP PEAK 25(19Q13.13) WILD-TYPE 19  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     15    0
  AMP PEAK 25(19Q13.13) WILD-TYPE   19    3
     clus
vv    AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  CGY                            15                              19
  GY                              0                               3
[1] 2 2
[1] FALSE
D25V25, continuous
D25V26, continuous
D25V27, continuous
D25V28, continuous
D25V29, continuous
D25V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                     3
  AMP PEAK 25(19Q13.13) WILD-TYPE                                   3
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 25(19Q13.13) MUTATED                         8
  AMP PEAK 25(19Q13.13) WILD-TYPE                      21
                                 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                       6
D25V31, multiclass
                                     clus
vv                                    AMP PEAK 25(19Q13.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                         8
  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                                          21
  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 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                                                3
  AMP PEAK 25(19Q13.13) WILD-TYPE                                             13
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 25(19Q13.13) MUTATED                                                                                  22
  AMP PEAK 25(19Q13.13) WILD-TYPE                                                                                46
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 25(19Q13.13) MUTATED                                                                                             33
  AMP PEAK 25(19Q13.13) WILD-TYPE                                                                                           72
D25V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 25(19Q13.13) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            33
                                                                                              clus
vv                                                                                             AMP PEAK 25(19Q13.13) 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)                                         46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V33, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   17 25
  AMP PEAK 25(19Q13.13) WILD-TYPE 51 45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     17   25
  AMP PEAK 25(19Q13.13) WILD-TYPE   51   45
         clus
vv        AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  ABSENT                             17                              51
  PRESENT                            25                              45
[1] 2 2
[1] FALSE
D25V34, continuous
D25V35, continuous
D25V36, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   16 29
  AMP PEAK 25(19Q13.13) WILD-TYPE 27 65
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     16   29
  AMP PEAK 25(19Q13.13) WILD-TYPE   27   65
                                          clus
vv                                         AMP PEAK 25(19Q13.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            29
                                          clus
vv                                         AMP PEAK 25(19Q13.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              65
[1] 2 2
[1] FALSE
D25V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 25(19Q13.13) MUTATED              2          17         21
  AMP PEAK 25(19Q13.13) WILD-TYPE            8          32         36
D25V38, multiclass
              clus
vv             AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  CURRENT USER                             2                               8
  FORMER USER                             17                              32
  NEVER USED                              21                              36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V39, continuous
D25V40, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.13) MUTATED   23  7
  AMP PEAK 25(19Q13.13) WILD-TYPE 66  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.13) MUTATED     23    7
  AMP PEAK 25(19Q13.13) WILD-TYPE   66    9
         clus
vv        AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  ABSENT                             23                              66
  PRESENT                             7                               9
[1] 2 2
[1] FALSE
D25V41, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 25(19Q13.13) MUTATED     0    0   6   18    6  1   3    3    2  10
  AMP PEAK 25(19Q13.13) WILD-TYPE   1    1  24   47   18  3   5    4    7  12
                                 vv
clus                              T3 T3B T4 TIS TX
  AMP PEAK 25(19Q13.13) MUTATED    1   5  1   0  3
  AMP PEAK 25(19Q13.13) WILD-TYPE  0   3  1   1 11
D25V42, multiclass
      clus
vv     AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  T1A                              0                               1
  T1A1                             0                               1
  T1B                              6                              24
  T1B1                            18                              47
  T1B2                             6                              18
  T2                               1                               3
  T2A                              3                               5
  T2A1                             3                               4
  T2A2                             2                               7
  T2B                             10                              12
  T3                               1                               0
  T3B                              5                               3
  T4                               1                               1
  TIS                              0                               1
  TX                               3                              11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        2         1         1       24
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 25(19Q13.13) MUTATED          17        11        2         2
  AMP PEAK 25(19Q13.13) WILD-TYPE        52        21        1         4
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 25(19Q13.13) MUTATED            2          3        14         1
  AMP PEAK 25(19Q13.13) WILD-TYPE          3          4        13         0
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 25(19Q13.13) MUTATED           11         2         1
  AMP PEAK 25(19Q13.13) WILD-TYPE         23         1         6
D25V44, multiclass
            clus
vv           AMP PEAK 25(19Q13.13) MUTATED AMP PEAK 25(19Q13.13) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                               0                               2
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               7                              24
  STAGE IB1                             17                              52
  STAGE IB2                             11                              21
  STAGE II                               2                               1
  STAGE IIA                              2                               4
  STAGE IIA1                             2                               3
  STAGE IIA2                             3                               4
  STAGE IIB                             14                              13
  STAGE III                              1                               0
  STAGE IIIB                            11                              23
  STAGE IVA                              2                               1
  STAGE IVB                              1                               6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = AMP PEAK 26(20Q11.21) MUTATION ANALYSIS
D26V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 26(20Q11.21) MUTATED   86 21
  AMP PEAK 26(20Q11.21) WILD-TYPE 97 29
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                            107                             126 
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                             21                              29 
$`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       182.93 
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        60.69        13.61 
TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        2.73        75.78        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         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A439 
       12.36         1.74         1.32         0.82        13.05        14.50 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ 
       14.89         1.48        14.96        13.58         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
       45.96        26.27         1.51         0.59         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN TCGA-FU-A23K 
       16.08         1.18         2.24         0.10         0.03         1.22 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A40J TCGA-GH-A9DA 
       23.84         2.17         0.66         1.45         1.35         9.01 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH 
       25.41        21.67        20.78       147.39        96.95        78.71 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AX 
       20.48        10.06        21.11       195.85         7.99         0.07 
TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        0.20         0.03         5.49         2.96        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 
       15.95         3.39        17.56        15.88        10.39         3.88 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ 
       93.99        12.16        61.28        34.52        14.07        19.96 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       23.28        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       44.88        42.58        39.35        38.96        18.05 

$`AMP PEAK 26(20Q11.21) WILD-TYPE`
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN 
       11.44        18.74        36.56       177.04        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH 
       19.86        67.46        46.32        30.21        53.16        38.99 
TCGA-C5-A1ML TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 
       20.91        73.45        83.05        78.35        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        18.02        17.85        20.42       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH 
       15.48        85.55        94.95         9.34        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
        8.35        99.91        23.51         6.12        20.91         4.47 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       87.75        58.88         2.66       117.99       118.65        16.83 
TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       16.18         8.28         0.62         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5O9 
        1.35         1.81        12.66        12.82         0.26        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R8 
       15.02        14.99        13.48         6.64         0.43         1.45 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN 
        0.07         4.04         0.03         0.36        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.07         0.10        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A3TQ 
       19.79         6.12         4.73         0.92         1.02         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.32         1.97         1.12 
TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
        7.13        14.93         9.44       137.16        66.81       117.40 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-LP-A4AU 
       21.44        15.58         5.13         6.71        30.31        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD 
        0.89         0.30         0.82        13.87         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R 
        0.07         4.34        16.14        14.07         5.88         6.25 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL 
       19.59        11.67        10.03        29.03        20.22        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A957 TCGA-VS-A958 
       32.15        46.03         4.73        23.24        42.08        43.82 

  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 
                         195.85                          177.04 
  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE 
                         17.520                          14.815 
[1] "0.0 - 195.8 (17.5)" "0.0 - 177.0 (14.8)"
[1] "hr=" "1.4"
D26V2, continuous
                                 vv
clus                              T1 T2 T3+T4
  AMP PEAK 26(20Q11.21) MUTATED   55 18     7
  AMP PEAK 26(20Q11.21) WILD-TYPE 66 32     4
D26V3, multiclass
       clus
vv      AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  T1                               55                              66
  T2                               18                              32
  T3+T4                             7                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   45 25
  AMP PEAK 26(20Q11.21) WILD-TYPE 66 22
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     45   25
  AMP PEAK 26(20Q11.21) WILD-TYPE   66   22
   clus
vv  AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  0                            45                              66
  1                            25                              22
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 26(20Q11.21) MUTATED   46  3 38
  AMP PEAK 26(20Q11.21) WILD-TYPE 45  5 55
D26V5, multiclass
    clus
vv   AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  M0                            46                              45
  M1                             3                               5
  MX                            38                              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  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                                 88
  AMP PEAK 26(20Q11.21) WILD-TYPE                              109
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 26(20Q11.21) MUTATED                                               3
  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                                              4
  AMP PEAK 26(20Q11.21) WILD-TYPE                                            2
D26V6, multiclass
                                               clus
vv                                              AMP PEAK 26(20Q11.21) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         88
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
                                               clus
vv                                              AMP PEAK 26(20Q11.21) WILD-TYPE
  ADENOSQUAMOUS                                                               3
  CERVICAL SQUAMOUS CELL CARCINOMA                                          109
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q11.21) MUTATED    13  97
  AMP PEAK 26(20Q11.21) WILD-TYPE  17 111
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     13   97
  AMP PEAK 26(20Q11.21) WILD-TYPE   17  111
     clus
vv    AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  NO                             13                              17
  YES                            97                             111
[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                          12
  AMP PEAK 26(20Q11.21) WILD-TYPE                        12
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 26(20Q11.21) MUTATED                                           0
  AMP PEAK 26(20Q11.21) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 26(20Q11.21) MUTATED      80
  AMP PEAK 26(20Q11.21) WILD-TYPE    89
D26V10, multiclass
                                           clus
vv                                          AMP PEAK 26(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                80
                                           clus
vv                                          AMP PEAK 26(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  12
  BLACK OR AFRICAN AMERICAN                                              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                  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"
D26V11, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED    5 68
  AMP PEAK 26(20Q11.21) WILD-TYPE 11 81
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED      5   68
  AMP PEAK 26(20Q11.21) WILD-TYPE   11   81
                        clus
vv                       AMP PEAK 26(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            68
                        clus
vv                       AMP PEAK 26(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                              81
[1] 2 2
[1] FALSE
D26V12, continuous
D26V13, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   32 11
  AMP PEAK 26(20Q11.21) WILD-TYPE 39 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     32   11
  AMP PEAK 26(20Q11.21) WILD-TYPE   39   14
            clus
vv           AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  TUMOR FREE                            32                              39
  WITH TUMOR                            11                              14
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 26(20Q11.21) MUTATED       13      5       1      6       2
  AMP PEAK 26(20Q11.21) WILD-TYPE     10      0       0      4       5
                                 vv
clus                              UNITED STATES VIETNAM
  AMP PEAK 26(20Q11.21) MUTATED              77       6
  AMP PEAK 26(20Q11.21) WILD-TYPE           101       8
D26V14, multiclass
               clus
vv              AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  BRAZIL                                   13                              10
  CANADA                                    5                               0
  NIGERIA                                   1                               0
  RUSSIA                                    6                               4
  UKRAINE                                   2                               5
  UNITED STATES                            77                             101
  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    7 44 49  1  8
  AMP PEAK 26(20Q11.21) WILD-TYPE 10 62 48  0  6
D26V15, multiclass
    clus
vv   AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  G1                             7                              10
  G2                            44                              62
  G3                            49                              48
  G4                             1                               0
  GX                             8                               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V16, continuous
D26V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 26(20Q11.21) MUTATED                                            18
  AMP PEAK 26(20Q11.21) WILD-TYPE                                          13
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 26(20Q11.21) MUTATED                                        5
  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                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 26(20Q11.21) MUTATED               18                  49
  AMP PEAK 26(20Q11.21) WILD-TYPE             34                  63
D26V18, multiclass
                                                 clus
vv                                                AMP PEAK 26(20Q11.21) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             18
  LIFELONG NON-SMOKER                                                        49
                                                 clus
vv                                                AMP PEAK 26(20Q11.21) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               34
  LIFELONG NON-SMOKER                                                          63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V19, continuous
D26V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 26(20Q11.21) MUTATED             7       34             7        6
  AMP PEAK 26(20Q11.21) WILD-TYPE          12       41             5        6
D26V21, multiclass
               clus
vv              AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  COMBINATION                               7                              12
  EXTERNAL                                 34                              41
  EXTERNAL BEAM                             7                               5
  INTERNAL                                  6                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    14             8
  AMP PEAK 26(20Q11.21) WILD-TYPE                  14             8
D26V23, multiclass
                     clus
vv                    AMP PEAK 26(20Q11.21) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                1
  PRIMARY TUMOR FIELD                            14
  REGIONAL SITE                                   8
                     clus
vv                    AMP PEAK 26(20Q11.21) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  1
  PRIMARY TUMOR FIELD                              14
  REGIONAL SITE                                     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"
D26V24, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   18  1
  AMP PEAK 26(20Q11.21) WILD-TYPE 16  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     18    1
  AMP PEAK 26(20Q11.21) WILD-TYPE   16    2
     clus
vv    AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  CGY                            18                              16
  GY                              1                               2
[1] 2 2
[1] FALSE
D26V25, continuous
D26V26, continuous
D26V27, continuous
D26V28, continuous
D26V29, continuous
D26V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                     1
  AMP PEAK 26(20Q11.21) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 26(20Q11.21) MUTATED                        10
  AMP PEAK 26(20Q11.21) WILD-TYPE                      19
                                 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                         5
  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                             1
  OTHER LOCATION, SPECIFY                                        10
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         5
                                     clus
vv                                    AMP PEAK 26(20Q11.21) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                          19
  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                                                8
  AMP PEAK 26(20Q11.21) WILD-TYPE                                              8
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 26(20Q11.21) MUTATED                                                                                  34
  AMP PEAK 26(20Q11.21) WILD-TYPE                                                                                34
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 26(20Q11.21) MUTATED                                                                                             44
  AMP PEAK 26(20Q11.21) WILD-TYPE                                                                                           61
D26V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 26(20Q11.21) 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)                                       34
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            44
                                                                                              clus
vv                                                                                             AMP PEAK 26(20Q11.21) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                             8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         34
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V33, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   30 34
  AMP PEAK 26(20Q11.21) WILD-TYPE 38 36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     30   34
  AMP PEAK 26(20Q11.21) WILD-TYPE   38   36
         clus
vv        AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  ABSENT                             30                              38
  PRESENT                            34                              36
[1] 2 2
[1] FALSE
D26V34, continuous
D26V35, continuous
D26V36, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   15 42
  AMP PEAK 26(20Q11.21) WILD-TYPE 28 52
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     15   42
  AMP PEAK 26(20Q11.21) WILD-TYPE   28   52
                                          clus
vv                                         AMP PEAK 26(20Q11.21) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            42
                                          clus
vv                                         AMP PEAK 26(20Q11.21) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              52
[1] 2 2
[1] FALSE
D26V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 26(20Q11.21) MUTATED              4          23         23
  AMP PEAK 26(20Q11.21) WILD-TYPE            6          26         34
D26V38, multiclass
              clus
vv             AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  CURRENT USER                             4                               6
  FORMER USER                             23                              26
  NEVER USED                              23                              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"
D26V39, continuous
D26V40, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q11.21) MUTATED   39  9
  AMP PEAK 26(20Q11.21) WILD-TYPE 50  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q11.21) MUTATED     39    9
  AMP PEAK 26(20Q11.21) WILD-TYPE   50    7
         clus
vv        AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  ABSENT                             39                              50
  PRESENT                             9                               7
[1] 2 2
[1] FALSE
D26V41, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 26(20Q11.21) MUTATED     0    1  14   32    8  1   4    4    1   8
  AMP PEAK 26(20Q11.21) WILD-TYPE   1    0  16   33   16  3   4    3    8  14
                                 vv
clus                              T3 T3B T4 TIS TX
  AMP PEAK 26(20Q11.21) MUTATED    1   6  0   1  9
  AMP PEAK 26(20Q11.21) WILD-TYPE  0   2  2   0  5
D26V42, multiclass
      clus
vv     AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  T1A                              0                               1
  T1A1                             1                               0
  T1B                             14                              16
  T1B1                            32                              33
  T1B2                             8                              16
  T2                               1                               3
  T2A                              4                               4
  T2A1                             4                               3
  T2A2                             1                               8
  T2B                              8                              14
  T3                               1                               0
  T3B                              6                               2
  T4                               0                               2
  TIS                              1                               0
  TX                               9                               5
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       2        2         0         1       17
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 26(20Q11.21) MUTATED          30        12        3         3
  AMP PEAK 26(20Q11.21) WILD-TYPE        39        20        0         3
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 26(20Q11.21) MUTATED            3          2        14         1
  AMP PEAK 26(20Q11.21) WILD-TYPE          2          5        13         0
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 26(20Q11.21) MUTATED           18         1         2
  AMP PEAK 26(20Q11.21) WILD-TYPE         16         2         5
D26V44, multiclass
            clus
vv           AMP PEAK 26(20Q11.21) MUTATED AMP PEAK 26(20Q11.21) WILD-TYPE
  STAGE I                                2                               2
  STAGE IA                               0                               2
  STAGE IA1                              1                               0
  STAGE IA2                              0                               1
  STAGE IB                              14                              17
  STAGE IB1                             30                              39
  STAGE IB2                             12                              20
  STAGE II                               3                               0
  STAGE IIA                              3                               3
  STAGE IIA1                             3                               2
  STAGE IIA2                             2                               5
  STAGE IIB                             14                              13
  STAGE III                              1                               0
  STAGE IIIB                            18                              16
  STAGE IVA                              1                               2
  STAGE IVB                              2                               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(21Q22.13) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 27(21Q22.13) MUTATED    27  11
  AMP PEAK 27(21Q22.13) WILD-TYPE 156  39
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                             38                             195 
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                             11                              39 
$`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-A2PM TCGA-EK-A2RA 
        0.76        12.36         1.74        13.91         0.59        16.08 
TCGA-EK-A2RM TCGA-FU-A3TX TCGA-HG-A9SC TCGA-HM-A3JK TCGA-IR-A3LL TCGA-JW-A5VJ 
        2.24         1.48         7.13        20.78        36.36        21.44 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE TCGA-MY-A913 
       21.11        30.31        11.28         0.30         0.07         5.49 
TCGA-Q1-A73R TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QA 
        6.25        34.52        20.22        14.07        19.96        23.28 
TCGA-VS-A8QF TCGA-VS-A94Y 
       49.55         4.73 

$`AMP PEAK 27(21Q22.13) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 
       36.56       144.16       177.04       173.29        82.85        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       46.32        30.21        35.01        57.73        53.16         0.46 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       182.93       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34        13.61        50.99         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
       23.51        27.52         6.12        20.91         4.47        58.88 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       50.76        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-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-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        8.28         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26        14.89         1.48        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         6.64         1.51         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.13         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       23.70         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.73         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.02         1.45         1.58         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.32         1.97         1.12         9.01        25.41        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-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        78.71        81.96        26.56        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU 
      195.85         7.99         0.89         0.07         0.82         0.20 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA 
       13.87         0.03         5.42        29.72         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88         5.88        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       11.67        93.99        12.16        61.28        10.03        29.03 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       53.52        32.15        46.03        11.51        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       16.64        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                           0.07                            0.03 
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                         100.14                          195.85 
  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE 
                          13.99                           15.95 
[1] "0.1 - 100.1 (14.0)" "0.0 - 195.8 (15.9)"
[1] "hr=" "2.1"
D27V2, continuous
                                 vv
clus                               T1  T2 T3+T4
  AMP PEAK 27(21Q22.13) MUTATED    14  11     3
  AMP PEAK 27(21Q22.13) WILD-TYPE 107  39     8
D27V3, multiclass
       clus
vv      AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  T1                               14                             107
  T2                               11                              39
  T3+T4                             3                               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED   17  6
  AMP PEAK 27(21Q22.13) WILD-TYPE 94 41
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     17    6
  AMP PEAK 27(21Q22.13) WILD-TYPE   94   41
   clus
vv  AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  0                            17                              94
  1                             6                              41
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 27(21Q22.13) MUTATED   15  2 14
  AMP PEAK 27(21Q22.13) WILD-TYPE 76  6 79
D27V5, multiclass
    clus
vv   AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  M0                            15                              76
  M1                             2                               6
  MX                            14                              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"
                                 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                                 34
  AMP PEAK 27(21Q22.13) WILD-TYPE                              163
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 27(21Q22.13) MUTATED                                               1
  AMP PEAK 27(21Q22.13) WILD-TYPE                                             4
                                 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                                            5
D27V6, multiclass
                                               clus
vv                                              AMP PEAK 27(21Q22.13) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         34
  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                                          163
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(21Q22.13) MUTATED     6  34
  AMP PEAK 27(21Q22.13) WILD-TYPE  24 174
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      6   34
  AMP PEAK 27(21Q22.13) WILD-TYPE   24  174
     clus
vv    AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  NO                              6                              24
  YES                            34                             174
[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                        21
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 27(21Q22.13) MUTATED                                           0
  AMP PEAK 27(21Q22.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 27(21Q22.13) MUTATED      27
  AMP PEAK 27(21Q22.13) WILD-TYPE   142
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                                                                27
                                           clus
vv                                          AMP PEAK 27(21Q22.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  15
  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"
D27V11, binary
                                 cls
clus                                0   1
  AMP PEAK 27(21Q22.13) MUTATED     3  21
  AMP PEAK 27(21Q22.13) WILD-TYPE  13 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      3   21
  AMP PEAK 27(21Q22.13) WILD-TYPE   13  128
                        clus
vv                       AMP PEAK 27(21Q22.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            21
                        clus
vv                       AMP PEAK 27(21Q22.13) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             128
[1] 2 2
[1] FALSE
D27V12, continuous
D27V13, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED    9  8
  AMP PEAK 27(21Q22.13) WILD-TYPE 62 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      9    8
  AMP PEAK 27(21Q22.13) WILD-TYPE   62   17
            clus
vv           AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  TUMOR FREE                             9                              62
  WITH TUMOR                             8                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 27(21Q22.13) MUTATED        7      2       0      3       1
  AMP PEAK 27(21Q22.13) WILD-TYPE     16      3       1      7       6
                                 vv
clus                              UNITED STATES VIETNAM
  AMP PEAK 27(21Q22.13) MUTATED              25       2
  AMP PEAK 27(21Q22.13) WILD-TYPE           153      12
D27V14, multiclass
               clus
vv              AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  BRAZIL                                    7                              16
  CANADA                                    2                               3
  NIGERIA                                   0                               1
  RUSSIA                                    3                               7
  UKRAINE                                   1                               6
  UNITED STATES                            25                             153
  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    1 14 19  0  5
  AMP PEAK 27(21Q22.13) WILD-TYPE 16 92 78  1  9
D27V15, multiclass
    clus
vv   AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  G1                             1                              16
  G2                            14                              92
  G3                            19                              78
  G4                             0                               1
  GX                             5                               9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V16, continuous
D27V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 27(21Q22.13) MUTATED                                             7
  AMP PEAK 27(21Q22.13) WILD-TYPE                                          24
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 27(21Q22.13) MUTATED                                        1
  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                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 27(21Q22.13) MUTATED                7                  19
  AMP PEAK 27(21Q22.13) WILD-TYPE             45                  93
D27V18, multiclass
                                                 clus
vv                                                AMP PEAK 27(21Q22.13) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                              7
  LIFELONG NON-SMOKER                                                        19
                                                 clus
vv                                                AMP PEAK 27(21Q22.13) 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                                                               45
  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"
D27V19, continuous
D27V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 27(21Q22.13) MUTATED             5       14             1        1
  AMP PEAK 27(21Q22.13) WILD-TYPE          14       61            11       11
D27V21, multiclass
               clus
vv              AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  COMBINATION                               5                              14
  EXTERNAL                                 14                              61
  EXTERNAL BEAM                             1                              11
  INTERNAL                                  1                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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             3
  AMP PEAK 27(21Q22.13) WILD-TYPE                  23            13
D27V23, multiclass
                     clus
vv                    AMP PEAK 27(21Q22.13) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                0
  PRIMARY TUMOR FIELD                             5
  REGIONAL SITE                                   3
                     clus
vv                    AMP PEAK 27(21Q22.13) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  2
  PRIMARY TUMOR FIELD                              23
  REGIONAL SITE                                    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"
D27V24, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED    5  1
  AMP PEAK 27(21Q22.13) WILD-TYPE 29  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      5    1
  AMP PEAK 27(21Q22.13) WILD-TYPE   29    2
     clus
vv    AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  CGY                             5                              29
  GY                              1                               2
[1] 2 2
[1] FALSE
D27V25, continuous
D27V26, continuous
D27V27, continuous
D27V28, continuous
D27V29, continuous
D27V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   6
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 27(21Q22.13) MUTATED                         3
  AMP PEAK 27(21Q22.13) WILD-TYPE                      26
                                 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                         2
  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                                         2
                                     clus
vv                                    AMP PEAK 27(21Q22.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               6
  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)
  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                                             12
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 27(21Q22.13) MUTATED                                                                                  17
  AMP PEAK 27(21Q22.13) WILD-TYPE                                                                                51
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 27(21Q22.13) MUTATED                                                                                             14
  AMP PEAK 27(21Q22.13) WILD-TYPE                                                                                           91
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)                                       17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            14
                                                                                              clus
vv                                                                                             AMP PEAK 27(21Q22.13) 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)                                         51
  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"
D27V33, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED   11 10
  AMP PEAK 27(21Q22.13) WILD-TYPE 57 60
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     11   10
  AMP PEAK 27(21Q22.13) WILD-TYPE   57   60
         clus
vv        AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  ABSENT                             11                              57
  PRESENT                            10                              60
[1] 2 2
[1] FALSE
D27V34, continuous
D27V35, continuous
D27V36, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED    9  7
  AMP PEAK 27(21Q22.13) WILD-TYPE 34 87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED      9    7
  AMP PEAK 27(21Q22.13) WILD-TYPE   34   87
                                          clus
vv                                         AMP PEAK 27(21Q22.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             7
                                          clus
vv                                         AMP PEAK 27(21Q22.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              87
[1] 2 2
[1] FALSE
D27V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 27(21Q22.13) MUTATED              1           4         11
  AMP PEAK 27(21Q22.13) WILD-TYPE            9          45         46
D27V38, multiclass
              clus
vv             AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  CURRENT USER                             1                               9
  FORMER USER                              4                              45
  NEVER USED                              11                              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V39, continuous
D27V40, binary
                                 cls
clus                               0  1
  AMP PEAK 27(21Q22.13) MUTATED   11  1
  AMP PEAK 27(21Q22.13) WILD-TYPE 78 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(21Q22.13) MUTATED     11    1
  AMP PEAK 27(21Q22.13) WILD-TYPE   78   15
         clus
vv        AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  ABSENT                             11                              78
  PRESENT                             1                              15
[1] 2 2
[1] FALSE
D27V41, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 27(21Q22.13) MUTATED     0    0   2    9    3  1   4    0    1   5
  AMP PEAK 27(21Q22.13) WILD-TYPE   1    1  28   56   21  3   4    7    8  17
                                 vv
clus                              T3 T3B T4 TIS TX
  AMP PEAK 27(21Q22.13) MUTATED    0   3  0   1  2
  AMP PEAK 27(21Q22.13) WILD-TYPE  1   5  2   0 12
D27V42, multiclass
      clus
vv     AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  T1A                              0                               1
  T1A1                             0                               1
  T1B                              2                              28
  T1B1                             9                              56
  T1B2                             3                              21
  T2                               1                               3
  T2A                              4                               4
  T2A1                             0                               7
  T2A2                             1                               8
  T2B                              5                              17
  T3                               0                               1
  T3B                              3                               5
  T4                               0                               2
  TIS                              1                               0
  TX                               2                              12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        2         1         0       28
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 27(21Q22.13) MUTATED           9         4        1         2
  AMP PEAK 27(21Q22.13) WILD-TYPE        60        28        2         4
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 27(21Q22.13) MUTATED            0          2         8         0
  AMP PEAK 27(21Q22.13) WILD-TYPE          5          5        19         1
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 27(21Q22.13) MUTATED            9         0         0
  AMP PEAK 27(21Q22.13) WILD-TYPE         25         3         7
D27V44, multiclass
            clus
vv           AMP PEAK 27(21Q22.13) MUTATED AMP PEAK 27(21Q22.13) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                               0                               2
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                               3                              28
  STAGE IB1                              9                              60
  STAGE IB2                              4                              28
  STAGE II                               1                               2
  STAGE IIA                              2                               4
  STAGE IIA1                             0                               5
  STAGE IIA2                             2                               5
  STAGE IIB                              8                              19
  STAGE III                              0                               1
  STAGE IIIB                             9                              25
  STAGE IVA                              0                               3
  STAGE IVB                              0                               7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = AMP PEAK 28(XQ28) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 28(XQ28) MUTATED    52   7
  AMP PEAK 28(XQ28) WILD-TYPE 131  43
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         59                         174 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                          7                          43 
$`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        60.69         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         1.74        13.05 
TCGA-EA-A3QE TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2H0 
        1.18        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         4.73 
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-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R3 
      195.85        30.31         0.30        29.72         4.34        15.95 
TCGA-Q1-A6DV TCGA-R2-A69V TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH 
       16.14        19.59        61.28        10.03        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A954 
       14.07        11.51        49.55        16.64        42.58 

$`AMP PEAK 28(XQ28) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      173.29        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       30.21        35.01        57.73        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY 
        2.43        20.91        40.93        44.22        73.18        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       20.42       182.93       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       17.19        85.55        94.95         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       50.99        45.83        75.78        99.91        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91         4.47        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR 
       16.83        17.52         8.28         0.76        12.36         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
        0.82         0.62        14.50         1.35         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.66        12.82         0.26         1.48        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2R7 
       13.58        13.48         0.36        12.59        26.27         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RL 
        1.45         0.13        16.08         4.04         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        2.24         0.10        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       19.79         6.12         1.22         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.02         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC 
       21.67        20.78        14.93         9.44       147.39       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       96.95        81.96        26.56        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       21.11         7.99        11.28         0.89         0.07         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A913 
        0.20        13.87         0.03         5.42         0.07         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O 
        2.96        15.58        13.35         3.39        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       15.88         5.88         6.25        10.39         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       93.99        12.16        34.52        19.96        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z 
       46.03        23.28        39.78        31.27         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       44.88        42.08        43.82        39.35        38.96        18.05 

  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                       0.03                        0.03 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                     195.85                      182.93 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                      16.14                       15.58 
[1] "0.0 - 195.8 (16.1)" "0.0 - 182.9 (15.6)"
[1] "hr=" "2.4"
D28V2, continuous
                             vv
clus                          T1 T2 T3+T4
  AMP PEAK 28(XQ28) MUTATED   27 12     6
  AMP PEAK 28(XQ28) WILD-TYPE 94 38     5
D28V3, multiclass
       clus
vv      AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  T1                           27                          94
  T2                           12                          38
  T3+T4                         6                           5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   30  8
  AMP PEAK 28(XQ28) WILD-TYPE 81 39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     30    8
  AMP PEAK 28(XQ28) WILD-TYPE   81   39
   clus
vv  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  0                        30                          81
  1                         8                          39
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK 28(XQ28) MUTATED   22  1 24
  AMP PEAK 28(XQ28) WILD-TYPE 69  7 69
D28V5, multiclass
    clus
vv   AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  M0                        22                          69
  M1                         1                           7
  MX                        24                          69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(XQ28) MUTATED               2                               49
  AMP PEAK 28(XQ28) WILD-TYPE             3                              148
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 28(XQ28) MUTATED                                               1
  AMP PEAK 28(XQ28) WILD-TYPE                                             4
                             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                                              1
  AMP PEAK 28(XQ28) WILD-TYPE                                            5
D28V6, multiclass
                                               clus
vv                                              AMP PEAK 28(XQ28) MUTATED
  ADENOSQUAMOUS                                                         2
  CERVICAL SQUAMOUS CELL CARCINOMA                                     49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          1
                                               clus
vv                                              AMP PEAK 28(XQ28) WILD-TYPE
  ADENOSQUAMOUS                                                           3
  CERVICAL SQUAMOUS CELL CARCINOMA                                      148
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED     5  54
  AMP PEAK 28(XQ28) WILD-TYPE  25 154
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED      5   54
  AMP PEAK 28(XQ28) WILD-TYPE   25  154
     clus
vv    AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  NO                          5                          25
  YES                        54                         154
[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                           8
  AMP PEAK 28(XQ28) WILD-TYPE                        16
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 28(XQ28) MUTATED                                           1    37
  AMP PEAK 28(XQ28) WILD-TYPE                                         0   132
D28V10, multiclass
                                           clus
vv                                          AMP PEAK 28(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                         8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            37
                                           clus
vv                                          AMP PEAK 28(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                          16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             132
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED     3  33
  AMP PEAK 28(XQ28) WILD-TYPE  13 116
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED      3   33
  AMP PEAK 28(XQ28) WILD-TYPE   13  116
                        clus
vv                       AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             3                          13
  NOT HISPANIC OR LATINO                        33                         116
[1] 2 2
[1] FALSE
D28V12, continuous
D28V13, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   21  2
  AMP PEAK 28(XQ28) WILD-TYPE 50 23
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     21    2
  AMP PEAK 28(XQ28) WILD-TYPE   50   23
            clus
vv           AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  TUMOR FREE                        21                          50
  WITH TUMOR                         2                          23
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  AMP PEAK 28(XQ28) MUTATED        8      1       0      3       1
  AMP PEAK 28(XQ28) WILD-TYPE     15      4       1      7       6
                             vv
clus                          UNITED STATES VIETNAM
  AMP PEAK 28(XQ28) MUTATED              43       3
  AMP PEAK 28(XQ28) WILD-TYPE           135      11
D28V14, multiclass
               clus
vv              AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  BRAZIL                                8                          15
  CANADA                                1                           4
  NIGERIA                               0                           1
  RUSSIA                                3                           7
  UKRAINE                               1                           6
  UNITED STATES                        43                         135
  VIETNAM                               3                          11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  AMP PEAK 28(XQ28) MUTATED    4 24 25  1  4
  AMP PEAK 28(XQ28) WILD-TYPE 13 82 72  0 10
D28V15, multiclass
    clus
vv   AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  G1                         4                          13
  G2                        24                          82
  G3                        25                          72
  G4                         1                           0
  GX                         4                          10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V16, continuous
D28V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 28(XQ28) MUTATED                                             6
  AMP PEAK 28(XQ28) WILD-TYPE                                          25
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 28(XQ28) MUTATED                                        2
  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                                               2
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 28(XQ28) MUTATED               14                  26
  AMP PEAK 28(XQ28) WILD-TYPE             38                  86
D28V18, multiclass
                                                 clus
vv                                                AMP PEAK 28(XQ28) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         0
  CURRENT SMOKER                                                         14
  LIFELONG NON-SMOKER                                                    26
                                                 clus
vv                                                AMP PEAK 28(XQ28) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           38
  LIFELONG NON-SMOKER                                                      86
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V19, continuous
D28V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 28(XQ28) MUTATED             3       19             2        3
  AMP PEAK 28(XQ28) WILD-TYPE          16       56            10        9
D28V21, multiclass
               clus
vv              AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  COMBINATION                           3                          16
  EXTERNAL                             19                          56
  EXTERNAL BEAM                         2                          10
  INTERNAL                              3                           9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     5             7
  AMP PEAK 28(XQ28) WILD-TYPE                  23             9
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                         5                          23
  REGIONAL SITE                               7                           9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V24, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   11  1
  AMP PEAK 28(XQ28) WILD-TYPE 23  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     11    1
  AMP PEAK 28(XQ28) WILD-TYPE   23    2
     clus
vv    AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  CGY                        11                          23
  GY                          1                           2
[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                                   6
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 28(XQ28) MUTATED                         7                       0
  AMP PEAK 28(XQ28) WILD-TYPE                      22                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK 28(XQ28) MUTATED                         2
  AMP PEAK 28(XQ28) WILD-TYPE                       5
D28V31, multiclass
                                     clus
vv                                    AMP PEAK 28(XQ28) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  OTHER LOCATION, SPECIFY                                     7
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     2
                                     clus
vv                                    AMP PEAK 28(XQ28) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           6
  OTHER LOCATION, SPECIFY                                      22
  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 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                                                5
  AMP PEAK 28(XQ28) WILD-TYPE                                             11
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 28(XQ28) MUTATED                                                                                  18
  AMP PEAK 28(XQ28) WILD-TYPE                                                                                50
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 28(XQ28) MUTATED                                                                                             26
  AMP PEAK 28(XQ28) WILD-TYPE                                                                                           79
D28V32, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 28(XQ28) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        26
                                                                                              clus
vv                                                                                             AMP PEAK 28(XQ28) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     50
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V33, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   17 18
  AMP PEAK 28(XQ28) WILD-TYPE 51 52
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     17   18
  AMP PEAK 28(XQ28) WILD-TYPE   51   52
         clus
vv        AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  ABSENT                         17                          51
  PRESENT                        18                          52
[1] 2 2
[1] FALSE
D28V34, continuous
D28V35, continuous
D28V36, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   11 20
  AMP PEAK 28(XQ28) WILD-TYPE 32 74
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     11   20
  AMP PEAK 28(XQ28) WILD-TYPE   32   74
                                          clus
vv                                         AMP PEAK 28(XQ28) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        20
                                          clus
vv                                         AMP PEAK 28(XQ28) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          74
[1] 2 2
[1] FALSE
D28V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK 28(XQ28) MUTATED              3          10         15
  AMP PEAK 28(XQ28) WILD-TYPE            7          39         42
D28V38, multiclass
              clus
vv             AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  CURRENT USER                         3                           7
  FORMER USER                         10                          39
  NEVER USED                          15                          42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V39, continuous
D28V40, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   24  3
  AMP PEAK 28(XQ28) WILD-TYPE 65 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     24    3
  AMP PEAK 28(XQ28) WILD-TYPE   65   13
         clus
vv        AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  ABSENT                         24                          65
  PRESENT                         3                          13
[1] 2 2
[1] FALSE
D28V41, continuous
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  AMP PEAK 28(XQ28) MUTATED     0    0   5   17    5  1   3    4    2   2  1
  AMP PEAK 28(XQ28) WILD-TYPE   1    1  25   48   19  3   5    3    7  20  0
                             vv
clus                          T3B T4 TIS TX
  AMP PEAK 28(XQ28) MUTATED     5  0   0  4
  AMP PEAK 28(XQ28) WILD-TYPE   3  2   1 10
D28V42, multiclass
      clus
vv     AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  T1A                          0                           1
  T1A1                         0                           1
  T1B                          5                          25
  T1B1                        17                          48
  T1B2                         5                          19
  T2                           1                           3
  T2A                          3                           5
  T2A1                         4                           3
  T2A2                         2                           7
  T2B                          2                          20
  T3                           1                           0
  T3B                          5                           3
  T4                           0                           2
  TIS                          0                           1
  TX                           4                          10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 28(XQ28) MUTATED         0        0         0         0        6
  AMP PEAK 28(XQ28) WILD-TYPE       4        2         1         1       25
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK 28(XQ28) MUTATED          18         5        1         2          3
  AMP PEAK 28(XQ28) WILD-TYPE        51        27        2         4          2
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIB
  AMP PEAK 28(XQ28) MUTATED            1         9         1          9
  AMP PEAK 28(XQ28) WILD-TYPE          6        18         0         25
                             vv
clus                          STAGE IVA STAGE IVB
  AMP PEAK 28(XQ28) MUTATED           1         1
  AMP PEAK 28(XQ28) WILD-TYPE         2         6
D28V44, multiclass
            clus
vv           AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  STAGE I                            0                           4
  STAGE IA                           0                           2
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           6                          25
  STAGE IB1                         18                          51
  STAGE IB2                          5                          27
  STAGE II                           1                           2
  STAGE IIA                          2                           4
  STAGE IIA1                         3                           2
  STAGE IIA2                         1                           6
  STAGE IIB                          9                          18
  STAGE III                          1                           0
  STAGE IIIB                         9                          25
  STAGE IVA                          1                           2
  STAGE IVB                          1                           6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.23) MUTATED    22   8
  DEL PEAK  1(1P36.23) WILD-TYPE 161  42
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            30                            203 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             8                             42 
$`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        60.69         9.34 
TCGA-C5-A8YQ TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A556 TCGA-EK-A2PG TCGA-EK-A2PM 
       23.51         1.32        14.50        14.89         1.51         0.59 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A3EO TCGA-IR-A3LF 
        1.18         2.24        14.70        19.79         2.17        96.95 
TCGA-JX-A3Q8 TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QH 
       30.31         5.49         3.39        19.96        46.03        39.78 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MH 
       67.46        31.40        46.32        30.21        35.01        38.99 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY 
        2.43        20.91        40.93         3.58        44.22        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43         0.82        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
      182.93       154.32       101.82       134.33        15.48       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       17.19        85.55        94.95        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35        75.78        99.91        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91         4.47         1.12        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        0.76        12.36         1.74         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S 
        1.18        14.50         1.35         1.35         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26         1.48        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       26.27         6.64         0.43         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       16.08         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        7.92         6.94         6.12         4.73         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
        9.44       147.39       137.16        66.81       117.40        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85         7.99        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         2.96        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        10.39        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       14.07        53.52        32.15        23.28        11.51        49.55 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       31.27        16.64         4.73        23.24        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.08        43.82        39.35        38.96        18.05 

  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 
                         96.95                         195.85 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        19.875                         15.580 
[1] "0.5 - 97.0 (19.9)"  "0.0 - 195.8 (15.6)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK  1(1P36.23) MUTATED    13   5     0
  DEL PEAK  1(1P36.23) WILD-TYPE 108  45    11
D29V3, multiclass
       clus
vv      DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1                              13                            108
  T2                               5                             45
  T3+T4                            0                             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   13  4
  DEL PEAK  1(1P36.23) WILD-TYPE 98 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     13    4
  DEL PEAK  1(1P36.23) WILD-TYPE   98   43
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           13                             98
  1                            4                             43
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK  1(1P36.23) MUTATED    8  3 11
  DEL PEAK  1(1P36.23) WILD-TYPE 83  5 82
D29V5, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  M0                            8                             83
  M1                            3                              5
  MX                           11                             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.23) MUTATED               0                               22
  DEL PEAK  1(1P36.23) WILD-TYPE             5                              175
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  1(1P36.23) MUTATED                                               2
  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                                              1
  DEL PEAK  1(1P36.23) WILD-TYPE                                            5
D29V6, multiclass
                                               clus
vv                                              DEL PEAK  1(1P36.23) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        22
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK  1(1P36.23) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         175
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED     6  26
  DEL PEAK  1(1P36.23) WILD-TYPE  24 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      6   26
  DEL PEAK  1(1P36.23) WILD-TYPE   24  182
     clus
vv    DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  NO                             6                             24
  YES                           26                            182
[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                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  1(1P36.23) MUTATED                                           0
  DEL PEAK  1(1P36.23) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK  1(1P36.23) MUTATED      25
  DEL PEAK  1(1P36.23) WILD-TYPE   144
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                                                               25
                                           clus
vv                                          DEL PEAK  1(1P36.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             20
  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"
D29V11, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED     3  21
  DEL PEAK  1(1P36.23) WILD-TYPE  13 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      3   21
  DEL PEAK  1(1P36.23) WILD-TYPE   13  128
                        clus
vv                       DEL PEAK  1(1P36.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       DEL PEAK  1(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE
D29V12, continuous
D29V13, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   13  3
  DEL PEAK  1(1P36.23) WILD-TYPE 58 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     13    3
  DEL PEAK  1(1P36.23) WILD-TYPE   58   22
            clus
vv           DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  TUMOR FREE                           13                             58
  WITH TUMOR                            3                             22
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  1(1P36.23) MUTATED        3      0       0      2       0
  DEL PEAK  1(1P36.23) WILD-TYPE     20      5       1      8       7
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK  1(1P36.23) MUTATED              26       1
  DEL PEAK  1(1P36.23) WILD-TYPE           152      13
D29V14, multiclass
               clus
vv              DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  BRAZIL                                   3                             20
  CANADA                                   0                              5
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  0                              7
  UNITED STATES                           26                            152
  VIETNAM                                  1                             13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK  1(1P36.23) MUTATED    2 15 14  0  1
  DEL PEAK  1(1P36.23) WILD-TYPE 15 91 83  1 13
D29V15, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  G1                            2                             15
  G2                           15                             91
  G3                           14                             83
  G4                            0                              1
  GX                            1                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V16, continuous
D29V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  1(1P36.23) MUTATED                                             4
  DEL PEAK  1(1P36.23) WILD-TYPE                                          27
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  1(1P36.23) MUTATED                                        0
  DEL PEAK  1(1P36.23) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  1(1P36.23) MUTATED                                                 1
  DEL PEAK  1(1P36.23) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  1(1P36.23) MUTATED                7                  14
  DEL PEAK  1(1P36.23) WILD-TYPE             45                  98
D29V18, multiclass
                                                 clus
vv                                                DEL PEAK  1(1P36.23) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             7
  LIFELONG NON-SMOKER                                                       14
                                                 clus
vv                                                DEL PEAK  1(1P36.23) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              45
  LIFELONG NON-SMOKER                                                         98
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V19, continuous
D29V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  1(1P36.23) MUTATED             4        8             2        2
  DEL PEAK  1(1P36.23) WILD-TYPE          15       67            10       10
D29V21, multiclass
               clus
vv              DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                 8                             67
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     7             1
  DEL PEAK  1(1P36.23) WILD-TYPE                  21            15
D29V23, multiclass
                     clus
vv                    DEL PEAK  1(1P36.23) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            7
  REGIONAL SITE                                  1
                     clus
vv                    DEL PEAK  1(1P36.23) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             21
  REGIONAL SITE                                   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"
D29V24, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    6  1
  DEL PEAK  1(1P36.23) WILD-TYPE 28  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      6    1
  DEL PEAK  1(1P36.23) WILD-TYPE   28    2
     clus
vv    DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  CGY                            6                             28
  GY                             1                              2
[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                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK  1(1P36.23) MUTATED                         5
  DEL PEAK  1(1P36.23) WILD-TYPE                      24
                                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                       5
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                              5
  OTHER LOCATION, SPECIFY                                         24
  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  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                                                1
  DEL PEAK  1(1P36.23) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  1(1P36.23) MUTATED                                                                                  13
  DEL PEAK  1(1P36.23) WILD-TYPE                                                                                55
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  1(1P36.23) MUTATED                                                                                             11
  DEL PEAK  1(1P36.23) WILD-TYPE                                                                                           94
D29V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  1(1P36.23) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           11
                                                                                              clus
vv                                                                                             DEL PEAK  1(1P36.23) 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)                                        55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V33, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    9  8
  DEL PEAK  1(1P36.23) WILD-TYPE 59 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      9    8
  DEL PEAK  1(1P36.23) WILD-TYPE   59   62
         clus
vv        DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  ABSENT                             9                             59
  PRESENT                            8                             62
[1] 2 2
[1] FALSE
D29V34, continuous
D29V35, continuous
D29V36, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    5  7
  DEL PEAK  1(1P36.23) WILD-TYPE 38 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      5    7
  DEL PEAK  1(1P36.23) WILD-TYPE   38   87
                                          clus
vv                                         DEL PEAK  1(1P36.23) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            7
                                          clus
vv                                         DEL PEAK  1(1P36.23) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             87
[1] 2 2
[1] FALSE
D29V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK  1(1P36.23) MUTATED              1           7          6
  DEL PEAK  1(1P36.23) WILD-TYPE            9          42         51
D29V38, multiclass
              clus
vv             DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  CURRENT USER                            1                              9
  FORMER USER                             7                             42
  NEVER USED                              6                             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V39, continuous
D29V40, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   15  1
  DEL PEAK  1(1P36.23) WILD-TYPE 74 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     15    1
  DEL PEAK  1(1P36.23) WILD-TYPE   74   15
         clus
vv        DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  ABSENT                            15                             74
  PRESENT                            1                             15
[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                             11 
                    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-MU-A51Y 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-MU-A8JM 
"DEL PEAK  1(1P36.23) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  1(1P36.23) MUTATED     0    0   3    8    2  1   1    1    0   2  0
  DEL PEAK  1(1P36.23) WILD-TYPE   1    1  27   57   22  3   7    6    9  20  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK  1(1P36.23) MUTATED     0  0   1  3
  DEL PEAK  1(1P36.23) WILD-TYPE   8  2   0 11
D29V42, multiclass
      clus
vv     DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             3                             27
  T1B1                            8                             57
  T1B2                            2                             22
  T2                              1                              3
  T2A                             1                              7
  T2A1                            1                              6
  T2A2                            0                              9
  T2B                             2                             20
  T3                              0                              1
  T3B                             0                              8
  T4                              0                              2
  TIS                             1                              0
  TX                              3                             11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        2         1         1       28
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  1(1P36.23) MUTATED          11         4        1         2
  DEL PEAK  1(1P36.23) WILD-TYPE        58        28        2         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  1(1P36.23) MUTATED            1          0         4         0
  DEL PEAK  1(1P36.23) WILD-TYPE          4          7        23         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.23) MUTATED            3         0         1
  DEL PEAK  1(1P36.23) WILD-TYPE         31         3         6
D29V44, multiclass
            clus
vv           DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              3                             28
  STAGE IB1                            11                             58
  STAGE IB2                             4                             28
  STAGE II                              1                              2
  STAGE IIA                             2                              4
  STAGE IIA1                            1                              4
  STAGE IIA2                            0                              7
  STAGE IIB                             4                             23
  STAGE III                             0                              1
  STAGE IIIB                            3                             31
  STAGE IVA                             0                              3
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    17  11
  DEL PEAK  2(1P13.2) WILD-TYPE 166  39
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           28                           205 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           11                            39 
$`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        60.69 
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         1.32 
TCGA-EA-A3QE TCGA-EK-A2PL TCGA-EX-A69L TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A6W2 
        1.18         0.43        19.79         1.45        25.41         9.44 
TCGA-LP-A4AW TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EL 
        0.89         5.49         3.39        10.03        34.52        53.52 
TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94Y 
       46.03        11.51        39.78         4.73 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        38.99         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
        3.58        44.22        73.45        83.05       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
       85.55         9.34         2.73        50.99         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       99.91        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       58.88        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
       17.52         8.28         0.76        12.36         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
        0.62        13.05        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
        0.36        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-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-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        7.92         6.94        14.70         6.12         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
       23.84         0.92         2.17         0.66         1.02         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12         9.01         7.13        21.67        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX 
       21.11       195.85        30.31         7.99        11.28         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         2.96        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        10.39        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       12.16        61.28        29.03        20.22        14.07        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z 
       32.15        23.28        49.55        31.27        16.64        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       44.88        42.58        42.08        43.82        39.35        38.96 
TCGA-WL-A834 
       18.05 

  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                        195.85 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        21.65                         15.58 
[1] "0.4 - 154.3 (21.6)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.7"
D30V2, continuous
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK  2(1P13.2) MUTATED    11   4     2
  DEL PEAK  2(1P13.2) WILD-TYPE 110  46     9
D30V3, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                             11                           110
  T2                              4                            46
  T3+T4                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   13  2
  DEL PEAK  2(1P13.2) WILD-TYPE 98 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     13    2
  DEL PEAK  2(1P13.2) WILD-TYPE   98   45
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          13                            98
  1                           2                            45
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  2(1P13.2) MUTATED   11  3  9
  DEL PEAK  2(1P13.2) WILD-TYPE 80  5 84
D30V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  M0                          11                            80
  M1                           3                             5
  MX                           9                            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.2) MUTATED               1                               27
  DEL PEAK  2(1P13.2) WILD-TYPE             4                              170
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  2(1P13.2) MUTATED                                               0
  DEL PEAK  2(1P13.2) WILD-TYPE                                             5
                               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                                            5
D30V6, multiclass
                                               clus
vv                                              DEL PEAK  2(1P13.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  2(1P13.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        170
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     5  25
  DEL PEAK  2(1P13.2) WILD-TYPE  25 183
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      5   25
  DEL PEAK  2(1P13.2) WILD-TYPE   25  183
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                            5                            25
  YES                          25                           183
[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                        19
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           0    23
  DEL PEAK  2(1P13.2) WILD-TYPE                                         1   146
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                                                              23
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               146
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     2  18
  DEL PEAK  2(1P13.2) WILD-TYPE  14 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      2   18
  DEL PEAK  2(1P13.2) WILD-TYPE   14  131
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           131
[1] 2 2
[1] FALSE
D30V12, continuous
D30V13, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6  3
  DEL PEAK  2(1P13.2) WILD-TYPE 65 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6    3
  DEL PEAK  2(1P13.2) WILD-TYPE   65   22
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  TUMOR FREE                           6                            65
  WITH TUMOR                           3                            22
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  2(1P13.2) MUTATED        7      0       0      2       0
  DEL PEAK  2(1P13.2) WILD-TYPE     16      5       1      8       7
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  2(1P13.2) MUTATED              20       1
  DEL PEAK  2(1P13.2) WILD-TYPE           158      13
D30V14, multiclass
               clus
vv              DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  BRAZIL                                  7                            16
  CANADA                                  0                             5
  NIGERIA                                 0                             1
  RUSSIA                                  2                             8
  UKRAINE                                 0                             7
  UNITED STATES                          20                           158
  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  8  0  3
  DEL PEAK  2(1P13.2) WILD-TYPE 15 91 89  1 11
D30V15, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  G1                           2                            15
  G2                          15                            91
  G3                           8                            89
  G4                           0                             1
  GX                           3                            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                            33 
                   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-MU-A5YI 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MU-A8JM                    TCGA-Q1-A6DW 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-Q1-A73S                    TCGA-RA-A741 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-VS-A8QF                    TCGA-VS-A94Z 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-WL-A834 
"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                                          30
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  2(1P13.2) MUTATED                                        0
  DEL PEAK  2(1P13.2) WILD-TYPE                                      8
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  2(1P13.2) MUTATED                                                 1
  DEL PEAK  2(1P13.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  2(1P13.2) MUTATED               11                  13
  DEL PEAK  2(1P13.2) WILD-TYPE             41                  99
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                                                           11
  LIFELONG NON-SMOKER                                                      13
                                                 clus
vv                                                DEL PEAK  2(1P13.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             41
  LIFELONG NON-SMOKER                                                        99
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V19, continuous
D30V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  2(1P13.2) MUTATED             3       10             2        2
  DEL PEAK  2(1P13.2) WILD-TYPE          16       65            10       10
D30V21, multiclass
               clus
vv              DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  COMBINATION                             3                            16
  EXTERNAL                               10                            65
  EXTERNAL BEAM                           2                            10
  INTERNAL                                2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V22, binary
                               cls
clus                             0  1
  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             3
  DEL PEAK  2(1P13.2) WILD-TYPE                  22            13
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                            22
  REGIONAL SITE                                 3                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V24, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6  1
  DEL PEAK  2(1P13.2) WILD-TYPE 28  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6    1
  DEL PEAK  2(1P13.2) WILD-TYPE   28    2
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CGY                           6                            28
  GY                            1                             2
[1] 2 2
[1] FALSE
D30V25, continuous
D30V26, continuous
D30V27, continuous
D30V28, continuous
D30V29, continuous
D30V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  2(1P13.2) MUTATED                                     0
  DEL PEAK  2(1P13.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  2(1P13.2) MUTATED                                     0
  DEL PEAK  2(1P13.2) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  2(1P13.2) MUTATED                         3                       0
  DEL PEAK  2(1P13.2) WILD-TYPE                      26                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  2(1P13.2) MUTATED                         0
  DEL PEAK  2(1P13.2) WILD-TYPE                       7
D30V31, multiclass
                                     clus
vv                                    DEL PEAK  2(1P13.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       3
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    DEL PEAK  2(1P13.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  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)
  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                                             12
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  2(1P13.2) MUTATED                                                                                   6
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                62
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  2(1P13.2) MUTATED                                                                                             12
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                           93
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)                                      6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          12
                                                                                              clus
vv                                                                                             DEL PEAK  2(1P13.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            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"
D30V33, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6  4
  DEL PEAK  2(1P13.2) WILD-TYPE 62 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6    4
  DEL PEAK  2(1P13.2) WILD-TYPE   62   66
         clus
vv        DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ABSENT                            6                            62
  PRESENT                           4                            66
[1] 2 2
[1] FALSE
D30V34, continuous
D30V35, continuous
D30V36, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    8  8
  DEL PEAK  2(1P13.2) WILD-TYPE 35 86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      8    8
  DEL PEAK  2(1P13.2) WILD-TYPE   35   86
                                          clus
vv                                         DEL PEAK  2(1P13.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           8
                                          clus
vv                                         DEL PEAK  2(1P13.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            86
[1] 2 2
[1] FALSE
D30V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  2(1P13.2) MUTATED              2           6          4
  DEL PEAK  2(1P13.2) WILD-TYPE            8          43         53
D30V38, multiclass
              clus
vv             DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CURRENT USER                           2                             8
  FORMER USER                            6                            43
  NEVER USED                             4                            53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V39, continuous
D30V40, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    7  1
  DEL PEAK  2(1P13.2) WILD-TYPE 82 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7    1
  DEL PEAK  2(1P13.2) WILD-TYPE   82   15
         clus
vv        DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ABSENT                            7                            82
  PRESENT                           1                            15
[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                            12 
                   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-MU-A51Y                    TCGA-MU-A8JM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  2(1P13.2) MUTATED     0    0   3    6    2  0   2    0    0   2  0
  DEL PEAK  2(1P13.2) WILD-TYPE   1    1  27   59   22  4   6    7    9  20  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  2(1P13.2) MUTATED     2  0   1  5
  DEL PEAK  2(1P13.2) WILD-TYPE   6  2   0  9
D30V42, multiclass
      clus
vv     DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                            3                            27
  T1B1                           6                            59
  T1B2                           2                            22
  T2                             0                             4
  T2A                            2                             6
  T2A1                           0                             7
  T2A2                           0                             9
  T2B                            2                            20
  T3                             0                             1
  T3B                            2                             6
  T4                             0                             2
  TIS                            1                             0
  TX                             5                             9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        1         1         1       27
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED           9         1        1         2
  DEL PEAK  2(1P13.2) WILD-TYPE        60        31        2         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  2(1P13.2) MUTATED            0          0         3         0
  DEL PEAK  2(1P13.2) WILD-TYPE          5          7        24         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  2(1P13.2) MUTATED            5         1         2
  DEL PEAK  2(1P13.2) WILD-TYPE         29         2         5
D30V44, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                             1                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             4                            27
  STAGE IB1                            9                            60
  STAGE IB2                            1                            31
  STAGE II                             1                             2
  STAGE IIA                            2                             4
  STAGE IIA1                           0                             5
  STAGE IIA2                           0                             7
  STAGE IIB                            3                            24
  STAGE III                            0                             1
  STAGE IIIB                           5                            29
  STAGE IVA                            1                             2
  STAGE IVB                            2                             5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    40   8
  DEL PEAK  3(2Q22.1) WILD-TYPE 143  42
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           48                           185 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            8                            42 
$`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       182.93        60.69        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         1.32         1.35 
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         4.73        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-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-R2-A69V 
        0.20         4.34         5.49        15.58        13.35        19.59 
TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A94Y TCGA-VS-A94Z 
       12.16        20.22        53.52        11.51         4.73        23.24 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       31.40        46.32        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43         0.82        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35        17.19        85.55        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        75.78 
TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK 
       99.91         6.12        20.91         4.47        58.88        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-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18         8.28         0.76        12.36         1.74 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       14.50         1.81        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       13.91        15.02        13.58        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA 
       26.27         0.43         0.59         0.59         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         4.04         0.03         0.36        23.70         2.24 
TCGA-EK-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-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        6.94        14.70         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA 
        9.01        25.41         7.13        20.78        14.93       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81       117.40        96.95        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AW 
       10.06         5.13         6.71        21.11        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.07         0.30         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       29.72         0.07         2.96        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
        3.88        11.67        93.99        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       29.03        14.07        19.96        32.15        46.03        23.28 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A954 
       49.55        39.78        31.27        16.64        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.08        43.82        39.35        38.96        18.05 

  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 
                       195.85                        177.04 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        16.55                         15.88 
[1] "0.1 - 195.8 (16.6)" "0.0 - 177.0 (15.9)"
[1] "hr=" "1.4"
D31V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  3(2Q22.1) MUTATED   24 12     4
  DEL PEAK  3(2Q22.1) WILD-TYPE 97 38     7
D31V3, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                             24                            97
  T2                             12                            38
  T3+T4                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   28  8
  DEL PEAK  3(2Q22.1) WILD-TYPE 83 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     28    8
  DEL PEAK  3(2Q22.1) WILD-TYPE   83   39
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          28                            83
  1                           8                            39
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  3(2Q22.1) MUTATED   24  2 17
  DEL PEAK  3(2Q22.1) WILD-TYPE 67  6 76
D31V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  M0                          24                            67
  M1                           2                             6
  MX                          17                            76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED               2                               42
  DEL PEAK  3(2Q22.1) WILD-TYPE             3                              155
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  3(2Q22.1) MUTATED                                               0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             5
                               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                                              1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                            5
D31V6, multiclass
                                               clus
vv                                              DEL PEAK  3(2Q22.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       42
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  3(2Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     8  40
  DEL PEAK  3(2Q22.1) WILD-TYPE  22 168
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      8   40
  DEL PEAK  3(2Q22.1) WILD-TYPE   22  168
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                            8                            22
  YES                          40                           168
[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                           8
  DEL PEAK  3(2Q22.1) WILD-TYPE                        16
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(2Q22.1) MUTATED                                           0    31
  DEL PEAK  3(2Q22.1) WILD-TYPE                                         1   138
D31V10, multiclass
                                           clus
vv                                          DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              31
                                           clus
vv                                          DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D31V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     1  32
  DEL PEAK  3(2Q22.1) WILD-TYPE  15 117
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      1   32
  DEL PEAK  3(2Q22.1) WILD-TYPE   15  117
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           117
[1] 2 2
[1] FALSE
D31V12, continuous
D31V13, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   15  4
  DEL PEAK  3(2Q22.1) WILD-TYPE 56 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     15    4
  DEL PEAK  3(2Q22.1) WILD-TYPE   56   21
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  TUMOR FREE                          15                            56
  WITH TUMOR                           4                            21
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  3(2Q22.1) MUTATED        5      2       0      2       2
  DEL PEAK  3(2Q22.1) WILD-TYPE     18      3       1      8       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  3(2Q22.1) MUTATED              34       3
  DEL PEAK  3(2Q22.1) WILD-TYPE           144      11
D31V14, multiclass
               clus
vv              DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  BRAZIL                                  5                            18
  CANADA                                  2                             3
  NIGERIA                                 0                             1
  RUSSIA                                  2                             8
  UKRAINE                                 2                             5
  UNITED STATES                          34                           144
  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 17 25  1  2
  DEL PEAK  3(2Q22.1) WILD-TYPE 14 89 72  0 12
D31V15, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  G1                           3                            14
  G2                          17                            89
  G3                          25                            72
  G4                           1                             0
  GX                           2                            12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V16, continuous
D31V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  3(2Q22.1) MUTATED                                             5
  DEL PEAK  3(2Q22.1) WILD-TYPE                                          26
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  3(2Q22.1) MUTATED                                        2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  3(2Q22.1) MUTATED                                                 1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  3(2Q22.1) MUTATED               11                  23
  DEL PEAK  3(2Q22.1) WILD-TYPE             41                  89
D31V18, multiclass
                                                 clus
vv                                                DEL PEAK  3(2Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           11
  LIFELONG NON-SMOKER                                                      23
                                                 clus
vv                                                DEL PEAK  3(2Q22.1) 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                                                             41
  LIFELONG NON-SMOKER                                                        89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V19, continuous
D31V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  3(2Q22.1) MUTATED             3       17             5        3
  DEL PEAK  3(2Q22.1) WILD-TYPE          16       58             7        9
D31V21, multiclass
               clus
vv              DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  COMBINATION                             3                            16
  EXTERNAL                               17                            58
  EXTERNAL BEAM                           5                             7
  INTERNAL                                3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     9             3
  DEL PEAK  3(2Q22.1) WILD-TYPE                  19            13
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                           9                            19
  REGIONAL SITE                                 3                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V24, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   10  2
  DEL PEAK  3(2Q22.1) WILD-TYPE 24  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     10    2
  DEL PEAK  3(2Q22.1) WILD-TYPE   24    1
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  CGY                          10                            24
  GY                            2                             1
[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                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  3(2Q22.1) MUTATED                         7                       0
  DEL PEAK  3(2Q22.1) WILD-TYPE                      22                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  3(2Q22.1) MUTATED                         2
  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                                       7
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK  3(2Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                        22
  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                                                5
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             11
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  3(2Q22.1) MUTATED                                                                                  11
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                                57
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  3(2Q22.1) MUTATED                                                                                             25
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                                           80
D31V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  3(2Q22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          25
                                                                                              clus
vv                                                                                             DEL PEAK  3(2Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            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"
D31V33, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   17 12
  DEL PEAK  3(2Q22.1) WILD-TYPE 51 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     17   12
  DEL PEAK  3(2Q22.1) WILD-TYPE   51   58
         clus
vv        DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  ABSENT                           17                            51
  PRESENT                          12                            58
[1] 2 2
[1] FALSE
D31V34, continuous
D31V35, continuous
D31V36, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED    9 20
  DEL PEAK  3(2Q22.1) WILD-TYPE 34 74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      9   20
  DEL PEAK  3(2Q22.1) WILD-TYPE   34   74
                                          clus
vv                                         DEL PEAK  3(2Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          20
                                          clus
vv                                         DEL PEAK  3(2Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            74
[1] 2 2
[1] FALSE
D31V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  3(2Q22.1) MUTATED              3          15         13
  DEL PEAK  3(2Q22.1) WILD-TYPE            7          34         44
D31V38, multiclass
              clus
vv             DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  CURRENT USER                           3                             7
  FORMER USER                           15                            34
  NEVER USED                            13                            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V39, continuous
D31V40, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   20  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 69 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     20    0
  DEL PEAK  3(2Q22.1) WILD-TYPE   69   16
         clus
vv        DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  ABSENT                           20                            69
  PRESENT                           0                            16
[1] 2 2
[1] FALSE
D31V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  3(2Q22.1) MUTATED     0    0   7   12    5  1   3    2    2   4  1
  DEL PEAK  3(2Q22.1) WILD-TYPE   1    1  23   53   19  3   5    5    7  18  0
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  3(2Q22.1) MUTATED     3  0   1  2
  DEL PEAK  3(2Q22.1) WILD-TYPE   5  2   0 12
D31V42, multiclass
      clus
vv     DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                            7                            23
  T1B1                          12                            53
  T1B2                           5                            19
  T2                             1                             3
  T2A                            3                             5
  T2A1                           2                             5
  T2A2                           2                             7
  T2B                            4                            18
  T3                             1                             0
  T3B                            3                             5
  T4                             0                             2
  TIS                            1                             0
  TX                             2                            12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        2         1         1       25
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  3(2Q22.1) MUTATED          16         5        2         2
  DEL PEAK  3(2Q22.1) WILD-TYPE        53        27        1         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  3(2Q22.1) MUTATED            1          1         3         1
  DEL PEAK  3(2Q22.1) WILD-TYPE          4          6        24         0
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  3(2Q22.1) MUTATED            7         1         1
  DEL PEAK  3(2Q22.1) WILD-TYPE         27         2         6
D31V44, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                             0                             2
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             6                            25
  STAGE IB1                           16                            53
  STAGE IB2                            5                            27
  STAGE II                             2                             1
  STAGE IIA                            2                             4
  STAGE IIA1                           1                             4
  STAGE IIA2                           1                             6
  STAGE IIB                            3                            24
  STAGE III                            1                             0
  STAGE IIIB                           7                            27
  STAGE IVA                            1                             2
  STAGE IVB                            1                             6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK  4(2Q37.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.1) MUTATED    81  21
  DEL PEAK  4(2Q37.1) WILD-TYPE 102  29
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          102                           131 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                           21                            29 
$`DEL PEAK  4(2Q37.1) MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       57.04        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A2LY 
      177.04         5.46        30.21        38.99        73.18        78.35 
TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7UE 
      100.14        52.01        18.02       182.93       134.33        85.55 
TCGA-C5-A7UH TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
       60.69        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         4.47         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         0.76 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A43B 
       12.36         1.32        13.05         1.18         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       12.66         0.26        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2RD TCGA-EK-A2RJ 
       45.96        26.27         1.51         1.45         0.03         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A69L TCGA-FU-A2QG 
        2.24         0.10         0.10         7.92        19.79         0.92 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A770 TCGA-HM-A3JJ 
        0.66         1.45         0.82         1.35         1.12        21.67 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A3PZ 
       26.56        36.36        27.42        21.44        15.58        21.11 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       30.31         7.99         0.07         0.30         0.82         0.20 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V 
        4.34         5.49        15.58        13.35         3.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
        3.88        11.67        93.99        12.16        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF 
       29.03        20.22        14.07        53.52        11.51        49.55 
TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
        4.73        42.08        43.82        39.35        38.96        18.05 

$`DEL PEAK  4(2Q37.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
       49.48       144.16       173.29        82.85        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       31.40        46.32        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL 
       73.45        83.05        38.43         0.82        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      154.32       101.82        15.48        20.35       147.35        17.19 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-C5-A8YT 
       94.95         9.34        13.61         2.73        75.78         6.12 
TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A3LQ 
       20.91        58.88        50.76        58.88        36.76        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 
       16.83        16.18         1.74         0.82         0.62        14.50 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35        14.50        12.82        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
       15.02        14.99        14.96         6.64         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
        0.59         0.13        16.08         0.07         4.04         0.36 
TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 
       23.70         0.07         0.10         0.03        20.35         6.94 
TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       14.70         6.12         4.73         1.22        23.84         2.17 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.02         1.58         1.48         3.52         1.32         1.97 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        9.01        25.41         7.13        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 
       81.96         3.29        24.56        20.48        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A5YI 
        6.71       195.85        11.28         0.89        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        5.42        29.72         0.07         2.96        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH 
       61.28        19.96        32.15        46.03        23.28        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       31.27        16.64        23.24        44.88        42.58 

  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 
                       182.93                        195.85 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                        15.58                         15.95 
[1] "0.0 - 182.9 (15.6)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.1"
D32V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  4(2Q37.1) MUTATED   57 18     6
  DEL PEAK  4(2Q37.1) WILD-TYPE 64 32     5
D32V3, multiclass
       clus
vv      DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  T1                             57                            64
  T2                             18                            32
  T3+T4                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   47 21
  DEL PEAK  4(2Q37.1) WILD-TYPE 64 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     47   21
  DEL PEAK  4(2Q37.1) WILD-TYPE   64   26
   clus
vv  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  0                          47                            64
  1                          21                            26
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  4(2Q37.1) MUTATED   44  2 39
  DEL PEAK  4(2Q37.1) WILD-TYPE 47  6 54
D32V5, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  M0                          44                            47
  M1                           2                             6
  MX                          39                            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q37.1) MUTATED               1                               94
  DEL PEAK  4(2Q37.1) WILD-TYPE             4                              103
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  4(2Q37.1) MUTATED                                               2
  DEL PEAK  4(2Q37.1) WILD-TYPE                                             3
                               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                                              1
  DEL PEAK  4(2Q37.1) WILD-TYPE                                            5
D32V6, multiclass
                                               clus
vv                                              DEL PEAK  4(2Q37.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       94
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  4(2Q37.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        103
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.1) MUTATED    13  91
  DEL PEAK  4(2Q37.1) WILD-TYPE  17 117
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     13   91
  DEL PEAK  4(2Q37.1) WILD-TYPE   17  117
     clus
vv    DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  NO                           13                            17
  YES                          91                           117
[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                           9
  DEL PEAK  4(2Q37.1) WILD-TYPE                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(2Q37.1) MUTATED                                           0    72
  DEL PEAK  4(2Q37.1) WILD-TYPE                                         1    97
D32V10, multiclass
                                           clus
vv                                          DEL PEAK  4(2Q37.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    5
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              72
                                           clus
vv                                          DEL PEAK  4(2Q37.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                97
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED    4 65
  DEL PEAK  4(2Q37.1) WILD-TYPE 12 84
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED      4   65
  DEL PEAK  4(2Q37.1) WILD-TYPE   12   84
                        clus
vv                       DEL PEAK  4(2Q37.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          65
                        clus
vv                       DEL PEAK  4(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                            84
[1] 2 2
[1] FALSE
D32V12, continuous
D32V13, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   26 13
  DEL PEAK  4(2Q37.1) WILD-TYPE 45 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     26   13
  DEL PEAK  4(2Q37.1) WILD-TYPE   45   12
            clus
vv           DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  TUMOR FREE                          26                            45
  WITH TUMOR                          13                            12
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  4(2Q37.1) MUTATED       13      3       0      5       3
  DEL PEAK  4(2Q37.1) WILD-TYPE     10      2       1      5       4
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  4(2Q37.1) MUTATED              72       8
  DEL PEAK  4(2Q37.1) WILD-TYPE           106       6
D32V14, multiclass
               clus
vv              DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  BRAZIL                                 13                            10
  CANADA                                  3                             2
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 3                             4
  UNITED STATES                          72                           106
  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    6 48 42  0  7
  DEL PEAK  4(2Q37.1) WILD-TYPE 11 58 55  1  7
D32V15, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  G1                           6                            11
  G2                          48                            58
  G3                          42                            55
  G4                           0                             1
  GX                           7                             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V16, continuous
D32V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  4(2Q37.1) MUTATED                                             9
  DEL PEAK  4(2Q37.1) WILD-TYPE                                          22
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  4(2Q37.1) MUTATED                                        2
  DEL PEAK  4(2Q37.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  4(2Q37.1) MUTATED                                                 2
  DEL PEAK  4(2Q37.1) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  4(2Q37.1) MUTATED               21                  55
  DEL PEAK  4(2Q37.1) WILD-TYPE             31                  57
D32V18, multiclass
                                                 clus
vv                                                DEL PEAK  4(2Q37.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           21
  LIFELONG NON-SMOKER                                                      55
                                                 clus
vv                                                DEL PEAK  4(2Q37.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             31
  LIFELONG NON-SMOKER                                                        57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V19, continuous
D32V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  4(2Q37.1) MUTATED             7       33             6        6
  DEL PEAK  4(2Q37.1) WILD-TYPE          12       42             6        6
D32V21, multiclass
               clus
vv              DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               33                            42
  EXTERNAL BEAM                           6                             6
  INTERNAL                                6                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    15             9
  DEL PEAK  4(2Q37.1) WILD-TYPE                  13             7
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                          15                            13
  REGIONAL SITE                                 9                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V24, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   19  2
  DEL PEAK  4(2Q37.1) WILD-TYPE 15  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     19    2
  DEL PEAK  4(2Q37.1) WILD-TYPE   15    1
     clus
vv    DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  CGY                          19                            15
  GY                            2                             1
[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                                     3
  DEL PEAK  4(2Q37.1) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  4(2Q37.1) MUTATED                        12                       1
  DEL PEAK  4(2Q37.1) WILD-TYPE                      17                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  4(2Q37.1) MUTATED                         1
  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                           3
  OTHER LOCATION, SPECIFY                                      12
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  4(2Q37.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        17
  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                                               10
  DEL PEAK  4(2Q37.1) WILD-TYPE                                              6
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  4(2Q37.1) MUTATED                                                                                  26
  DEL PEAK  4(2Q37.1) WILD-TYPE                                                                                42
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  4(2Q37.1) MUTATED                                                                                             47
  DEL PEAK  4(2Q37.1) WILD-TYPE                                                                                           58
D32V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  4(2Q37.1) 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)                                     26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          47
                                                                                              clus
vv                                                                                             DEL PEAK  4(2Q37.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V33, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   28 29
  DEL PEAK  4(2Q37.1) WILD-TYPE 40 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     28   29
  DEL PEAK  4(2Q37.1) WILD-TYPE   40   41
         clus
vv        DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  ABSENT                           28                            40
  PRESENT                          29                            41
[1] 2 2
[1] FALSE
D32V34, continuous
D32V35, continuous
D32V36, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   19 43
  DEL PEAK  4(2Q37.1) WILD-TYPE 24 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     19   43
  DEL PEAK  4(2Q37.1) WILD-TYPE   24   51
                                          clus
vv                                         DEL PEAK  4(2Q37.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          43
                                          clus
vv                                         DEL PEAK  4(2Q37.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            51
[1] 2 2
[1] FALSE
D32V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  4(2Q37.1) MUTATED              6          22         29
  DEL PEAK  4(2Q37.1) WILD-TYPE            4          27         28
D32V38, multiclass
              clus
vv             DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  CURRENT USER                           6                             4
  FORMER USER                           22                            27
  NEVER USED                            29                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V39, continuous
D32V40, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   37  4
  DEL PEAK  4(2Q37.1) WILD-TYPE 52 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     37    4
  DEL PEAK  4(2Q37.1) WILD-TYPE   52   12
         clus
vv        DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  ABSENT                           37                            52
  PRESENT                           4                            12
[1] 2 2
[1] FALSE
D32V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  4(2Q37.1) MUTATED     1    0  15   32    9  1   4    1    5   7  0
  DEL PEAK  4(2Q37.1) WILD-TYPE   0    1  15   33   15  3   4    6    4  15  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  4(2Q37.1) MUTATED     5  1   1  5
  DEL PEAK  4(2Q37.1) WILD-TYPE   3  1   0  9
D32V42, multiclass
      clus
vv     DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  T1A                            1                             0
  T1A1                           0                             1
  T1B                           15                            15
  T1B1                          32                            33
  T1B2                           9                            15
  T2                             1                             3
  T2A                            4                             4
  T2A1                           1                             6
  T2A2                           5                             4
  T2B                            7                            15
  T3                             0                             1
  T3B                            5                             3
  T4                             1                             1
  TIS                            1                             0
  TX                             5                             9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  4(2Q37.1) MUTATED         1        1         0         0       17
  DEL PEAK  4(2Q37.1) WILD-TYPE       3        1         1         1       14
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  4(2Q37.1) MUTATED          30        13        2         3
  DEL PEAK  4(2Q37.1) WILD-TYPE        39        19        1         3
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  4(2Q37.1) MUTATED            0          3        11         0
  DEL PEAK  4(2Q37.1) WILD-TYPE          5          4        16         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  4(2Q37.1) MUTATED           16         3         0
  DEL PEAK  4(2Q37.1) WILD-TYPE         18         0         7
D32V44, multiclass
            clus
vv           DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                             1                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            17                            14
  STAGE IB1                           30                            39
  STAGE IB2                           13                            19
  STAGE II                             2                             1
  STAGE IIA                            3                             3
  STAGE IIA1                           0                             5
  STAGE IIA2                           3                             4
  STAGE IIB                           11                            16
  STAGE III                            0                             1
  STAGE IIIB                          16                            18
  STAGE IVA                            3                             0
  STAGE IVB                            0                             7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  5(3P14.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P14.2) MUTATED    77  27
  DEL PEAK  5(3P14.2) WILD-TYPE 106  23
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                          104                           129 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           27                            23 
$`DEL PEAK  5(3P14.2) MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        23.67        11.44        18.74        36.56       144.16 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MI 
      173.29         5.46        31.40        30.21        53.16        35.61 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CH 
       20.91        40.93        73.18        83.05        52.01       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH 
      101.82       134.33        15.48       147.35        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8YQ 
       94.95        13.61         2.73        45.83        75.78        23.51 
TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM 
       20.91        58.88        40.04        87.75        36.76       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3QD 
      118.65        16.83        17.52        12.36         0.82        13.05 
TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 
        1.18         1.35        14.50        12.66         0.26        14.89 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58         0.36        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RB 
        6.64         1.51         0.43         0.59         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI 
        4.04         0.36        20.35        23.84         0.66         1.45 
TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3L7 
        3.52         1.97        25.41         7.13        21.67       147.39 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-AAVH TCGA-JX-A3PZ 
       78.71        26.56        24.56        21.44         6.71        21.11 
TCGA-JX-A3Q8 TCGA-MU-A5YI TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73Q 
       30.31         0.03         5.49        13.35         3.39         5.88 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
       10.39         3.88        93.99        12.16        10.03        34.52 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       20.22        14.07        32.15        46.03        23.28        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A957 
       49.55        39.78        31.27         4.73        23.24        42.08 
TCGA-VS-A959 TCGA-VS-A9U5 
       39.35        38.96 

$`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 
        0.82        18.02        17.85        20.42       182.93        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 
        6.12         4.47         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         0.76         1.74 
TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA 
        1.32         0.62        14.50         1.35         1.81        12.82 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2R8 
        1.48        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        23.70         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         6.12         4.73         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.92         2.17         1.02         1.58         1.48         0.82 
TCGA-FU-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        10.06 
TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
        5.13       195.85         7.99        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD 
        0.30         0.82         0.20        13.87         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        0.07         4.34         2.96        15.58        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD 
       17.56        14.07        15.88         6.25        19.59        11.67 
TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A94X TCGA-VS-A952 
       61.28        29.03        19.96        53.52        16.64        44.88 
TCGA-VS-A954 TCGA-VS-A958 TCGA-WL-A834 
       42.58        43.82        18.05 

  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                       173.29                        195.85 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                        21.01                         14.07 
[1] "0.0 - 173.3 (21.0)" "0.0 - 195.8 (14.1)"
[1] "hr=" "1"  
D33V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  5(3P14.2) MUTATED   48 17     6
  DEL PEAK  5(3P14.2) WILD-TYPE 73 33     5
D33V3, multiclass
       clus
vv      DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  T1                             48                            73
  T2                             17                            33
  T3+T4                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   35 25
  DEL PEAK  5(3P14.2) WILD-TYPE 76 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     35   25
  DEL PEAK  5(3P14.2) WILD-TYPE   76   22
   clus
vv  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  0                          35                            76
  1                          25                            22
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  5(3P14.2) MUTATED   38  3 40
  DEL PEAK  5(3P14.2) WILD-TYPE 53  5 53
D33V5, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  M0                          38                            53
  M1                           3                             5
  MX                          40                            53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(3P14.2) MUTATED               2                               99
  DEL PEAK  5(3P14.2) WILD-TYPE             3                               98
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  5(3P14.2) MUTATED                                               0
  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                                              2
  DEL PEAK  5(3P14.2) WILD-TYPE                                            4
D33V6, multiclass
                                               clus
vv                                              DEL PEAK  5(3P14.2) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       99
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              DEL PEAK  5(3P14.2) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         98
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P14.2) MUTATED    19  87
  DEL PEAK  5(3P14.2) WILD-TYPE  11 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     19   87
  DEL PEAK  5(3P14.2) WILD-TYPE   11  121
     clus
vv    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  NO                           19                            11
  YES                          87                           121
[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                          10
  DEL PEAK  5(3P14.2) WILD-TYPE                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(3P14.2) MUTATED                                           0    78
  DEL PEAK  5(3P14.2) WILD-TYPE                                         1    91
D33V10, multiclass
                                           clus
vv                                          DEL PEAK  5(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              78
                                           clus
vv                                          DEL PEAK  5(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED    4 63
  DEL PEAK  5(3P14.2) WILD-TYPE 12 86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED      4   63
  DEL PEAK  5(3P14.2) WILD-TYPE   12   86
                        clus
vv                       DEL PEAK  5(3P14.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK  5(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                            86
[1] 2 2
[1] FALSE
D33V12, continuous
D33V13, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   31 14
  DEL PEAK  5(3P14.2) WILD-TYPE 40 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     31   14
  DEL PEAK  5(3P14.2) WILD-TYPE   40   11
            clus
vv           DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  TUMOR FREE                          31                            40
  WITH TUMOR                          14                            11
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  5(3P14.2) MUTATED       16      2       0      5       2
  DEL PEAK  5(3P14.2) WILD-TYPE      7      3       1      5       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  5(3P14.2) MUTATED              75       6
  DEL PEAK  5(3P14.2) WILD-TYPE           103       8
D33V14, multiclass
               clus
vv              DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  BRAZIL                                 16                             7
  CANADA                                  2                             3
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 2                             5
  UNITED STATES                          75                           103
  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 49 41  1  8
  DEL PEAK  5(3P14.2) WILD-TYPE 13 57 56  0  6
D33V15, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  G1                           4                            13
  G2                          49                            57
  G3                          41                            56
  G4                           1                             0
  GX                           8                             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V16, continuous
D33V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  5(3P14.2) MUTATED                                            13
  DEL PEAK  5(3P14.2) WILD-TYPE                                          18
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  5(3P14.2) MUTATED                                        2
  DEL PEAK  5(3P14.2) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  5(3P14.2) MUTATED                                                 2
  DEL PEAK  5(3P14.2) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  5(3P14.2) MUTATED               34                  40
  DEL PEAK  5(3P14.2) WILD-TYPE             18                  72
D33V18, multiclass
                                                 clus
vv                                                DEL PEAK  5(3P14.2) 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                                                           34
  LIFELONG NON-SMOKER                                                      40
                                                 clus
vv                                                DEL PEAK  5(3P14.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             18
  LIFELONG NON-SMOKER                                                        72
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V19, continuous
D33V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  5(3P14.2) MUTATED            12       38             7        5
  DEL PEAK  5(3P14.2) WILD-TYPE           7       37             5        7
D33V21, multiclass
               clus
vv              DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  COMBINATION                            12                             7
  EXTERNAL                               38                            37
  EXTERNAL BEAM                           7                             5
  INTERNAL                                5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    14            11
  DEL PEAK  5(3P14.2) WILD-TYPE                  14             5
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                          14                            14
  REGIONAL SITE                                11                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V24, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   19  2
  DEL PEAK  5(3P14.2) WILD-TYPE 15  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     19    2
  DEL PEAK  5(3P14.2) WILD-TYPE   15    1
     clus
vv    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CGY                          19                            15
  GY                            2                             1
[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                                   2
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  5(3P14.2) MUTATED                         8                       1
  DEL PEAK  5(3P14.2) WILD-TYPE                      21                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  5(3P14.2) MUTATED                         4
  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                                       8
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       4
                                     clus
vv                                    DEL PEAK  5(3P14.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        21
  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                                                9
  DEL PEAK  5(3P14.2) WILD-TYPE                                              7
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  5(3P14.2) MUTATED                                                                                  26
  DEL PEAK  5(3P14.2) WILD-TYPE                                                                                42
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  5(3P14.2) MUTATED                                                                                             47
  DEL PEAK  5(3P14.2) WILD-TYPE                                                                                           58
D33V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  5(3P14.2) 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)                                     26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          47
                                                                                              clus
vv                                                                                             DEL PEAK  5(3P14.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V33, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   17 33
  DEL PEAK  5(3P14.2) WILD-TYPE 51 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     17   33
  DEL PEAK  5(3P14.2) WILD-TYPE   51   37
         clus
vv        DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  ABSENT                           17                            51
  PRESENT                          33                            37
[1] 2 2
[1] FALSE
D33V34, continuous
D33V35, continuous
D33V36, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   22 38
  DEL PEAK  5(3P14.2) WILD-TYPE 21 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     22   38
  DEL PEAK  5(3P14.2) WILD-TYPE   21   56
                                          clus
vv                                         DEL PEAK  5(3P14.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          38
                                          clus
vv                                         DEL PEAK  5(3P14.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            56
[1] 2 2
[1] FALSE
D33V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  5(3P14.2) MUTATED              3          28         22
  DEL PEAK  5(3P14.2) WILD-TYPE            7          21         35
D33V38, multiclass
              clus
vv             DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CURRENT USER                           3                             7
  FORMER USER                           28                            21
  NEVER USED                            22                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V39, continuous
D33V40, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   31  8
  DEL PEAK  5(3P14.2) WILD-TYPE 58  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     31    8
  DEL PEAK  5(3P14.2) WILD-TYPE   58    8
         clus
vv        DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  ABSENT                           31                            58
  PRESENT                           8                             8
[1] 2 2
[1] FALSE
D33V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  5(3P14.2) MUTATED     0    1  12   28    7  1   2    3    2   9  0
  DEL PEAK  5(3P14.2) WILD-TYPE   1    0  18   37   17  3   6    4    7  13  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  5(3P14.2) MUTATED     5  1   1  9
  DEL PEAK  5(3P14.2) WILD-TYPE   3  1   0  5
D33V42, multiclass
      clus
vv     DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  T1A                            0                             1
  T1A1                           1                             0
  T1B                           12                            18
  T1B1                          28                            37
  T1B2                           7                            17
  T2                             1                             3
  T2A                            2                             6
  T2A1                           3                             4
  T2A2                           2                             7
  T2B                            9                            13
  T3                             0                             1
  T3B                            5                             3
  T4                             1                             1
  TIS                            1                             0
  TX                             9                             5
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  5(3P14.2) MUTATED         2        0         1         0       15
  DEL PEAK  5(3P14.2) WILD-TYPE       2        2         0         1       16
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  5(3P14.2) MUTATED          30         9        0         3
  DEL PEAK  5(3P14.2) WILD-TYPE        39        23        3         3
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  5(3P14.2) MUTATED            3          0        18         0
  DEL PEAK  5(3P14.2) WILD-TYPE          2          7         9         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  5(3P14.2) MUTATED           17         3         3
  DEL PEAK  5(3P14.2) WILD-TYPE         17         0         4
D33V44, multiclass
            clus
vv           DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                             0                             2
  STAGE IA1                            1                             0
  STAGE IA2                            0                             1
  STAGE IB                            15                            16
  STAGE IB1                           30                            39
  STAGE IB2                            9                            23
  STAGE II                             0                             3
  STAGE IIA                            3                             3
  STAGE IIA1                           3                             2
  STAGE IIA2                           0                             7
  STAGE IIB                           18                             9
  STAGE III                            0                             1
  STAGE IIIB                          17                            17
  STAGE IVA                            3                             0
  STAGE IVB                            3                             4
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK  6(4Q21.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4Q21.3) MUTATED    55  23
  DEL PEAK  6(4Q21.3) WILD-TYPE 128  27
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                           78                           155 
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                           23                            27 
$`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 
       60.69         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         1.35        14.50         1.81         0.26        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-MY-A913 
       21.67        20.48         7.99        11.28         0.89         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB 
        2.96        13.35        10.39        11.67        12.16        10.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QM TCGA-VS-A94X 
       20.22        14.07        19.96        32.15        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
        4.73        42.08        43.82        39.35        38.96        18.05 

$`DEL PEAK  6(4Q21.3) WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       57.04        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       82.85        19.86        67.46        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       57.73        53.16        38.99         0.46         2.43        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
        3.58        44.22        78.35       100.14        38.43         0.82 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UE 
       17.85        20.42       182.93       154.32       101.82        85.55 
TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YT 
       94.95        50.99         8.35        75.78        23.51         6.12 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK 
        4.47         1.12        50.76        44.94        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28         0.76         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA 
       13.05         1.18        14.50         1.35        12.66        12.82 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2H0 
        1.48        13.91        14.99        14.96        13.58        45.96 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        6.64         0.43         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        23.70         0.07         0.10         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        7.92        14.70        19.79         6.12         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
       23.84         0.92         2.17         0.66         1.02         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
        1.48         0.82         3.52         1.35         1.32         1.12 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41         7.13        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       26.56        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        10.06         5.13         6.71        21.11       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       30.31         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
        0.03         5.42        29.72         0.07         4.34        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI 
        5.88         6.25        19.59         3.88        93.99        61.28 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       34.52        29.03        53.52        46.03        23.28        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       49.55        39.78        23.24        44.88        42.58 

  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                        195.85 
  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE 
                        15.78                         15.88 
[1] "0.1 - 147.3 (15.8)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.8"
D34V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  6(4Q21.3) MUTATED   37 16     5
  DEL PEAK  6(4Q21.3) WILD-TYPE 84 34     6
D34V3, multiclass
       clus
vv      DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  T1                             37                            84
  T2                             16                            34
  T3+T4                           5                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   26 21
  DEL PEAK  6(4Q21.3) WILD-TYPE 85 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     26   21
  DEL PEAK  6(4Q21.3) WILD-TYPE   85   26
   clus
vv  DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  0                          26                            85
  1                          21                            26
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  6(4Q21.3) MUTATED   30  4 26
  DEL PEAK  6(4Q21.3) WILD-TYPE 61  4 67
D34V5, multiclass
    clus
vv   DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  M0                          30                            61
  M1                           4                             4
  MX                          26                            67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(4Q21.3) MUTATED               1                               76
  DEL PEAK  6(4Q21.3) WILD-TYPE             4                              121
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  6(4Q21.3) MUTATED                                               1
  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                                              1
  DEL PEAK  6(4Q21.3) WILD-TYPE                                            5
D34V6, multiclass
                                               clus
vv                                              DEL PEAK  6(4Q21.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       76
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  6(4Q21.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        121
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q21.3) MUTATED    12  69
  DEL PEAK  6(4Q21.3) WILD-TYPE  18 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     12   69
  DEL PEAK  6(4Q21.3) WILD-TYPE   18  139
     clus
vv    DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  NO                           12                            18
  YES                          69                           139
[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                          12
  DEL PEAK  6(4Q21.3) WILD-TYPE                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(4Q21.3) MUTATED                                           0    55
  DEL PEAK  6(4Q21.3) WILD-TYPE                                         1   114
D34V10, multiclass
                                           clus
vv                                          DEL PEAK  6(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              55
                                           clus
vv                                          DEL PEAK  6(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            12
  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"
D34V11, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED    4 50
  DEL PEAK  6(4Q21.3) WILD-TYPE 12 99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED      4   50
  DEL PEAK  6(4Q21.3) WILD-TYPE   12   99
                        clus
vv                       DEL PEAK  6(4Q21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       DEL PEAK  6(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                            99
[1] 2 2
[1] FALSE
D34V12, continuous
D34V13, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   20 10
  DEL PEAK  6(4Q21.3) WILD-TYPE 51 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     20   10
  DEL PEAK  6(4Q21.3) WILD-TYPE   51   15
            clus
vv           DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  TUMOR FREE                          20                            51
  WITH TUMOR                          10                            15
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  6(4Q21.3) MUTATED       12      2       1      3       2
  DEL PEAK  6(4Q21.3) WILD-TYPE     11      3       0      7       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  6(4Q21.3) MUTATED              55       6
  DEL PEAK  6(4Q21.3) WILD-TYPE           123       8
D34V14, multiclass
               clus
vv              DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  BRAZIL                                 12                            11
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  3                             7
  UKRAINE                                 2                             5
  UNITED STATES                          55                           123
  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 30 44  0  4
  DEL PEAK  6(4Q21.3) WILD-TYPE 15 76 53  1 10
D34V15, multiclass
    clus
vv   DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  G1                           2                            15
  G2                          30                            76
  G3                          44                            53
  G4                           0                             1
  GX                           4                            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V16, continuous
D34V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  6(4Q21.3) MUTATED                                             7
  DEL PEAK  6(4Q21.3) WILD-TYPE                                          24
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  6(4Q21.3) MUTATED                                        3
  DEL PEAK  6(4Q21.3) WILD-TYPE                                      5
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  6(4Q21.3) MUTATED                                                 2
  DEL PEAK  6(4Q21.3) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  6(4Q21.3) MUTATED               20                  31
  DEL PEAK  6(4Q21.3) WILD-TYPE             32                  81
D34V18, multiclass
                                                 clus
vv                                                DEL PEAK  6(4Q21.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           20
  LIFELONG NON-SMOKER                                                      31
                                                 clus
vv                                                DEL PEAK  6(4Q21.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             32
  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"
D34V19, continuous
D34V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  6(4Q21.3) MUTATED             7       26             4        9
  DEL PEAK  6(4Q21.3) WILD-TYPE          12       49             8        3
D34V21, multiclass
               clus
vv              DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               26                            49
  EXTERNAL BEAM                           4                             8
  INTERNAL                                9                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    11            10
  DEL PEAK  6(4Q21.3) WILD-TYPE                  17             6
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                          11                            17
  REGIONAL SITE                                10                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V24, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   15  2
  DEL PEAK  6(4Q21.3) WILD-TYPE 19  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     15    2
  DEL PEAK  6(4Q21.3) WILD-TYPE   19    1
     clus
vv    DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  CGY                          15                            19
  GY                            2                             1
[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                                     3
  DEL PEAK  6(4Q21.3) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  6(4Q21.3) MUTATED                        10                       1
  DEL PEAK  6(4Q21.3) WILD-TYPE                      19                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  6(4Q21.3) MUTATED                         1
  DEL PEAK  6(4Q21.3) WILD-TYPE                       6
D34V31, multiclass
                                     clus
vv                                    DEL PEAK  6(4Q21.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                      10
  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                                        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  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                                                5
  DEL PEAK  6(4Q21.3) WILD-TYPE                                             11
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  6(4Q21.3) MUTATED                                                                                  20
  DEL PEAK  6(4Q21.3) WILD-TYPE                                                                                48
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  6(4Q21.3) MUTATED                                                                                             33
  DEL PEAK  6(4Q21.3) WILD-TYPE                                                                                           72
D34V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  6(4Q21.3) 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)                                     20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          33
                                                                                              clus
vv                                                                                             DEL PEAK  6(4Q21.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       48
  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"
D34V33, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   18 23
  DEL PEAK  6(4Q21.3) WILD-TYPE 50 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     18   23
  DEL PEAK  6(4Q21.3) WILD-TYPE   50   47
         clus
vv        DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  ABSENT                           18                            50
  PRESENT                          23                            47
[1] 2 2
[1] FALSE
D34V34, continuous
D34V35, continuous
D34V36, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   17 34
  DEL PEAK  6(4Q21.3) WILD-TYPE 26 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     17   34
  DEL PEAK  6(4Q21.3) WILD-TYPE   26   60
                                          clus
vv                                         DEL PEAK  6(4Q21.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          34
                                          clus
vv                                         DEL PEAK  6(4Q21.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            60
[1] 2 2
[1] FALSE
D34V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  6(4Q21.3) MUTATED              4          15         18
  DEL PEAK  6(4Q21.3) WILD-TYPE            6          34         39
D34V38, multiclass
              clus
vv             DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  CURRENT USER                           4                             6
  FORMER USER                           15                            34
  NEVER USED                            18                            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V39, continuous
D34V40, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q21.3) MUTATED   21  7
  DEL PEAK  6(4Q21.3) WILD-TYPE 68  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q21.3) MUTATED     21    7
  DEL PEAK  6(4Q21.3) WILD-TYPE   68    9
         clus
vv        DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  ABSENT                           21                            68
  PRESENT                           7                             9
[1] 2 2
[1] FALSE
D34V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  6(4Q21.3) MUTATED     0    0  12   18    7  2   1    2    1  10  0
  DEL PEAK  6(4Q21.3) WILD-TYPE   1    1  18   47   17  2   7    5    8  12  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  6(4Q21.3) MUTATED     4  1   1  2
  DEL PEAK  6(4Q21.3) WILD-TYPE   4  1   0 12
D34V42, multiclass
      clus
vv     DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                           12                            18
  T1B1                          18                            47
  T1B2                           7                            17
  T2                             2                             2
  T2A                            1                             7
  T2A1                           2                             5
  T2A2                           1                             8
  T2B                           10                            12
  T3                             0                             1
  T3B                            4                             4
  T4                             1                             1
  TIS                            1                             0
  TX                             2                            12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  6(4Q21.3) MUTATED         0        1         0         1       11
  DEL PEAK  6(4Q21.3) WILD-TYPE       4        1         1         0       20
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  6(4Q21.3) MUTATED          19        12        0         2
  DEL PEAK  6(4Q21.3) WILD-TYPE        50        20        3         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  6(4Q21.3) MUTATED            2          1        13         0
  DEL PEAK  6(4Q21.3) WILD-TYPE          3          6        14         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  6(4Q21.3) MUTATED           11         2         2
  DEL PEAK  6(4Q21.3) WILD-TYPE         23         1         5
D34V44, multiclass
            clus
vv           DEL PEAK  6(4Q21.3) MUTATED DEL PEAK  6(4Q21.3) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                             1                             1
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            11                            20
  STAGE IB1                           19                            50
  STAGE IB2                           12                            20
  STAGE II                             0                             3
  STAGE IIA                            2                             4
  STAGE IIA1                           2                             3
  STAGE IIA2                           1                             6
  STAGE IIB                           13                            14
  STAGE III                            0                             1
  STAGE IIIB                          11                            23
  STAGE IVA                            2                             1
  STAGE IVB                            2                             5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK  7(4Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q22.1) MUTATED    56  20
  DEL PEAK  7(4Q22.1) WILD-TYPE 127  30
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           76                           157 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           20                            30 
$`DEL PEAK  7(4Q22.1) MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MI 
       49.48        23.67        11.44         5.46        31.40        35.61 
TCGA-C5-A1ML TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE 
       20.91        73.18        73.45        83.05        52.01        18.02 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 
       15.48        20.35       147.35        17.19        60.69         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8ZZ 
       13.61         2.73        45.83        99.91        27.52        20.91 
TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 
       58.88        40.04        87.75        12.36         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
        1.81        14.89        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA 
       26.27         1.51         0.59         0.59         1.45        16.08 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A3NI 
        1.18         2.24         0.10        20.35         6.94         1.45 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3LK TCGA-JW-A5VK TCGA-JX-A5QV 
        1.97         9.01        21.67        26.56        20.48         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73S 
       11.28         0.89         5.49         2.96        13.35        10.39 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI 
       11.67        12.16        10.03        34.52        20.22        14.07 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A957 
       19.96        32.15        49.55        31.27         4.73        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

$`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 
        0.82        17.85        20.42       182.93       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
      134.33        85.55        94.95        50.99         8.35        75.78 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       23.51         6.12         4.47         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         0.76         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35        12.66        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PL 
       15.02        14.99        14.96        13.58         6.64         0.43 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        0.13         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 
        0.07         0.10         0.10         0.03         7.92        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
        3.52         1.35         1.32         1.12        25.41         7.13 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        21.44        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-LP-A5U2 
        6.71        21.11       195.85        30.31         0.07         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.82         0.20        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        0.07         4.34        15.58        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
       17.56        14.07        15.88         5.88         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q9 
        3.88        93.99        61.28        29.03        53.52        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       23.28        11.51        39.78        16.64        23.24        44.88 
TCGA-VS-A954 
       42.58 

  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                        195.85 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                       16.635                        15.580 
[1] "0.1 - 147.3 (16.6)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.6"
D35V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  7(4Q22.1) MUTATED   35 15     5
  DEL PEAK  7(4Q22.1) WILD-TYPE 86 35     6
D35V3, multiclass
       clus
vv      DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  T1                             35                            86
  T2                             15                            35
  T3+T4                           5                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   25 19
  DEL PEAK  7(4Q22.1) WILD-TYPE 86 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     25   19
  DEL PEAK  7(4Q22.1) WILD-TYPE   86   28
   clus
vv  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  0                          25                            86
  1                          19                            28
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  7(4Q22.1) MUTATED   29  4 25
  DEL PEAK  7(4Q22.1) WILD-TYPE 62  4 68
D35V5, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  M0                          29                            62
  M1                           4                             4
  MX                          25                            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(4Q22.1) MUTATED               1                               74
  DEL PEAK  7(4Q22.1) WILD-TYPE             4                              123
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  7(4Q22.1) MUTATED                                               1
  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                                              1
  DEL PEAK  7(4Q22.1) WILD-TYPE                                            5
D35V6, multiclass
                                               clus
vv                                              DEL PEAK  7(4Q22.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       74
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  7(4Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    11  68
  DEL PEAK  7(4Q22.1) WILD-TYPE  19 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     11   68
  DEL PEAK  7(4Q22.1) WILD-TYPE   19  140
     clus
vv    DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  NO                           11                            19
  YES                          68                           140
[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                          11
  DEL PEAK  7(4Q22.1) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(4Q22.1) MUTATED                                           0    56
  DEL PEAK  7(4Q22.1) WILD-TYPE                                         1   113
D35V10, multiclass
                                           clus
vv                                          DEL PEAK  7(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              56
                                           clus
vv                                          DEL PEAK  7(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED     4  47
  DEL PEAK  7(4Q22.1) WILD-TYPE  12 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED      4   47
  DEL PEAK  7(4Q22.1) WILD-TYPE   12  102
                        clus
vv                       DEL PEAK  7(4Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          47
                        clus
vv                       DEL PEAK  7(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           102
[1] 2 2
[1] FALSE
D35V12, continuous
D35V13, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   19  9
  DEL PEAK  7(4Q22.1) WILD-TYPE 52 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     19    9
  DEL PEAK  7(4Q22.1) WILD-TYPE   52   16
            clus
vv           DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  TUMOR FREE                          19                            52
  WITH TUMOR                           9                            16
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  7(4Q22.1) MUTATED       13      2       1      3       2
  DEL PEAK  7(4Q22.1) WILD-TYPE     10      3       0      7       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  7(4Q22.1) MUTATED              54       4
  DEL PEAK  7(4Q22.1) WILD-TYPE           124      10
D35V14, multiclass
               clus
vv              DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  BRAZIL                                 13                            10
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  3                             7
  UKRAINE                                 2                             5
  UNITED STATES                          54                           124
  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 26 46  0  4
  DEL PEAK  7(4Q22.1) WILD-TYPE 15 80 51  1 10
D35V15, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  G1                           2                            15
  G2                          26                            80
  G3                          46                            51
  G4                           0                             1
  GX                           4                            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V16, continuous
D35V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  7(4Q22.1) MUTATED                                             8
  DEL PEAK  7(4Q22.1) WILD-TYPE                                          23
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  7(4Q22.1) MUTATED                                        2
  DEL PEAK  7(4Q22.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  7(4Q22.1) MUTATED                                                 1
  DEL PEAK  7(4Q22.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  7(4Q22.1) MUTATED               20                  28
  DEL PEAK  7(4Q22.1) WILD-TYPE             32                  84
D35V18, multiclass
                                                 clus
vv                                                DEL PEAK  7(4Q22.1) 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                                                           20
  LIFELONG NON-SMOKER                                                      28
                                                 clus
vv                                                DEL PEAK  7(4Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             32
  LIFELONG NON-SMOKER                                                        84
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V19, continuous
D35V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  7(4Q22.1) MUTATED             6       28             4        8
  DEL PEAK  7(4Q22.1) WILD-TYPE          13       47             8        4
D35V21, multiclass
               clus
vv              DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  COMBINATION                             6                            13
  EXTERNAL                               28                            47
  EXTERNAL BEAM                           4                             8
  INTERNAL                                8                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    10            11
  DEL PEAK  7(4Q22.1) WILD-TYPE                  18             5
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                          10                            18
  REGIONAL SITE                                11                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V24, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   16  2
  DEL PEAK  7(4Q22.1) WILD-TYPE 18  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     16    2
  DEL PEAK  7(4Q22.1) WILD-TYPE   18    1
     clus
vv    DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  CGY                          16                            18
  GY                            2                             1
[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                                     4
  DEL PEAK  7(4Q22.1) WILD-TYPE                                   2
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  7(4Q22.1) MUTATED                         8                       0
  DEL PEAK  7(4Q22.1) WILD-TYPE                      21                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  7(4Q22.1) MUTATED                         1
  DEL PEAK  7(4Q22.1) WILD-TYPE                       6
D35V31, multiclass
                                     clus
vv                                    DEL PEAK  7(4Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                       8
  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                                        21
  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  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                                                6
  DEL PEAK  7(4Q22.1) WILD-TYPE                                             10
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  7(4Q22.1) MUTATED                                                                                  20
  DEL PEAK  7(4Q22.1) WILD-TYPE                                                                                48
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  7(4Q22.1) MUTATED                                                                                             32
  DEL PEAK  7(4Q22.1) WILD-TYPE                                                                                           73
D35V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  7(4Q22.1) 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)                                     20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          32
                                                                                              clus
vv                                                                                             DEL PEAK  7(4Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V33, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   16 21
  DEL PEAK  7(4Q22.1) WILD-TYPE 52 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     16   21
  DEL PEAK  7(4Q22.1) WILD-TYPE   52   49
         clus
vv        DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  ABSENT                           16                            52
  PRESENT                          21                            49
[1] 2 2
[1] FALSE
D35V34, continuous
D35V35, continuous
D35V36, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   15 32
  DEL PEAK  7(4Q22.1) WILD-TYPE 28 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     15   32
  DEL PEAK  7(4Q22.1) WILD-TYPE   28   62
                                          clus
vv                                         DEL PEAK  7(4Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          32
                                          clus
vv                                         DEL PEAK  7(4Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            62
[1] 2 2
[1] FALSE
D35V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  7(4Q22.1) MUTATED              4          14         19
  DEL PEAK  7(4Q22.1) WILD-TYPE            6          35         38
D35V38, multiclass
              clus
vv             DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  CURRENT USER                           4                             6
  FORMER USER                           14                            35
  NEVER USED                            19                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V39, continuous
D35V40, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q22.1) MUTATED   20  5
  DEL PEAK  7(4Q22.1) WILD-TYPE 69 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     20    5
  DEL PEAK  7(4Q22.1) WILD-TYPE   69   11
         clus
vv        DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  ABSENT                           20                            69
  PRESENT                           5                            11
[1] 2 2
[1] FALSE
D35V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  7(4Q22.1) MUTATED     0    0  11   17    7  2   1    2    1   9  0
  DEL PEAK  7(4Q22.1) WILD-TYPE   1    1  19   48   17  2   7    5    8  13  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  7(4Q22.1) MUTATED     5  0   1  3
  DEL PEAK  7(4Q22.1) WILD-TYPE   3  2   0 11
D35V42, multiclass
      clus
vv     DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                           11                            19
  T1B1                          17                            48
  T1B2                           7                            17
  T2                             2                             2
  T2A                            1                             7
  T2A1                           2                             5
  T2A2                           1                             8
  T2B                            9                            13
  T3                             0                             1
  T3B                            5                             3
  T4                             0                             2
  TIS                            1                             0
  TX                             3                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  7(4Q22.1) MUTATED         0        1         0         1       10
  DEL PEAK  7(4Q22.1) WILD-TYPE       4        1         1         0       21
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  7(4Q22.1) MUTATED          18        12        0         2
  DEL PEAK  7(4Q22.1) WILD-TYPE        51        20        3         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  7(4Q22.1) MUTATED            2          1        14         0
  DEL PEAK  7(4Q22.1) WILD-TYPE          3          6        13         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  7(4Q22.1) MUTATED           12         0         2
  DEL PEAK  7(4Q22.1) WILD-TYPE         22         3         5
D35V44, multiclass
            clus
vv           DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                             1                             1
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            10                            21
  STAGE IB1                           18                            51
  STAGE IB2                           12                            20
  STAGE II                             0                             3
  STAGE IIA                            2                             4
  STAGE IIA1                           2                             3
  STAGE IIA2                           1                             6
  STAGE IIB                           14                            13
  STAGE III                            0                             1
  STAGE IIIB                          12                            22
  STAGE IVA                            0                             3
  STAGE IVB                            2                             5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK  8(4Q35.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q35.2) MUTATED    67  22
  DEL PEAK  8(4Q35.2) WILD-TYPE 116  28
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                           89                           144 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                           22                            28 
$`DEL PEAK  8(4Q35.2) MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
       57.04        23.67        11.44         5.46        67.46        31.40 
TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV 
       57.73        35.61        20.91        40.93        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       83.05        52.01        18.02       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
      147.35        17.19        60.69         9.34        13.61         2.73 
TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
       45.83        99.91        27.52        20.91         4.47        58.88 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HT 
       40.04        87.75        16.83         0.76        12.36         0.62 
TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 
       13.05         1.35        14.50         1.81        12.66        14.89 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RJ 
       26.27         1.51         0.59         0.59         1.45         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-FU-A2QG 
        2.24         0.10        20.35         6.94         4.73         0.92 
TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-JW-A5VG 
        1.45         1.97         9.01        21.67       137.16        27.42 
TCGA-JW-A5VK TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MY-A913 
       20.48        21.11         7.99        11.28         0.89         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD 
        2.96        13.35         6.25        10.39        19.59        11.67 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8QM 
       12.16        10.03        20.22        14.07        32.15        31.27 
TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
        4.73        42.08        39.35        38.96        18.05 

$`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         0.82        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC 
      182.93       154.32       101.82        85.55        94.95        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KK 
        8.35        75.78        23.51         6.12         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         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E 
        0.82         1.18        14.50         1.35        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PL 
        1.48        13.91        15.02        13.58         6.64         0.43 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
       23.70         0.07         0.10         0.10         0.03         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       14.70        19.79         6.12         1.22        23.84         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
        1.35         1.32         1.12        25.41         7.13        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-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       21.44        15.58        10.06         5.13         6.71       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       30.31         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
        0.03         5.42        29.72         0.07         4.34        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
        5.88         3.88        93.99        61.28        34.52        29.03 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        53.52        46.03        23.28        11.51        49.55 
TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       39.78        16.64        23.24        44.88        42.58        43.82 

  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                        195.85 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                        14.96                         16.11 
[1] "0.1 - 147.3 (15.0)" "0.0 - 195.8 (16.1)"
[1] "hr=" "1.5"
D36V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  8(4Q35.2) MUTATED   47 14     4
  DEL PEAK  8(4Q35.2) WILD-TYPE 74 36     7
D36V3, multiclass
       clus
vv      DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  T1                             47                            74
  T2                             14                            36
  T3+T4                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   35 20
  DEL PEAK  8(4Q35.2) WILD-TYPE 76 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     35   20
  DEL PEAK  8(4Q35.2) WILD-TYPE   76   27
   clus
vv  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  0                          35                            76
  1                          20                            27
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  8(4Q35.2) MUTATED   39  3 25
  DEL PEAK  8(4Q35.2) WILD-TYPE 52  5 68
D36V5, multiclass
    clus
vv   DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  M0                          39                            52
  M1                           3                             5
  MX                          25                            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(4Q35.2) MUTATED               1                               84
  DEL PEAK  8(4Q35.2) WILD-TYPE             4                              113
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  8(4Q35.2) MUTATED                                               1
  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                                              1
  DEL PEAK  8(4Q35.2) WILD-TYPE                                            5
D36V6, multiclass
                                               clus
vv                                              DEL PEAK  8(4Q35.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  8(4Q35.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        113
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  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"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q35.2) MUTATED    12  80
  DEL PEAK  8(4Q35.2) WILD-TYPE  18 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     12   80
  DEL PEAK  8(4Q35.2) WILD-TYPE   18  128
     clus
vv    DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  NO                           12                            18
  YES                          80                           128
[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                          11
  DEL PEAK  8(4Q35.2) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(4Q35.2) MUTATED                                           0    67
  DEL PEAK  8(4Q35.2) WILD-TYPE                                         1   102
D36V10, multiclass
                                           clus
vv                                          DEL PEAK  8(4Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              67
                                           clus
vv                                          DEL PEAK  8(4Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               102
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED    4 60
  DEL PEAK  8(4Q35.2) WILD-TYPE 12 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED      4   60
  DEL PEAK  8(4Q35.2) WILD-TYPE   12   89
                        clus
vv                       DEL PEAK  8(4Q35.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       DEL PEAK  8(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                            89
[1] 2 2
[1] FALSE
D36V12, continuous
D36V13, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   27  9
  DEL PEAK  8(4Q35.2) WILD-TYPE 44 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     27    9
  DEL PEAK  8(4Q35.2) WILD-TYPE   44   16
            clus
vv           DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  TUMOR FREE                          27                            44
  WITH TUMOR                           9                            16
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  8(4Q35.2) MUTATED        9      2       1      5       3
  DEL PEAK  8(4Q35.2) WILD-TYPE     14      3       0      5       4
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  8(4Q35.2) MUTATED              66       6
  DEL PEAK  8(4Q35.2) WILD-TYPE           112       8
D36V14, multiclass
               clus
vv              DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  BRAZIL                                  9                            14
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  5                             5
  UKRAINE                                 3                             4
  UNITED STATES                          66                           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  8(4Q35.2) MUTATED    4 33 49  0  5
  DEL PEAK  8(4Q35.2) WILD-TYPE 13 73 48  1  9
D36V15, multiclass
    clus
vv   DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  G1                           4                            13
  G2                          33                            73
  G3                          49                            48
  G4                           0                             1
  GX                           5                             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V16, continuous
D36V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  8(4Q35.2) MUTATED                                             8
  DEL PEAK  8(4Q35.2) WILD-TYPE                                          23
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  8(4Q35.2) MUTATED                                        2
  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                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  8(4Q35.2) MUTATED               23                  38
  DEL PEAK  8(4Q35.2) WILD-TYPE             29                  74
D36V18, multiclass
                                                 clus
vv                                                DEL PEAK  8(4Q35.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           23
  LIFELONG NON-SMOKER                                                      38
                                                 clus
vv                                                DEL PEAK  8(4Q35.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             29
  LIFELONG NON-SMOKER                                                        74
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V19, continuous
D36V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  8(4Q35.2) MUTATED             8       33             4        7
  DEL PEAK  8(4Q35.2) WILD-TYPE          11       42             8        5
D36V21, multiclass
               clus
vv              DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  COMBINATION                             8                            11
  EXTERNAL                               33                            42
  EXTERNAL BEAM                           4                             8
  INTERNAL                                7                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    14             8
  DEL PEAK  8(4Q35.2) WILD-TYPE                  14             8
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                          14                            14
  REGIONAL SITE                                 8                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V24, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   15  3
  DEL PEAK  8(4Q35.2) WILD-TYPE 19  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     15    3
  DEL PEAK  8(4Q35.2) WILD-TYPE   19    0
     clus
vv    DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  CGY                          15                            19
  GY                            3                             0
[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                                     3
  DEL PEAK  8(4Q35.2) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  8(4Q35.2) MUTATED                        10                       0
  DEL PEAK  8(4Q35.2) WILD-TYPE                      19                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  8(4Q35.2) MUTATED                         1
  DEL PEAK  8(4Q35.2) WILD-TYPE                       6
D36V31, multiclass
                                     clus
vv                                    DEL PEAK  8(4Q35.2) 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  8(4Q35.2) 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)
  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                                                9
  DEL PEAK  8(4Q35.2) WILD-TYPE                                              7
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  8(4Q35.2) MUTATED                                                                                  22
  DEL PEAK  8(4Q35.2) WILD-TYPE                                                                                46
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  8(4Q35.2) MUTATED                                                                                             38
  DEL PEAK  8(4Q35.2) WILD-TYPE                                                                                           67
D36V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  8(4Q35.2) 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)                          38
                                                                                              clus
vv                                                                                             DEL PEAK  8(4Q35.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       46
  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"
D36V33, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   23 27
  DEL PEAK  8(4Q35.2) WILD-TYPE 45 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     23   27
  DEL PEAK  8(4Q35.2) WILD-TYPE   45   43
         clus
vv        DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  ABSENT                           23                            45
  PRESENT                          27                            43
[1] 2 2
[1] FALSE
D36V34, continuous
D36V35, continuous
D36V36, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   22 39
  DEL PEAK  8(4Q35.2) WILD-TYPE 21 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     22   39
  DEL PEAK  8(4Q35.2) WILD-TYPE   21   55
                                          clus
vv                                         DEL PEAK  8(4Q35.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          39
                                          clus
vv                                         DEL PEAK  8(4Q35.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            55
[1] 2 2
[1] FALSE
D36V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  8(4Q35.2) MUTATED              4          19         23
  DEL PEAK  8(4Q35.2) WILD-TYPE            6          30         34
D36V38, multiclass
              clus
vv             DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  CURRENT USER                           4                             6
  FORMER USER                           19                            30
  NEVER USED                            23                            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"
D36V39, continuous
D36V40, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED   30  3
  DEL PEAK  8(4Q35.2) WILD-TYPE 59 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED     30    3
  DEL PEAK  8(4Q35.2) WILD-TYPE   59   13
         clus
vv        DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  ABSENT                           30                            59
  PRESENT                           3                            13
[1] 2 2
[1] FALSE
D36V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  8(4Q35.2) MUTATED     0    0  15   26    6  2   2    3    1   6  0
  DEL PEAK  8(4Q35.2) WILD-TYPE   1    1  15   39   18  2   6    4    8  16  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  8(4Q35.2) MUTATED     4  0   1  3
  DEL PEAK  8(4Q35.2) WILD-TYPE   4  2   0 11
D36V42, multiclass
      clus
vv     DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                           15                            15
  T1B1                          26                            39
  T1B2                           6                            18
  T2                             2                             2
  T2A                            2                             6
  T2A1                           3                             4
  T2A2                           1                             8
  T2B                            6                            16
  T3                             0                             1
  T3B                            4                             4
  T4                             0                             2
  TIS                            1                             0
  TX                             3                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        1         1         0       16
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  8(4Q35.2) MUTATED          26        12        0         3
  DEL PEAK  8(4Q35.2) WILD-TYPE        43        20        3         3
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  8(4Q35.2) MUTATED            2          0        11         0
  DEL PEAK  8(4Q35.2) WILD-TYPE          3          7        16         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  8(4Q35.2) MUTATED           13         1         2
  DEL PEAK  8(4Q35.2) WILD-TYPE         21         2         5
D36V44, multiclass
            clus
vv           DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                             1                             1
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            15                            16
  STAGE IB1                           26                            43
  STAGE IB2                           12                            20
  STAGE II                             0                             3
  STAGE IIA                            3                             3
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           11                            16
  STAGE III                            0                             1
  STAGE IIIB                          13                            21
  STAGE IVA                            1                             2
  STAGE IVB                            2                             5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(5Q12.1) MUTATED    42  17
  DEL PEAK  9(5Q12.1) WILD-TYPE 141  33
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           59                           174 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           17                            33 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M6 
       11.44        68.84       144.16       177.04         5.46        31.40 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A3HE 
       30.21        35.01        38.99        35.61        40.93        18.02 
TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-DG-A2KJ TCGA-DR-A0ZL 
      154.32        17.19         9.34        45.83        58.88        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR 
       36.76         2.66       117.99         0.76        12.36         1.32 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2GZ 
        1.35        14.50        14.89        14.96         0.36        12.59 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN 
        6.64         0.43         1.18         2.24         0.10         0.03 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV 
       20.35        23.84         0.92         0.66         1.45         1.97 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-JW-A5VI TCGA-LP-A4AW TCGA-MY-A913 
       25.41         7.13        21.67        24.56         0.89         5.49 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF 
       15.95         3.39        20.22        14.07        19.96        49.55 
TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       39.78         4.73        43.82        38.96        18.05 

$`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         0.82 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        17.85        20.42       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48        20.35       147.35        85.55        60.69        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        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-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         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B 
        0.62        13.05         1.18        14.50         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.66        12.82         0.26         1.48        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-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        23.70         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         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        4.73         1.22         2.17         1.02         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        26.56        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        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        5.13         6.71        21.11       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       11.28         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        13.35        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM 
       53.52        32.15        46.03        23.28        11.51        31.27 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 
       16.64        23.24        44.88        42.58        42.08        39.35 

  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                        195.85 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                        15.95                         15.73 
[1] "0.0 - 177.0 (15.9)" "0.0 - 195.8 (15.7)"
[1] "hr=" "1.6"
D37V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  9(5Q12.1) MUTATED   31 10     3
  DEL PEAK  9(5Q12.1) WILD-TYPE 90 40     8
D37V3, multiclass
       clus
vv      DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T1                             31                            90
  T2                             10                            40
  T3+T4                           3                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   24 13
  DEL PEAK  9(5Q12.1) WILD-TYPE 87 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     24   13
  DEL PEAK  9(5Q12.1) WILD-TYPE   87   34
   clus
vv  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  0                          24                            87
  1                          13                            34
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  9(5Q12.1) MUTATED   21  2 24
  DEL PEAK  9(5Q12.1) WILD-TYPE 70  6 69
D37V5, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  M0                          21                            70
  M1                           2                             6
  MX                          24                            69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(5Q12.1) MUTATED               1                               56
  DEL PEAK  9(5Q12.1) WILD-TYPE             4                              141
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  9(5Q12.1) MUTATED                                               0
  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                                              1
  DEL PEAK  9(5Q12.1) WILD-TYPE                                            5
D37V6, multiclass
                                               clus
vv                                              DEL PEAK  9(5Q12.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       56
  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                                              DEL PEAK  9(5Q12.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        141
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    12  49
  DEL PEAK  9(5Q12.1) WILD-TYPE  18 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     12   49
  DEL PEAK  9(5Q12.1) WILD-TYPE   18  159
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                           12                            18
  YES                          49                           159
[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                           6
  DEL PEAK  9(5Q12.1) WILD-TYPE                        18
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(5Q12.1) MUTATED                                           0    48
  DEL PEAK  9(5Q12.1) WILD-TYPE                                         1   121
D37V10, multiclass
                                           clus
vv                                          DEL PEAK  9(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              48
                                           clus
vv                                          DEL PEAK  9(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               121
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED     2  41
  DEL PEAK  9(5Q12.1) WILD-TYPE  14 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      2   41
  DEL PEAK  9(5Q12.1) WILD-TYPE   14  108
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           108
[1] 2 2
[1] FALSE
D37V12, continuous
D37V13, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   14 12
  DEL PEAK  9(5Q12.1) WILD-TYPE 57 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     14   12
  DEL PEAK  9(5Q12.1) WILD-TYPE   57   13
            clus
vv           DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  TUMOR FREE                          14                            57
  WITH TUMOR                          12                            13
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK  9(5Q12.1) MUTATED        8      1       0      5       1
  DEL PEAK  9(5Q12.1) WILD-TYPE     15      4       1      5       6
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK  9(5Q12.1) MUTATED              43       3
  DEL PEAK  9(5Q12.1) WILD-TYPE           135      11
D37V14, multiclass
               clus
vv              DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  BRAZIL                                  8                            15
  CANADA                                  1                             4
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 1                             6
  UNITED STATES                          43                           135
  VIETNAM                                 3                            11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  9(5Q12.1) MUTATED    1 26 29  0  3
  DEL PEAK  9(5Q12.1) WILD-TYPE 16 80 68  1 11
D37V15, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  G1                           1                            16
  G2                          26                            80
  G3                          29                            68
  G4                           0                             1
  GX                           3                            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V16, continuous
D37V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  9(5Q12.1) MUTATED                                             6
  DEL PEAK  9(5Q12.1) WILD-TYPE                                          25
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  9(5Q12.1) MUTATED                                        2
  DEL PEAK  9(5Q12.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  9(5Q12.1) MUTATED                                                 1
  DEL PEAK  9(5Q12.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  9(5Q12.1) MUTATED               12                  28
  DEL PEAK  9(5Q12.1) WILD-TYPE             40                  84
D37V18, multiclass
                                                 clus
vv                                                DEL PEAK  9(5Q12.1) 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                                                           12
  LIFELONG NON-SMOKER                                                      28
                                                 clus
vv                                                DEL PEAK  9(5Q12.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             40
  LIFELONG NON-SMOKER                                                        84
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V19, continuous
D37V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  9(5Q12.1) MUTATED             7       14             5        2
  DEL PEAK  9(5Q12.1) WILD-TYPE          12       61             7       10
D37V21, multiclass
               clus
vv              DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               14                            61
  EXTERNAL BEAM                           5                             7
  INTERNAL                                2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     6             3
  DEL PEAK  9(5Q12.1) WILD-TYPE                  22            13
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                           6                            22
  REGIONAL SITE                                 3                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V24, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED    9  1
  DEL PEAK  9(5Q12.1) WILD-TYPE 25  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      9    1
  DEL PEAK  9(5Q12.1) WILD-TYPE   25    2
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  CGY                           9                            25
  GY                            1                             2
[1] 2 2
[1] FALSE
D37V25, continuous
D37V26, continuous
D37V27, continuous
D37V28, continuous
D37V29, continuous
D37V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                     2
  DEL PEAK  9(5Q12.1) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  9(5Q12.1) MUTATED                         8                       0
  DEL PEAK  9(5Q12.1) WILD-TYPE                      21                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  9(5Q12.1) MUTATED                         1
  DEL PEAK  9(5Q12.1) WILD-TYPE                       6
D37V31, multiclass
                                     clus
vv                                    DEL PEAK  9(5Q12.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  OTHER LOCATION, SPECIFY                                       8
  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                                        21
  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  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                                                6
  DEL PEAK  9(5Q12.1) WILD-TYPE                                             10
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  9(5Q12.1) MUTATED                                                                                  17
  DEL PEAK  9(5Q12.1) WILD-TYPE                                                                                51
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  9(5Q12.1) MUTATED                                                                                             24
  DEL PEAK  9(5Q12.1) WILD-TYPE                                                                                           81
D37V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  9(5Q12.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          24
                                                                                              clus
vv                                                                                             DEL PEAK  9(5Q12.1) 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)                                       51
  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"
D37V33, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   13 20
  DEL PEAK  9(5Q12.1) WILD-TYPE 55 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     13   20
  DEL PEAK  9(5Q12.1) WILD-TYPE   55   50
         clus
vv        DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  ABSENT                           13                            55
  PRESENT                          20                            50
[1] 2 2
[1] FALSE
D37V34, continuous
D37V35, continuous
D37V36, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   10 29
  DEL PEAK  9(5Q12.1) WILD-TYPE 33 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     10   29
  DEL PEAK  9(5Q12.1) WILD-TYPE   33   65
                                          clus
vv                                         DEL PEAK  9(5Q12.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          29
                                          clus
vv                                         DEL PEAK  9(5Q12.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            65
[1] 2 2
[1] FALSE
D37V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  9(5Q12.1) MUTATED              2          13         16
  DEL PEAK  9(5Q12.1) WILD-TYPE            8          36         41
D37V38, multiclass
              clus
vv             DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  CURRENT USER                           2                             8
  FORMER USER                           13                            36
  NEVER USED                            16                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V39, continuous
D37V40, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   20  4
  DEL PEAK  9(5Q12.1) WILD-TYPE 69 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     20    4
  DEL PEAK  9(5Q12.1) WILD-TYPE   69   12
         clus
vv        DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  ABSENT                           20                            69
  PRESENT                           4                            12
[1] 2 2
[1] FALSE
D37V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK  9(5Q12.1) MUTATED     0    0   8   17    6  0   1    2    0   7  0
  DEL PEAK  9(5Q12.1) WILD-TYPE   1    1  22   48   18  4   7    5    9  15  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK  9(5Q12.1) MUTATED     3  0   1  5
  DEL PEAK  9(5Q12.1) WILD-TYPE   5  2   0  9
D37V42, multiclass
      clus
vv     DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                            8                            22
  T1B1                          17                            48
  T1B2                           6                            18
  T2                             0                             4
  T2A                            1                             7
  T2A1                           2                             5
  T2A2                           0                             9
  T2B                            7                            15
  T3                             0                             1
  T3B                            3                             5
  T4                             0                             2
  TIS                            1                             0
  TX                             5                             9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  9(5Q12.1) MUTATED         1        1         0         1        8
  DEL PEAK  9(5Q12.1) WILD-TYPE       3        1         1         0       23
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  9(5Q12.1) MUTATED          14         8        1         1
  DEL PEAK  9(5Q12.1) WILD-TYPE        55        24        2         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  9(5Q12.1) MUTATED            2          0        12         0
  DEL PEAK  9(5Q12.1) WILD-TYPE          3          7        15         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  9(5Q12.1) MUTATED           10         0         0
  DEL PEAK  9(5Q12.1) WILD-TYPE         24         3         7
D37V44, multiclass
            clus
vv           DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                             1                             1
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             8                            23
  STAGE IB1                           14                            55
  STAGE IB2                            8                            24
  STAGE II                             1                             2
  STAGE IIA                            1                             5
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           12                            15
  STAGE III                            0                             1
  STAGE IIIB                          10                            24
  STAGE IVA                            0                             3
  STAGE IVB                            0                             7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK 10(5Q35.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q35.2) MUTATED    44  13
  DEL PEAK 10(5Q35.2) WILD-TYPE 139  37
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                           57                           176 
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                           13                            37 
$`DEL PEAK 10(5Q35.2) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 
       11.44       144.16       173.29         5.46        31.40        35.01 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7UC 
       38.99        35.61        40.93        18.02       154.32        17.19 
TCGA-C5-A7UE TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       85.55        58.88        87.75        36.76         2.66       117.99 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 
        0.76        12.36         1.32        14.50         1.35        14.50 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PL 
       14.89        14.96         0.36        12.59         6.64         0.43 
TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A23L 
        0.03         1.18         2.24         0.10        20.35        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC 
        0.92         0.66         1.35         1.97        25.41         7.13 
TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-JW-A5VI TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MY-A913 
       21.67       137.16        24.56         0.89         0.82         5.49 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A8QH 
       15.95         3.39        20.22        14.07        49.55        39.78 
TCGA-VS-A94Y TCGA-VS-A9U5 TCGA-WL-A834 
        4.73        38.96        18.05 

$`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         0.82        52.01        17.85        20.42       182.93 
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        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       94.95         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35        75.78        99.91        23.51        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91         4.47         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         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35         1.81        12.66        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       13.91        15.02        14.99        13.58        13.48        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       26.27         1.51         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN 
       16.08         0.07         4.04         0.36        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.07         0.10         0.03         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ 
       19.79         6.12         4.73         1.22         2.17         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        1.45         1.58         1.48         0.82         3.52         1.32 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.12         9.01        20.78        14.93         9.44       147.39 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        27.42         3.29        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y 
        7.99        11.28         0.07         0.30         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        13.35        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       19.96        53.52        32.15        46.03        23.28        11.51 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       31.27        16.64        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 
       43.82        39.35 

  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                        195.85 
  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE 
                        14.89                         16.11 
[1] "0.0 - 173.3 (14.9)" "0.0 - 195.8 (16.1)"
[1] "hr=" "1.1"
D38V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 10(5Q35.2) MUTATED   31  9     3
  DEL PEAK 10(5Q35.2) WILD-TYPE 90 41     8
D38V3, multiclass
       clus
vv      DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  T1                             31                            90
  T2                              9                            41
  T3+T4                           3                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   25 13
  DEL PEAK 10(5Q35.2) WILD-TYPE 86 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     25   13
  DEL PEAK 10(5Q35.2) WILD-TYPE   86   34
   clus
vv  DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  0                          25                            86
  1                          13                            34
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 10(5Q35.2) MUTATED   25  1 20
  DEL PEAK 10(5Q35.2) WILD-TYPE 66  7 73
D38V5, multiclass
    clus
vv   DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  M0                          25                            66
  M1                           1                             7
  MX                          20                            73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(5Q35.2) MUTATED               1                               51
  DEL PEAK 10(5Q35.2) WILD-TYPE             4                              146
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 10(5Q35.2) MUTATED                                               0
  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                                              1
  DEL PEAK 10(5Q35.2) WILD-TYPE                                            5
D38V6, multiclass
                                               clus
vv                                              DEL PEAK 10(5Q35.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       51
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK 10(5Q35.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        146
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q35.2) MUTATED    11  47
  DEL PEAK 10(5Q35.2) WILD-TYPE  19 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     11   47
  DEL PEAK 10(5Q35.2) WILD-TYPE   19  161
     clus
vv    DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  NO                           11                            19
  YES                          47                           161
[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                           5
  DEL PEAK 10(5Q35.2) WILD-TYPE                        19
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(5Q35.2) MUTATED                                           0    44
  DEL PEAK 10(5Q35.2) WILD-TYPE                                         1   125
D38V10, multiclass
                                           clus
vv                                          DEL PEAK 10(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              44
                                           clus
vv                                          DEL PEAK 10(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D38V11, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q35.2) MUTATED     2  40
  DEL PEAK 10(5Q35.2) WILD-TYPE  14 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED      2   40
  DEL PEAK 10(5Q35.2) WILD-TYPE   14  109
                        clus
vv                       DEL PEAK 10(5Q35.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       DEL PEAK 10(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           109
[1] 2 2
[1] FALSE
D38V12, continuous
D38V13, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   15 11
  DEL PEAK 10(5Q35.2) WILD-TYPE 56 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     15   11
  DEL PEAK 10(5Q35.2) WILD-TYPE   56   14
            clus
vv           DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  TUMOR FREE                          15                            56
  WITH TUMOR                          11                            14
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 10(5Q35.2) MUTATED        6      1       0      5       2
  DEL PEAK 10(5Q35.2) WILD-TYPE     17      4       1      5       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 10(5Q35.2) MUTATED              40       4
  DEL PEAK 10(5Q35.2) WILD-TYPE           138      10
D38V14, multiclass
               clus
vv              DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  BRAZIL                                  6                            17
  CANADA                                  1                             4
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 2                             5
  UNITED STATES                          40                           138
  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    1 22 31  0  3
  DEL PEAK 10(5Q35.2) WILD-TYPE 16 84 66  1 11
D38V15, multiclass
    clus
vv   DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  G1                           1                            16
  G2                          22                            84
  G3                          31                            66
  G4                           0                             1
  GX                           3                            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V16, continuous
D38V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 10(5Q35.2) MUTATED                                             6
  DEL PEAK 10(5Q35.2) WILD-TYPE                                          25
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 10(5Q35.2) MUTATED                                        1
  DEL PEAK 10(5Q35.2) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 10(5Q35.2) MUTATED                                                 1
  DEL PEAK 10(5Q35.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 10(5Q35.2) MUTATED               12                  27
  DEL PEAK 10(5Q35.2) WILD-TYPE             40                  85
D38V18, multiclass
                                                 clus
vv                                                DEL PEAK 10(5Q35.2) 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                                                           12
  LIFELONG NON-SMOKER                                                      27
                                                 clus
vv                                                DEL PEAK 10(5Q35.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             40
  LIFELONG NON-SMOKER                                                        85
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V19, continuous
D38V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 10(5Q35.2) MUTATED             7       15             4        1
  DEL PEAK 10(5Q35.2) WILD-TYPE          12       60             8       11
D38V21, multiclass
               clus
vv              DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               15                            60
  EXTERNAL BEAM                           4                             8
  INTERNAL                                1                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     6             2
  DEL PEAK 10(5Q35.2) WILD-TYPE                  22            14
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                           6                            22
  REGIONAL SITE                                 2                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V24, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED    8  1
  DEL PEAK 10(5Q35.2) WILD-TYPE 26  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED      8    1
  DEL PEAK 10(5Q35.2) WILD-TYPE   26    2
     clus
vv    DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  CGY                           8                            26
  GY                            1                             2
[1] 2 2
[1] FALSE
D38V25, continuous
D38V26, continuous
D38V27, continuous
D38V28, continuous
D38V29, continuous
D38V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                     2
  DEL PEAK 10(5Q35.2) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 10(5Q35.2) MUTATED                         5                       0
  DEL PEAK 10(5Q35.2) WILD-TYPE                      24                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 10(5Q35.2) MUTATED                         1
  DEL PEAK 10(5Q35.2) WILD-TYPE                       6
D38V31, multiclass
                                     clus
vv                                    DEL PEAK 10(5Q35.2) 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 10(5Q35.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                        24
  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 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                                             10
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 10(5Q35.2) MUTATED                                                                                  17
  DEL PEAK 10(5Q35.2) WILD-TYPE                                                                                51
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 10(5Q35.2) MUTATED                                                                                             25
  DEL PEAK 10(5Q35.2) WILD-TYPE                                                                                           80
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)                                     17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          25
                                                                                              clus
vv                                                                                             DEL PEAK 10(5Q35.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            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"
D38V33, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   13 21
  DEL PEAK 10(5Q35.2) WILD-TYPE 55 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     13   21
  DEL PEAK 10(5Q35.2) WILD-TYPE   55   49
         clus
vv        DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  ABSENT                           13                            55
  PRESENT                          21                            49
[1] 2 2
[1] FALSE
D38V34, continuous
D38V35, continuous
D38V36, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED    7 31
  DEL PEAK 10(5Q35.2) WILD-TYPE 36 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED      7   31
  DEL PEAK 10(5Q35.2) WILD-TYPE   36   63
                                          clus
vv                                         DEL PEAK 10(5Q35.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          31
                                          clus
vv                                         DEL PEAK 10(5Q35.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            63
[1] 2 2
[1] FALSE
D38V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 10(5Q35.2) MUTATED              2          13         16
  DEL PEAK 10(5Q35.2) WILD-TYPE            8          36         41
D38V38, multiclass
              clus
vv             DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  CURRENT USER                           2                             8
  FORMER USER                           13                            36
  NEVER USED                            16                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V39, continuous
D38V40, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q35.2) MUTATED   22  3
  DEL PEAK 10(5Q35.2) WILD-TYPE 67 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q35.2) MUTATED     22    3
  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                           22                            67
  PRESENT                           3                            13
[1] 2 2
[1] FALSE
D38V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 10(5Q35.2) MUTATED     1    0   7   17    6  0   1    3    0   5  0
  DEL PEAK 10(5Q35.2) WILD-TYPE   0    1  23   48   18  4   7    4    9  17  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 10(5Q35.2) MUTATED     3  0   1  4
  DEL PEAK 10(5Q35.2) WILD-TYPE   5  2   0 10
D38V42, multiclass
      clus
vv     DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  T1A                            1                             0
  T1A1                           0                             1
  T1B                            7                            23
  T1B1                          17                            48
  T1B2                           6                            18
  T2                             0                             4
  T2A                            1                             7
  T2A1                           3                             4
  T2A2                           0                             9
  T2B                            5                            17
  T3                             0                             1
  T3B                            3                             5
  T4                             0                             2
  TIS                            1                             0
  TX                             4                            10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 10(5Q35.2) MUTATED         1        2         0         1        9
  DEL PEAK 10(5Q35.2) WILD-TYPE       3        0         1         0       22
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 10(5Q35.2) MUTATED          14         7        1         1
  DEL PEAK 10(5Q35.2) WILD-TYPE        55        25        2         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 10(5Q35.2) MUTATED            2          0        10         0
  DEL PEAK 10(5Q35.2) WILD-TYPE          3          7        17         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 10(5Q35.2) MUTATED            8         0         0
  DEL PEAK 10(5Q35.2) WILD-TYPE         26         3         7
D38V44, multiclass
            clus
vv           DEL PEAK 10(5Q35.2) MUTATED DEL PEAK 10(5Q35.2) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                             2                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             9                            22
  STAGE IB1                           14                            55
  STAGE IB2                            7                            25
  STAGE II                             1                             2
  STAGE IIA                            1                             5
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           10                            17
  STAGE III                            0                             1
  STAGE IIIB                           8                            26
  STAGE IVA                            0                             3
  STAGE IVB                            0                             7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK 11(6P24.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(6P24.2) MUTATED    26   9
  DEL PEAK 11(6P24.2) WILD-TYPE 157  41
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                           35                           198 
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                            9                            41 
$`DEL PEAK 11(6P24.2) MUTATED`
TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7CO TCGA-C5-A7X3 
       19.86        30.21        73.18       182.93       147.35         9.34 
TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       45.83        23.51        27.52         1.12        50.76        44.94 
TCGA-DG-A2KM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3QE TCGA-EA-A44S 
       40.04        36.76       117.99        22.98         1.18        12.66 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2RC TCGA-EK-A2RN TCGA-EX-A1H6 
       14.89        14.96        13.58         4.04         0.10         7.92 
TCGA-FU-A3HY TCGA-HG-A2PA TCGA-IR-A3L7 TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A5QV 
        0.66        25.41       147.39        21.44        21.11         7.99 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A94Y TCGA-VS-A957 
       93.99        12.16        53.52         4.73        42.08 

$`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         0.82        52.01        18.02        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-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 
       85.55        60.69        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        75.78        99.91         6.12        20.91         4.47 
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         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
        1.32         0.82         0.62        13.05        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35        14.50         1.81        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-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        23.70         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 
        6.12         4.73         1.22        23.84         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC 
        1.35         1.32         1.97         1.12         9.01         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-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        26.56        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        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
        5.13         6.71       195.85        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
        5.42        29.72         0.07         4.34         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        3.88        11.67        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       20.22        14.07        19.96        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z 
       11.51        49.55        39.78        31.27        16.64        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       44.88        42.58        43.82        39.35        38.96        18.05 

  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 
                       182.93                        195.85 
  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE 
                        22.98                         15.25 
[1] "0.1 - 182.9 (23.0)" "0.0 - 195.8 (15.2)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 11(6P24.2) MUTATED   22  6     2
  DEL PEAK 11(6P24.2) WILD-TYPE 99 44     9
D39V3, multiclass
       clus
vv      DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  T1                             22                            99
  T2                              6                            44
  T3+T4                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED   14 11
  DEL PEAK 11(6P24.2) WILD-TYPE 97 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     14   11
  DEL PEAK 11(6P24.2) WILD-TYPE   97   36
   clus
vv  DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  0                          14                            97
  1                          11                            36
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 11(6P24.2) MUTATED   20  0 10
  DEL PEAK 11(6P24.2) WILD-TYPE 71  8 83
D39V5, multiclass
    clus
vv   DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  M0                          20                            71
  M1                           0                             8
  MX                          10                            83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(6P24.2) MUTATED               1                               33
  DEL PEAK 11(6P24.2) WILD-TYPE             4                              164
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 11(6P24.2) MUTATED                                               0
  DEL PEAK 11(6P24.2) WILD-TYPE                                             5
                               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                                            6
D39V6, multiclass
                                               clus
vv                                              DEL PEAK 11(6P24.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       33
  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                                        164
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P24.2) MUTATED     3  33
  DEL PEAK 11(6P24.2) WILD-TYPE  27 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED      3   33
  DEL PEAK 11(6P24.2) WILD-TYPE   27  175
     clus
vv    DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  NO                            3                            27
  YES                          33                           175
[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                        23
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(6P24.2) MUTATED                                           0    25
  DEL PEAK 11(6P24.2) WILD-TYPE                                         1   144
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                                                              25
                                           clus
vv                                          DEL PEAK 11(6P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                16
  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"
D39V11, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P24.2) MUTATED     1  19
  DEL PEAK 11(6P24.2) WILD-TYPE  15 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED      1   19
  DEL PEAK 11(6P24.2) WILD-TYPE   15  130
                        clus
vv                       DEL PEAK 11(6P24.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK 11(6P24.2) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           130
[1] 2 2
[1] FALSE
D39V12, continuous
D39V13, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED   12  2
  DEL PEAK 11(6P24.2) WILD-TYPE 59 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     12    2
  DEL PEAK 11(6P24.2) WILD-TYPE   59   23
            clus
vv           DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  TUMOR FREE                          12                            59
  WITH TUMOR                           2                            23
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 11(6P24.2) MUTATED        3      4       0      2       1
  DEL PEAK 11(6P24.2) WILD-TYPE     20      1       1      8       6
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 11(6P24.2) MUTATED              24       2
  DEL PEAK 11(6P24.2) WILD-TYPE           154      12
D39V14, multiclass
               clus
vv              DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  BRAZIL                                  3                            20
  CANADA                                  4                             1
  NIGERIA                                 0                             1
  RUSSIA                                  2                             8
  UKRAINE                                 1                             6
  UNITED STATES                          24                           154
  VIETNAM                                 2                            12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 11(6P24.2) MUTATED    3 16 14  0  2
  DEL PEAK 11(6P24.2) WILD-TYPE 14 90 83  1 12
D39V15, multiclass
    clus
vv   DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  G1                           3                            14
  G2                          16                            90
  G3                          14                            83
  G4                           0                             1
  GX                           2                            12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                                          25
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 11(6P24.2) MUTATED                                        2
  DEL PEAK 11(6P24.2) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 11(6P24.2) MUTATED                                                 0
  DEL PEAK 11(6P24.2) WILD-TYPE                                               2
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 11(6P24.2) MUTATED                9                  16
  DEL PEAK 11(6P24.2) WILD-TYPE             43                  96
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                                                            9
  LIFELONG NON-SMOKER                                                      16
                                                 clus
vv                                                DEL PEAK 11(6P24.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             43
  LIFELONG NON-SMOKER                                                        96
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V19, continuous
D39V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 11(6P24.2) MUTATED             0       12             4        2
  DEL PEAK 11(6P24.2) WILD-TYPE          19       63             8       10
D39V21, multiclass
               clus
vv              DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  COMBINATION                             0                            19
  EXTERNAL                               12                            63
  EXTERNAL BEAM                           4                             8
  INTERNAL                                2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     7             2
  DEL PEAK 11(6P24.2) WILD-TYPE                  21            14
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                           7                            21
  REGIONAL SITE                                 2                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V24, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED    7  0
  DEL PEAK 11(6P24.2) WILD-TYPE 27  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED      7    0
  DEL PEAK 11(6P24.2) WILD-TYPE   27    3
     clus
vv    DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  CGY                           7                            27
  GY                            0                             3
[1] 2 2
[1] FALSE
D39V25, continuous
D39V26, continuous
D39V27, continuous
D39V28, continuous
D39V29, continuous
D39V30, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 11(6P24.2) MUTATED                         6                       0
  DEL PEAK 11(6P24.2) WILD-TYPE                      23                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 11(6P24.2) MUTATED                         2
  DEL PEAK 11(6P24.2) WILD-TYPE                       5
D39V31, multiclass
                                     clus
vv                                    DEL PEAK 11(6P24.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       6
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK 11(6P24.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                        23
  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 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                                             14
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 11(6P24.2) MUTATED                                                                                   9
  DEL PEAK 11(6P24.2) WILD-TYPE                                                                                59
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 11(6P24.2) MUTATED                                                                                             17
  DEL PEAK 11(6P24.2) WILD-TYPE                                                                                           88
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)                                      9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          17
                                                                                              clus
vv                                                                                             DEL PEAK 11(6P24.2) 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)                                       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"
D39V33, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED    9 14
  DEL PEAK 11(6P24.2) WILD-TYPE 59 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED      9   14
  DEL PEAK 11(6P24.2) WILD-TYPE   59   56
         clus
vv        DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  ABSENT                            9                            59
  PRESENT                          14                            56
[1] 2 2
[1] FALSE
D39V34, continuous
D39V35, continuous
D39V36, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED    9 12
  DEL PEAK 11(6P24.2) WILD-TYPE 34 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED      9   12
  DEL PEAK 11(6P24.2) WILD-TYPE   34   82
                                          clus
vv                                         DEL PEAK 11(6P24.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          12
                                          clus
vv                                         DEL PEAK 11(6P24.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            82
[1] 2 2
[1] FALSE
D39V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 11(6P24.2) MUTATED              3           7         11
  DEL PEAK 11(6P24.2) WILD-TYPE            7          42         46
D39V38, multiclass
              clus
vv             DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  CURRENT USER                           3                             7
  FORMER USER                            7                            42
  NEVER USED                            11                            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V39, continuous
D39V40, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P24.2) MUTATED   17  2
  DEL PEAK 11(6P24.2) WILD-TYPE 72 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P24.2) MUTATED     17    2
  DEL PEAK 11(6P24.2) WILD-TYPE   72   14
         clus
vv        DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  ABSENT                           17                            72
  PRESENT                           2                            14
[1] 2 2
[1] FALSE
D39V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 11(6P24.2) MUTATED     0    0   6   14    2  0   1    0    1   4  0
  DEL PEAK 11(6P24.2) WILD-TYPE   1    1  24   51   22  4   7    7    8  18  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 11(6P24.2) MUTATED     2  0   0  0
  DEL PEAK 11(6P24.2) WILD-TYPE   6  2   1 14
D39V42, multiclass
      clus
vv     DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  T1A                            0                             1
  T1A1                           0                             1
  T1B                            6                            24
  T1B1                          14                            51
  T1B2                           2                            22
  T2                             0                             4
  T2A                            1                             7
  T2A1                           0                             7
  T2A2                           1                             8
  T2B                            4                            18
  T3                             0                             1
  T3B                            2                             6
  T4                             0                             2
  TIS                            0                             1
  TX                             0                            14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        2         1         1       24
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 11(6P24.2) MUTATED          14         3        0         1
  DEL PEAK 11(6P24.2) WILD-TYPE        55        29        3         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 11(6P24.2) MUTATED            0          0         3         0
  DEL PEAK 11(6P24.2) WILD-TYPE          5          7        24         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 11(6P24.2) MUTATED            8         0         0
  DEL PEAK 11(6P24.2) WILD-TYPE         26         3         7
D39V44, multiclass
            clus
vv           DEL PEAK 11(6P24.2) MUTATED DEL PEAK 11(6P24.2) WILD-TYPE
  STAGE I                              0                             4
  STAGE IA                             0                             2
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             7                            24
  STAGE IB1                           14                            55
  STAGE IB2                            3                            29
  STAGE II                             0                             3
  STAGE IIA                            1                             5
  STAGE IIA1                           0                             5
  STAGE IIA2                           0                             7
  STAGE IIB                            3                            24
  STAGE III                            0                             1
  STAGE IIIB                           8                            26
  STAGE IVA                            0                             3
  STAGE IVB                            0                             7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = DEL PEAK 12(6Q26) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q26) MUTATED    62  17
  DEL PEAK 12(6Q26) WILD-TYPE 121  33
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         79                         154 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         17                          33 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 
       49.48        23.67        36.56       173.29        82.85        67.46 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LZ 
       30.21        35.01        57.73        73.18        73.45       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CO 
       38.43        52.01        17.85       182.93       154.32       147.35 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XK TCGA-C5-A8YQ 
       60.69        94.95         9.34        50.99        99.91        23.51 
TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VM 
       27.52         1.12        58.88        44.94        40.04       117.99 
TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 
       12.36         1.18        14.50         1.81        12.66        14.89 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
       14.96        13.58        12.59         1.51         0.43         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H6 
        0.07         4.04         2.24         0.10         0.10         7.92 
TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3YQ TCGA-FU-A40J 
       14.70         4.73        23.84         0.66         3.52         1.35 
TCGA-FU-A57G TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH TCGA-JW-A5VJ 
        1.32        20.78       147.39       117.40        78.71        21.44 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX TCGA-MU-A5YI TCGA-MY-A913 TCGA-Q1-A5R2 
       21.11         7.99         0.07         0.03         5.49        13.35 
TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EJ 
        3.39        19.59        11.67        12.16        10.03        19.96 
TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A959 
       53.52        11.51        49.55         4.73        42.08        39.35 
TCGA-VS-A9U5 
       38.96 

$`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         0.82        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        85.55 
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        75.78         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       20.91         4.47        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         0.76         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E 
       13.05        14.50         1.35         1.35        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N 
        1.48        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        23.70         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         6.12 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        1.22         0.92         2.17         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-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 
        7.13        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        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 
      195.85        30.31        11.28         0.89         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.20        13.87         5.42        29.72         0.07         4.34 
TCGA-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         5.88         6.25        10.39         3.88        93.99 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 
       61.28        34.52        29.03        20.22        14.07        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z 
       46.03        23.28        39.78        31.27        16.64        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-WL-A834 
       44.88        42.58        43.82        18.05 

  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                       0.03                        0.03 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     182.93                      195.85 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                      19.96                       15.53 
[1] "0.0 - 182.9 (20.0)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.4"
D40V2, continuous
                             vv
clus                          T1 T2 T3+T4
  DEL PEAK 12(6Q26) MUTATED   39 17     3
  DEL PEAK 12(6Q26) WILD-TYPE 82 33     8
D40V3, multiclass
       clus
vv      DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T1                           39                          82
  T2                           17                          33
  T3+T4                         3                           8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   33 16
  DEL PEAK 12(6Q26) WILD-TYPE 78 31
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     33   16
  DEL PEAK 12(6Q26) WILD-TYPE   78   31
   clus
vv  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  0                        33                          78
  1                        16                          31
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK 12(6Q26) MUTATED   33  4 26
  DEL PEAK 12(6Q26) WILD-TYPE 58  4 67
D40V5, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  M0                        33                          58
  M1                         4                           4
  MX                        26                          67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(6Q26) MUTATED               1                               72
  DEL PEAK 12(6Q26) WILD-TYPE             4                              125
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 12(6Q26) MUTATED                                               0
  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                                              1
  DEL PEAK 12(6Q26) WILD-TYPE                                            5
D40V6, multiclass
                                               clus
vv                                              DEL PEAK 12(6Q26) MUTATED
  ADENOSQUAMOUS                                                         1
  CERVICAL SQUAMOUS CELL CARCINOMA                                     72
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          1
                                               clus
vv                                              DEL PEAK 12(6Q26) WILD-TYPE
  ADENOSQUAMOUS                                                           4
  CERVICAL SQUAMOUS CELL CARCINOMA                                      125
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED     9  74
  DEL PEAK 12(6Q26) WILD-TYPE  21 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED      9   74
  DEL PEAK 12(6Q26) WILD-TYPE   21  134
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  NO                          9                          21
  YES                        74                         134
[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                          10
  DEL PEAK 12(6Q26) WILD-TYPE                        14
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(6Q26) MUTATED                                           1    60
  DEL PEAK 12(6Q26) WILD-TYPE                                         0   109
D40V10, multiclass
                                           clus
vv                                          DEL PEAK 12(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             4
  BLACK OR AFRICAN AMERICAN                                        10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            60
                                           clus
vv                                          DEL PEAK 12(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  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"
D40V11, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED     3  49
  DEL PEAK 12(6Q26) WILD-TYPE  13 100
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED      3   49
  DEL PEAK 12(6Q26) WILD-TYPE   13  100
                        clus
vv                       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             3                          13
  NOT HISPANIC OR LATINO                        49                         100
[1] 2 2
[1] FALSE
D40V12, continuous
D40V13, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   27  8
  DEL PEAK 12(6Q26) WILD-TYPE 44 17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     27    8
  DEL PEAK 12(6Q26) WILD-TYPE   44   17
            clus
vv           DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  TUMOR FREE                        27                          44
  WITH TUMOR                         8                          17
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 12(6Q26) MUTATED        9      4       0      3       2
  DEL PEAK 12(6Q26) WILD-TYPE     14      1       1      7       5
                             vv
clus                          UNITED STATES VIETNAM
  DEL PEAK 12(6Q26) MUTATED              61       4
  DEL PEAK 12(6Q26) WILD-TYPE           117      10
D40V14, multiclass
               clus
vv              DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  BRAZIL                                9                          14
  CANADA                                4                           1
  NIGERIA                               0                           1
  RUSSIA                                3                           7
  UKRAINE                               2                           5
  UNITED STATES                        61                         117
  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    6 32 39  1  4
  DEL PEAK 12(6Q26) WILD-TYPE 11 74 58  0 10
D40V15, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  G1                         6                          11
  G2                        32                          74
  G3                        39                          58
  G4                         1                           0
  GX                         4                          10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V16, continuous
D40V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 12(6Q26) MUTATED                                            10
  DEL PEAK 12(6Q26) WILD-TYPE                                          21
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 12(6Q26) MUTATED                                        2
  DEL PEAK 12(6Q26) WILD-TYPE                                      6
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 12(6Q26) MUTATED                                                 1
  DEL PEAK 12(6Q26) WILD-TYPE                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 12(6Q26) MUTATED               18                  37
  DEL PEAK 12(6Q26) WILD-TYPE             34                  75
D40V18, multiclass
                                                 clus
vv                                                DEL PEAK 12(6Q26) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                            10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         1
  CURRENT SMOKER                                                         18
  LIFELONG NON-SMOKER                                                    37
                                                 clus
vv                                                DEL PEAK 12(6Q26) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           34
  LIFELONG NON-SMOKER                                                      75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V19, continuous
D40V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 12(6Q26) MUTATED             6       26             4        5
  DEL PEAK 12(6Q26) WILD-TYPE          13       49             8        7
D40V21, multiclass
               clus
vv              DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  COMBINATION                           6                          13
  EXTERNAL                             26                          49
  EXTERNAL BEAM                         4                           8
  INTERNAL                              5                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    13             6
  DEL PEAK 12(6Q26) WILD-TYPE                  15            10
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                        13                          15
  REGIONAL SITE                               6                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V24, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   13  2
  DEL PEAK 12(6Q26) WILD-TYPE 21  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     13    2
  DEL PEAK 12(6Q26) WILD-TYPE   21    1
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  CGY                        13                          21
  GY                          2                           1
[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                                   5
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 12(6Q26) MUTATED                        11                       0
  DEL PEAK 12(6Q26) WILD-TYPE                      18                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  DEL PEAK 12(6Q26) MUTATED                         3
  DEL PEAK 12(6Q26) WILD-TYPE                       4
D40V31, multiclass
                                     clus
vv                                    DEL PEAK 12(6Q26) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  OTHER LOCATION, SPECIFY                                    11
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     3
                                     clus
vv                                    DEL PEAK 12(6Q26) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           5
  OTHER LOCATION, SPECIFY                                      18
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 12(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                                                6
  DEL PEAK 12(6Q26) WILD-TYPE                                             10
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 12(6Q26) MUTATED                                                                                  23
  DEL PEAK 12(6Q26) WILD-TYPE                                                                                45
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 12(6Q26) MUTATED                                                                                             33
  DEL PEAK 12(6Q26) WILD-TYPE                                                                                           72
D40V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 12(6Q26) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        33
                                                                                              clus
vv                                                                                             DEL PEAK 12(6Q26) WILD-TYPE
  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)                                     45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V33, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   21 23
  DEL PEAK 12(6Q26) WILD-TYPE 47 47
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     21   23
  DEL PEAK 12(6Q26) WILD-TYPE   47   47
         clus
vv        DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  ABSENT                         21                          47
  PRESENT                        23                          47
[1] 2 2
[1] FALSE
D40V34, continuous
D40V35, continuous
D40V36, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   13 29
  DEL PEAK 12(6Q26) WILD-TYPE 30 65
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     13   29
  DEL PEAK 12(6Q26) WILD-TYPE   30   65
                                          clus
vv                                         DEL PEAK 12(6Q26) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        29
                                          clus
vv                                         DEL PEAK 12(6Q26) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          65
[1] 2 2
[1] FALSE
D40V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  DEL PEAK 12(6Q26) MUTATED              4          17         18
  DEL PEAK 12(6Q26) WILD-TYPE            6          32         39
D40V38, multiclass
              clus
vv             DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  CURRENT USER                         4                           6
  FORMER USER                         17                          32
  NEVER USED                          18                          39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V39, continuous
D40V40, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   31  5
  DEL PEAK 12(6Q26) WILD-TYPE 58 11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     31    5
  DEL PEAK 12(6Q26) WILD-TYPE   58   11
         clus
vv        DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  ABSENT                         31                          58
  PRESENT                         5                          11
[1] 2 2
[1] FALSE
D40V41, continuous
[1] "Remove cluster labels:"    "DEL PEAK 12(6Q26) MUTATED"
clus
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                          2                          11 
                 TCGA-C5-A1BN                  TCGA-C5-A1MH 
"DEL PEAK 12(6Q26) WILD-TYPE" "DEL PEAK 12(6Q26) WILD-TYPE" 
                 TCGA-C5-A1ML                  TCGA-C5-A1MN 
"DEL PEAK 12(6Q26) WILD-TYPE" "DEL PEAK 12(6Q26) WILD-TYPE" 
                 TCGA-C5-A1MP                  TCGA-EK-A2RO 
"DEL PEAK 12(6Q26) WILD-TYPE" "DEL PEAK 12(6Q26) WILD-TYPE" 
                 TCGA-GH-A9DA                  TCGA-JW-A852 
"DEL PEAK 12(6Q26) WILD-TYPE" "DEL PEAK 12(6Q26) WILD-TYPE" 
                 TCGA-JX-A3Q8                  TCGA-MU-A51Y 
"DEL PEAK 12(6Q26) WILD-TYPE" "DEL PEAK 12(6Q26) WILD-TYPE" 
                 TCGA-MU-A8JM 
"DEL PEAK 12(6Q26) WILD-TYPE" 
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 12(6Q26) MUTATED     0    1  15   21    2  1   1    5    1   9  0
  DEL PEAK 12(6Q26) WILD-TYPE   1    0  15   44   22  3   7    2    8  13  1
                             vv
clus                          T3B T4 TIS TX
  DEL PEAK 12(6Q26) MUTATED     3  0   1  4
  DEL PEAK 12(6Q26) WILD-TYPE   5  2   0 10
D40V42, multiclass
      clus
vv     DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T1A                          0                           1
  T1A1                         1                           0
  T1B                         15                          15
  T1B1                        21                          44
  T1B2                         2                          22
  T2                           1                           3
  T2A                          1                           7
  T2A1                         5                           2
  T2A2                         1                           8
  T2B                          9                          13
  T3                           0                           1
  T3B                          3                           5
  T4                           0                           2
  TIS                          1                           0
  TX                           4                          10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V43, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 12(6Q26) MUTATED         1        0         1         1       14
  DEL PEAK 12(6Q26) WILD-TYPE       3        2         0         0       17
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  DEL PEAK 12(6Q26) MUTATED          25         4        0         3          3
  DEL PEAK 12(6Q26) WILD-TYPE        44        28        3         3          2
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIB
  DEL PEAK 12(6Q26) MUTATED            1        10         0         14
  DEL PEAK 12(6Q26) WILD-TYPE          6        17         1         20
                             vv
clus                          STAGE IVA STAGE IVB
  DEL PEAK 12(6Q26) MUTATED           1         2
  DEL PEAK 12(6Q26) WILD-TYPE         2         5
D40V44, multiclass
            clus
vv           DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  STAGE I                            1                           3
  STAGE IA                           0                           2
  STAGE IA1                          1                           0
  STAGE IA2                          1                           0
  STAGE IB                          14                          17
  STAGE IB1                         25                          44
  STAGE IB2                          4                          28
  STAGE II                           0                           3
  STAGE IIA                          3                           3
  STAGE IIA1                         3                           2
  STAGE IIA2                         1                           6
  STAGE IIB                         10                          17
  STAGE III                          0                           1
  STAGE IIIB                        14                          20
  STAGE IVA                          1                           2
  STAGE IVB                          2                           5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 13(7Q34) MUTATION ANALYSIS
D41V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(7Q34) MUTATED    35  16
  DEL PEAK 13(7Q34) WILD-TYPE 148  34
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                         51                         182 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                         16                          34 
$`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         0.76         0.62        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-MU-A51Y TCGA-MY-A5BF 
       21.67        27.42        30.31         0.20        13.87         4.34 
TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-RA-A741 TCGA-UC-A7PF TCGA-VS-A8EH 
        5.49        13.35         3.39         3.88        93.99        20.22 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A957 
       14.07        32.15        42.08 

$`DEL PEAK 13(7Q34) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        23.67        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M8 
      177.04       173.29        82.85        19.86        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP 
       57.73        53.16         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       44.22        73.18        78.35        38.43         0.82        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO 
       17.85        20.42       182.93       101.82       134.33       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
       17.19        85.55        60.69        94.95         9.34         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99         8.35        75.78        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
        6.12        20.91         4.47         1.12        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT 
      118.65        22.98        16.83        16.18         8.28        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.74         1.32         0.82        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89         1.48        13.91        15.02        14.99        13.58 
TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       12.59         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ 
        1.45         0.13        16.08         0.07         4.04         1.18 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H6 
       23.70         0.10         0.07         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         6.12         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA 
        1.48         0.82         3.52         1.32         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41         7.13        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        10.06         5.13         6.71        21.11       195.85 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        11.28         0.89         0.07         0.30         0.82 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 
        0.03         5.42        29.72         0.07         2.96        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI 
        6.25        10.39        19.59        11.67        12.16        61.28 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 
       10.03        34.52        29.03        19.96        53.52        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       23.28        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 
        4.73        23.24        44.88        42.58        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  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                      195.85 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                      17.52                       15.73 
[1] "0.0 - 154.3 (17.5)" "0.0 - 195.8 (15.7)"
[1] "hr=" "1.7"
D41V2, continuous
                             vv
clus                          T1 T2 T3+T4
  DEL PEAK 13(7Q34) MUTATED   22  9     3
  DEL PEAK 13(7Q34) WILD-TYPE 99 41     8
D41V3, multiclass
       clus
vv      DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  T1                           22                          99
  T2                            9                          41
  T3+T4                         3                           8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   17 12
  DEL PEAK 13(7Q34) WILD-TYPE 94 35
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     17   12
  DEL PEAK 13(7Q34) WILD-TYPE   94   35
   clus
vv  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  0                        17                          94
  1                        12                          35
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK 13(7Q34) MUTATED   14  1 21
  DEL PEAK 13(7Q34) WILD-TYPE 77  7 72
D41V5, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  M0                        14                          77
  M1                         1                           7
  MX                        21                          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"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(7Q34) MUTATED               0                               44
  DEL PEAK 13(7Q34) WILD-TYPE             5                              153
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 13(7Q34) MUTATED                                               1
  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                                              0
  DEL PEAK 13(7Q34) WILD-TYPE                                            6
D41V6, multiclass
                                               clus
vv                                              DEL PEAK 13(7Q34) MUTATED
  ADENOSQUAMOUS                                                         0
  CERVICAL SQUAMOUS CELL CARCINOMA                                     44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          0
                                               clus
vv                                              DEL PEAK 13(7Q34) WILD-TYPE
  ADENOSQUAMOUS                                                           5
  CERVICAL SQUAMOUS CELL CARCINOMA                                      153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED    13  38
  DEL PEAK 13(7Q34) WILD-TYPE  17 170
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     13   38
  DEL PEAK 13(7Q34) WILD-TYPE   17  170
     clus
vv    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  NO                         13                          17
  YES                        38                         170
[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                        18
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(7Q34) MUTATED                                           0    35
  DEL PEAK 13(7Q34) WILD-TYPE                                         1   134
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                                                            35
                                           clus
vv                                          DEL PEAK 13(7Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                          18
  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"
D41V11, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     3  36
  DEL PEAK 13(7Q34) WILD-TYPE  13 113
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      3   36
  DEL PEAK 13(7Q34) WILD-TYPE   13  113
                        clus
vv                       DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             3                          13
  NOT HISPANIC OR LATINO                        36                         113
[1] 2 2
[1] FALSE
D41V12, continuous
D41V13, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   15 12
  DEL PEAK 13(7Q34) WILD-TYPE 56 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     15   12
  DEL PEAK 13(7Q34) WILD-TYPE   56   13
            clus
vv           DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  TUMOR FREE                        15                          56
  WITH TUMOR                        12                          13
[1] 2 2
[1] FALSE
                             vv
clus                          BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 13(7Q34) MUTATED        4      1       0      2       1
  DEL PEAK 13(7Q34) WILD-TYPE     19      4       1      8       6
                             vv
clus                          UNITED STATES VIETNAM
  DEL PEAK 13(7Q34) MUTATED              39       4
  DEL PEAK 13(7Q34) WILD-TYPE           139      10
D41V14, multiclass
               clus
vv              DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  BRAZIL                                4                          19
  CANADA                                1                           4
  NIGERIA                               0                           1
  RUSSIA                                2                           8
  UKRAINE                               1                           6
  UNITED STATES                        39                         139
  VIETNAM                               4                          10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  DEL PEAK 13(7Q34) MUTATED    2 22 23  0  3
  DEL PEAK 13(7Q34) WILD-TYPE 15 84 74  1 11
D41V15, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  G1                         2                          15
  G2                        22                          84
  G3                        23                          74
  G4                         0                           1
  GX                         3                          11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                                          26
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 13(7Q34) MUTATED                                        2
  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                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 13(7Q34) MUTATED               11                  23
  DEL PEAK 13(7Q34) WILD-TYPE             41                  89
D41V18, multiclass
                                                 clus
vv                                                DEL PEAK 13(7Q34) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         1
  CURRENT SMOKER                                                         11
  LIFELONG NON-SMOKER                                                    23
                                                 clus
vv                                                DEL PEAK 13(7Q34) 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                                                           41
  LIFELONG NON-SMOKER                                                      89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V19, continuous
D41V20, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 13(7Q34) MUTATED             9       12             4        2
  DEL PEAK 13(7Q34) WILD-TYPE          10       63             8       10
D41V21, multiclass
               clus
vv              DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  COMBINATION                           9                          10
  EXTERNAL                             12                          63
  EXTERNAL BEAM                         4                           8
  INTERNAL                              2                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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             4
  DEL PEAK 13(7Q34) WILD-TYPE                  22            12
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                          22
  REGIONAL SITE                               4                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V24, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED    8  2
  DEL PEAK 13(7Q34) WILD-TYPE 26  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      8    2
  DEL PEAK 13(7Q34) WILD-TYPE   26    1
     clus
vv    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  CGY                         8                          26
  GY                          2                           1
[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                                   4
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 13(7Q34) MUTATED                         5                       0
  DEL PEAK 13(7Q34) WILD-TYPE                      24                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  DEL PEAK 13(7Q34) MUTATED                         1
  DEL PEAK 13(7Q34) WILD-TYPE                       6
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                           4
  OTHER LOCATION, SPECIFY                                      24
  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 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                                                5
  DEL PEAK 13(7Q34) WILD-TYPE                                             11
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 13(7Q34) MUTATED                                                                                  14
  DEL PEAK 13(7Q34) WILD-TYPE                                                                                54
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 13(7Q34) MUTATED                                                                                             22
  DEL PEAK 13(7Q34) WILD-TYPE                                                                                           83
D41V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 13(7Q34) 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)                                   14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        22
                                                                                              clus
vv                                                                                             DEL PEAK 13(7Q34) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V33, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   11 18
  DEL PEAK 13(7Q34) WILD-TYPE 57 52
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     11   18
  DEL PEAK 13(7Q34) WILD-TYPE   57   52
         clus
vv        DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  ABSENT                         11                          57
  PRESENT                        18                          52
[1] 2 2
[1] FALSE
D41V34, continuous
D41V35, continuous
D41V36, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   13 20
  DEL PEAK 13(7Q34) WILD-TYPE 30 74
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     13   20
  DEL PEAK 13(7Q34) WILD-TYPE   30   74
                                          clus
vv                                         DEL PEAK 13(7Q34) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        20
                                          clus
vv                                         DEL PEAK 13(7Q34) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          74
[1] 2 2
[1] FALSE
D41V37, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  DEL PEAK 13(7Q34) MUTATED              1          12         11
  DEL PEAK 13(7Q34) WILD-TYPE            9          37         46
D41V38, multiclass
              clus
vv             DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  CURRENT USER                         1                           9
  FORMER USER                         12                          37
  NEVER USED                          11                          46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V39, continuous
D41V40, binary
                             cls
clus                           0  1
  DEL PEAK 13(7Q34) MUTATED   18  3
  DEL PEAK 13(7Q34) WILD-TYPE 71 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED     18    3
  DEL PEAK 13(7Q34) WILD-TYPE   71   13
         clus
vv        DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  ABSENT                         18                          71
  PRESENT                         3                          13
[1] 2 2
[1] FALSE
D41V41, continuous
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 13(7Q34) MUTATED     0    0   7   13    2  2   1    3    2   1  0
  DEL PEAK 13(7Q34) WILD-TYPE   1    1  23   52   22  2   7    4    7  21  1
                             vv
clus                          T3B T4 TIS TX
  DEL PEAK 13(7Q34) MUTATED     3  0   1  2
  DEL PEAK 13(7Q34) WILD-TYPE   5  2   0 12
D41V42, multiclass
      clus
vv     DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  T1A                          0                           1
  T1A1                         0                           1
  T1B                          7                          23
  T1B1                        13                          52
  T1B2                         2                          22
  T2                           2                           2
  T2A                          1                           7
  T2A1                         3                           4
  T2A2                         2                           7
  T2B                          1                          21
  T3                           0                           1
  T3B                          3                           5
  T4                           0                           2
  TIS                          1                           0
  TX                           2                          12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        2         1         1       26
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  DEL PEAK 13(7Q34) MUTATED          15         6        1         3          2
  DEL PEAK 13(7Q34) WILD-TYPE        54        26        2         3          3
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIB
  DEL PEAK 13(7Q34) MUTATED            1         7         0          8
  DEL PEAK 13(7Q34) WILD-TYPE          6        20         1         26
                             vv
clus                          STAGE IVA STAGE IVB
  DEL PEAK 13(7Q34) MUTATED           0         1
  DEL PEAK 13(7Q34) WILD-TYPE         3         6
D41V44, multiclass
            clus
vv           DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  STAGE I                            1                           3
  STAGE IA                           0                           2
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           5                          26
  STAGE IB1                         15                          54
  STAGE IB2                          6                          26
  STAGE II                           1                           2
  STAGE IIA                          3                           3
  STAGE IIA1                         2                           3
  STAGE IIA2                         1                           6
  STAGE IIB                          7                          20
  STAGE III                          0                           1
  STAGE IIIB                         8                          26
  STAGE IVA                          0                           3
  STAGE IVB                          1                           6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.3) MUTATED    58  24
  DEL PEAK 14(8P23.3) WILD-TYPE 125  26
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           82                           151 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           24                            26 
$`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         0.82        52.01       134.33 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       60.69        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         4.47         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         1.32        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2RM TCGA-EK-A2RO 
       12.66        14.89        12.59        45.96         2.24         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        0.10         0.03         6.94         6.12         1.22        23.84 
TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        1.45         0.82         1.32         1.12         9.01        25.41 
TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VL 
       21.67        14.93       137.16        78.71        26.56        15.58 
TCGA-JW-A852 TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A5YI 
        5.13        30.31         0.89         0.82         0.20         0.03 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V 
        5.49         2.96         3.39         5.88        10.39        19.59 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA 
       11.67        10.03        34.52        19.96        53.52        23.28 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z 
       49.55        39.78         4.73        23.24 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        23.67        11.44        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1MH 
      177.04       173.29        82.85        19.86        67.46        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ 
       35.61         0.46         3.58        44.22        83.05       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       38.43        18.02        17.85        20.42       182.93       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82        15.48        20.35       147.35        17.19        85.55 
TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ 
        9.34         8.35        75.78        23.51         6.12        20.91 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       50.76        44.94        40.04        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
      117.99        22.98        16.83        16.18        17.52         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.74         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35         1.35        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H5 
        0.36         1.18        23.70         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         4.73         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J 
        0.66         1.02         1.58         1.48         3.52         1.35 
TCGA-FU-A5XV TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
        1.97         7.13        20.78         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        96.95        81.96        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ 
       24.56        21.44        20.48        10.06         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-MU-A51Y 
      195.85         7.99        11.28         0.07         0.30        13.87 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         0.07         4.34        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R 
       15.95        16.14        17.56        14.07        15.88         6.25 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH 
        3.88        93.99        12.16        61.28        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94X 
       14.07        32.15        46.03        11.51        31.27        16.64 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       44.88        42.58        42.08        43.82        39.35        38.96 
TCGA-WL-A834 
       18.05 

  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                        195.85 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       15.255                        15.950 
[1] "0.0 - 137.2 (15.3)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.7"
D42V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 14(8P23.3) MUTATED   41 17     3
  DEL PEAK 14(8P23.3) WILD-TYPE 80 33     8
D42V3, multiclass
       clus
vv      DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  T1                             41                            80
  T2                             17                            33
  T3+T4                           3                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   39 15
  DEL PEAK 14(8P23.3) WILD-TYPE 72 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     39   15
  DEL PEAK 14(8P23.3) WILD-TYPE   72   32
   clus
vv  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  0                          39                            72
  1                          15                            32
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 14(8P23.3) MUTATED   32  3 30
  DEL PEAK 14(8P23.3) WILD-TYPE 59  5 63
D42V5, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  M0                          32                            59
  M1                           3                             5
  MX                          30                            63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(8P23.3) MUTATED               2                               71
  DEL PEAK 14(8P23.3) WILD-TYPE             3                              126
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 14(8P23.3) MUTATED                                               1
  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                                              2
  DEL PEAK 14(8P23.3) WILD-TYPE                                            4
D42V6, multiclass
                                               clus
vv                                              DEL PEAK 14(8P23.3) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       71
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              DEL PEAK 14(8P23.3) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        126
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED    15  70
  DEL PEAK 14(8P23.3) WILD-TYPE  15 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     15   70
  DEL PEAK 14(8P23.3) WILD-TYPE   15  138
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  NO                           15                            15
  YES                          70                           138
[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                          11
  DEL PEAK 14(8P23.3) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(8P23.3) MUTATED                                           1    62
  DEL PEAK 14(8P23.3) WILD-TYPE                                         0   107
D42V10, multiclass
                                           clus
vv                                          DEL PEAK 14(8P23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              62
                                           clus
vv                                          DEL PEAK 14(8P23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED    5 54
  DEL PEAK 14(8P23.3) WILD-TYPE 11 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      5   54
  DEL PEAK 14(8P23.3) WILD-TYPE   11   95
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                            95
[1] 2 2
[1] FALSE
D42V12, continuous
D42V13, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   23 11
  DEL PEAK 14(8P23.3) WILD-TYPE 48 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     23   11
  DEL PEAK 14(8P23.3) WILD-TYPE   48   14
            clus
vv           DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  TUMOR FREE                          23                            48
  WITH TUMOR                          11                            14
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 14(8P23.3) MUTATED        9      2       1      3       2
  DEL PEAK 14(8P23.3) WILD-TYPE     14      3       0      7       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 14(8P23.3) MUTATED              64       4
  DEL PEAK 14(8P23.3) WILD-TYPE           114      10
D42V14, multiclass
               clus
vv              DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  BRAZIL                                  9                            14
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  3                             7
  UKRAINE                                 2                             5
  UNITED STATES                          64                           114
  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 34 39  1  6
  DEL PEAK 14(8P23.3) WILD-TYPE 13 72 58  0  8
D42V15, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  G1                           4                            13
  G2                          34                            72
  G3                          39                            58
  G4                           1                             0
  GX                           6                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V16, continuous
D42V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 14(8P23.3) MUTATED                                            14
  DEL PEAK 14(8P23.3) WILD-TYPE                                          17
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 14(8P23.3) MUTATED                                        3
  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                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 14(8P23.3) MUTATED               19                  33
  DEL PEAK 14(8P23.3) WILD-TYPE             33                  79
D42V18, multiclass
                                                 clus
vv                                                DEL PEAK 14(8P23.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           2
  CURRENT SMOKER                                                           19
  LIFELONG NON-SMOKER                                                      33
                                                 clus
vv                                                DEL PEAK 14(8P23.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             33
  LIFELONG NON-SMOKER                                                        79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V19, continuous
D42V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 14(8P23.3) MUTATED             9       27             7        3
  DEL PEAK 14(8P23.3) WILD-TYPE          10       48             5        9
D42V21, multiclass
               clus
vv              DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  COMBINATION                             9                            10
  EXTERNAL                               27                            48
  EXTERNAL BEAM                           7                             5
  INTERNAL                                3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    13             3
  DEL PEAK 14(8P23.3) WILD-TYPE                  15            13
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                          13                            15
  REGIONAL SITE                                 3                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V24, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   11  2
  DEL PEAK 14(8P23.3) WILD-TYPE 23  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     11    2
  DEL PEAK 14(8P23.3) WILD-TYPE   23    1
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  CGY                          11                            23
  GY                            2                             1
[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                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 14(8P23.3) MUTATED                        14                       0
  DEL PEAK 14(8P23.3) WILD-TYPE                      15                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 14(8P23.3) MUTATED                         3
  DEL PEAK 14(8P23.3) WILD-TYPE                       4
D42V31, multiclass
                                     clus
vv                                    DEL PEAK 14(8P23.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                      14
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    DEL PEAK 14(8P23.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  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)
  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                                                4
  DEL PEAK 14(8P23.3) WILD-TYPE                                             12
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 14(8P23.3) MUTATED                                                                                  20
  DEL PEAK 14(8P23.3) WILD-TYPE                                                                                48
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 14(8P23.3) MUTATED                                                                                             42
  DEL PEAK 14(8P23.3) WILD-TYPE                                                                                           63
D42V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 14(8P23.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          42
                                                                                              clus
vv                                                                                             DEL PEAK 14(8P23.3) 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)                                       48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V33, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   26 19
  DEL PEAK 14(8P23.3) WILD-TYPE 42 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     26   19
  DEL PEAK 14(8P23.3) WILD-TYPE   42   51
         clus
vv        DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  ABSENT                           26                            42
  PRESENT                          19                            51
[1] 2 2
[1] FALSE
D42V34, continuous
D42V35, continuous
D42V36, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   16 31
  DEL PEAK 14(8P23.3) WILD-TYPE 27 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     16   31
  DEL PEAK 14(8P23.3) WILD-TYPE   27   63
                                          clus
vv                                         DEL PEAK 14(8P23.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          31
                                          clus
vv                                         DEL PEAK 14(8P23.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            63
[1] 2 2
[1] FALSE
D42V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 14(8P23.3) MUTATED              3          22         18
  DEL PEAK 14(8P23.3) WILD-TYPE            7          27         39
D42V38, multiclass
              clus
vv             DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  CURRENT USER                           3                             7
  FORMER USER                           22                            27
  NEVER USED                            18                            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V39, continuous
D42V40, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   32  5
  DEL PEAK 14(8P23.3) WILD-TYPE 57 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     32    5
  DEL PEAK 14(8P23.3) WILD-TYPE   57   11
         clus
vv        DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  ABSENT                           32                            57
  PRESENT                           5                            11
[1] 2 2
[1] FALSE
D42V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 14(8P23.3) MUTATED     1    1  13   18    8  1   2    4    4   6  0
  DEL PEAK 14(8P23.3) WILD-TYPE   0    0  17   47   16  3   6    3    5  16  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 14(8P23.3) MUTATED     3  0   1  5
  DEL PEAK 14(8P23.3) WILD-TYPE   5  2   0  9
D42V42, multiclass
      clus
vv     DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  T1A                            1                             0
  T1A1                           1                             0
  T1B                           13                            17
  T1B1                          18                            47
  T1B2                           8                            16
  T2                             1                             3
  T2A                            2                             6
  T2A1                           4                             3
  T2A2                           4                             5
  T2B                            6                            16
  T3                             0                             1
  T3B                            3                             5
  T4                             0                             2
  TIS                            1                             0
  TX                             5                             9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 14(8P23.3) MUTATED         2        2         1         1       11
  DEL PEAK 14(8P23.3) WILD-TYPE       2        0         0         0       20
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 14(8P23.3) MUTATED          20        11        2         2
  DEL PEAK 14(8P23.3) WILD-TYPE        49        21        1         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 14(8P23.3) MUTATED            4          2        11         0
  DEL PEAK 14(8P23.3) WILD-TYPE          1          5        16         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 14(8P23.3) MUTATED           13         1         1
  DEL PEAK 14(8P23.3) WILD-TYPE         21         2         6
D42V44, multiclass
            clus
vv           DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                             2                             0
  STAGE IA1                            1                             0
  STAGE IA2                            1                             0
  STAGE IB                            11                            20
  STAGE IB1                           20                            49
  STAGE IB2                           11                            21
  STAGE II                             2                             1
  STAGE IIA                            2                             4
  STAGE IIA1                           4                             1
  STAGE IIA2                           2                             5
  STAGE IIB                           11                            16
  STAGE III                            0                             1
  STAGE IIIB                          13                            21
  STAGE IVA                            1                             2
  STAGE IVB                            1                             6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 15(8P23.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P23.1) MUTATED    55  20
  DEL PEAK 15(8P23.1) WILD-TYPE 128  30
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                           75                           158 
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                           20                            30 
$`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         4.47         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         1.32        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PM TCGA-EK-A2RM 
       12.66        14.89        12.59        45.96         0.59         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         6.12         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-IR-A3LA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VL 
       25.41        21.67       137.16        78.71        26.56        15.58 
TCGA-JW-A852 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MY-A913 TCGA-PN-A8MA 
        5.13         0.82         0.20         0.03         5.49         2.96 
TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        3.39         5.88        10.39        19.59         3.88        11.67 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QF 
       10.03        34.52        19.96        53.52        23.28        49.55 
TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78         4.73        23.24 

$`DEL PEAK 15(8P23.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        23.67        11.44        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        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-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       182.93       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19        85.55        60.69         9.34 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        75.78        23.51        27.52         6.12        20.91 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       50.76        44.94        40.04        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
      117.99        22.98        16.83        16.18        17.52         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.74         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35         1.35        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         6.64         1.51         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        1.18        23.70         0.10         0.10        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       14.70        19.79         4.73         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV 
        1.02         1.58         1.48         3.52         1.35         1.97 
TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
        7.13        20.78        14.93         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        96.95        81.96        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ 
       24.56        21.44        20.48        10.06         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
      195.85        30.31         7.99        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.30        13.87         5.42        29.72         0.07         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        13.35        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG 
       15.88         6.25        93.99        12.16        61.28        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QM 
       20.22        14.07        32.15        46.03        11.51        31.27 
TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       16.64        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  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                        195.85 
  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE 
                        14.50                         16.11 
[1] "0.0 - 137.2 (14.5)" "0.0 - 195.8 (16.1)"
[1] "hr=" "1.5"
D43V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 15(8P23.1) MUTATED   37 17     3
  DEL PEAK 15(8P23.1) WILD-TYPE 84 33     8
D43V3, multiclass
       clus
vv      DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  T1                             37                            84
  T2                             17                            33
  T3+T4                           3                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   36 14
  DEL PEAK 15(8P23.1) WILD-TYPE 75 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     36   14
  DEL PEAK 15(8P23.1) WILD-TYPE   75   33
   clus
vv  DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  0                          36                            75
  1                          14                            33
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 15(8P23.1) MUTATED   30  3 28
  DEL PEAK 15(8P23.1) WILD-TYPE 61  5 65
D43V5, multiclass
    clus
vv   DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  M0                          30                            61
  M1                           3                             5
  MX                          28                            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(8P23.1) MUTATED               2                               66
  DEL PEAK 15(8P23.1) WILD-TYPE             3                              131
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 15(8P23.1) MUTATED                                               1
  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                                              2
  DEL PEAK 15(8P23.1) WILD-TYPE                                            4
D43V6, multiclass
                                               clus
vv                                              DEL PEAK 15(8P23.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       66
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              DEL PEAK 15(8P23.1) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        131
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.1) MUTATED    13  65
  DEL PEAK 15(8P23.1) WILD-TYPE  17 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     13   65
  DEL PEAK 15(8P23.1) WILD-TYPE   17  143
     clus
vv    DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  NO                           13                            17
  YES                          65                           143
[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                          11
  DEL PEAK 15(8P23.1) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(8P23.1) MUTATED                                           1    57
  DEL PEAK 15(8P23.1) WILD-TYPE                                         0   112
D43V10, multiclass
                                           clus
vv                                          DEL PEAK 15(8P23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              57
                                           clus
vv                                          DEL PEAK 15(8P23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               112
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.1) MUTATED     5  47
  DEL PEAK 15(8P23.1) WILD-TYPE  11 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED      5   47
  DEL PEAK 15(8P23.1) WILD-TYPE   11  102
                        clus
vv                       DEL PEAK 15(8P23.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          47
                        clus
vv                       DEL PEAK 15(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           102
[1] 2 2
[1] FALSE
D43V12, continuous
D43V13, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   20 10
  DEL PEAK 15(8P23.1) WILD-TYPE 51 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     20   10
  DEL PEAK 15(8P23.1) WILD-TYPE   51   15
            clus
vv           DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  TUMOR FREE                          20                            51
  WITH TUMOR                          10                            15
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 15(8P23.1) MUTATED        9      2       1      3       2
  DEL PEAK 15(8P23.1) WILD-TYPE     14      3       0      7       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 15(8P23.1) MUTATED              58       3
  DEL PEAK 15(8P23.1) WILD-TYPE           120      11
D43V14, multiclass
               clus
vv              DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  BRAZIL                                  9                            14
  CANADA                                  2                             3
  NIGERIA                                 1                             0
  RUSSIA                                  3                             7
  UKRAINE                                 2                             5
  UNITED STATES                          58                           120
  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 31 35  1  7
  DEL PEAK 15(8P23.1) WILD-TYPE 14 75 62  0  7
D43V15, multiclass
    clus
vv   DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  G1                           3                            14
  G2                          31                            75
  G3                          35                            62
  G4                           1                             0
  GX                           7                             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V16, continuous
D43V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 15(8P23.1) MUTATED                                            13
  DEL PEAK 15(8P23.1) WILD-TYPE                                          18
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 15(8P23.1) MUTATED                                        2
  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                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 15(8P23.1) MUTATED               18                  29
  DEL PEAK 15(8P23.1) WILD-TYPE             34                  83
D43V18, multiclass
                                                 clus
vv                                                DEL PEAK 15(8P23.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           18
  LIFELONG NON-SMOKER                                                      29
                                                 clus
vv                                                DEL PEAK 15(8P23.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             34
  LIFELONG NON-SMOKER                                                        83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V19, continuous
D43V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 15(8P23.1) MUTATED             7       26             7        2
  DEL PEAK 15(8P23.1) WILD-TYPE          12       49             5       10
D43V21, multiclass
               clus
vv              DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  COMBINATION                             7                            12
  EXTERNAL                               26                            49
  EXTERNAL BEAM                           7                             5
  INTERNAL                                2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    11             2
  DEL PEAK 15(8P23.1) WILD-TYPE                  17            14
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                          11                            17
  REGIONAL SITE                                 2                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V24, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   10  2
  DEL PEAK 15(8P23.1) WILD-TYPE 24  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     10    2
  DEL PEAK 15(8P23.1) WILD-TYPE   24    1
     clus
vv    DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  CGY                          10                            24
  GY                            2                             1
[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                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 15(8P23.1) MUTATED                        13                       0
  DEL PEAK 15(8P23.1) WILD-TYPE                      16                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 15(8P23.1) MUTATED                         3
  DEL PEAK 15(8P23.1) WILD-TYPE                       4
D43V31, multiclass
                                     clus
vv                                    DEL PEAK 15(8P23.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                      13
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    DEL PEAK 15(8P23.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                        16
  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 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                                                3
  DEL PEAK 15(8P23.1) WILD-TYPE                                             13
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 15(8P23.1) MUTATED                                                                                  20
  DEL PEAK 15(8P23.1) WILD-TYPE                                                                                48
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 15(8P23.1) MUTATED                                                                                             40
  DEL PEAK 15(8P23.1) WILD-TYPE                                                                                           65
D43V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 15(8P23.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          40
                                                                                              clus
vv                                                                                             DEL PEAK 15(8P23.1) 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)                                       48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V33, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   25 17
  DEL PEAK 15(8P23.1) WILD-TYPE 43 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     25   17
  DEL PEAK 15(8P23.1) WILD-TYPE   43   53
         clus
vv        DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  ABSENT                           25                            43
  PRESENT                          17                            53
[1] 2 2
[1] FALSE
D43V34, continuous
D43V35, continuous
D43V36, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   15 31
  DEL PEAK 15(8P23.1) WILD-TYPE 28 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     15   31
  DEL PEAK 15(8P23.1) WILD-TYPE   28   63
                                          clus
vv                                         DEL PEAK 15(8P23.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          31
                                          clus
vv                                         DEL PEAK 15(8P23.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            63
[1] 2 2
[1] FALSE
D43V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 15(8P23.1) MUTATED              3          17         17
  DEL PEAK 15(8P23.1) WILD-TYPE            7          32         40
D43V38, multiclass
              clus
vv             DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  CURRENT USER                           3                             7
  FORMER USER                           17                            32
  NEVER USED                            17                            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V39, continuous
D43V40, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.1) MUTATED   30  5
  DEL PEAK 15(8P23.1) WILD-TYPE 59 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.1) MUTATED     30    5
  DEL PEAK 15(8P23.1) WILD-TYPE   59   11
         clus
vv        DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  ABSENT                           30                            59
  PRESENT                           5                            11
[1] 2 2
[1] FALSE
D43V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 15(8P23.1) MUTATED     1    1  11   17    7  1   2    4    4   6  0
  DEL PEAK 15(8P23.1) WILD-TYPE   0    0  19   48   17  3   6    3    5  16  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 15(8P23.1) MUTATED     3  0   1  5
  DEL PEAK 15(8P23.1) WILD-TYPE   5  2   0  9
D43V42, multiclass
      clus
vv     DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  T1A                            1                             0
  T1A1                           1                             0
  T1B                           11                            19
  T1B1                          17                            48
  T1B2                           7                            17
  T2                             1                             3
  T2A                            2                             6
  T2A1                           4                             3
  T2A2                           4                             5
  T2B                            6                            16
  T3                             0                             1
  T3B                            3                             5
  T4                             0                             2
  TIS                            1                             0
  TX                             5                             9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 15(8P23.1) MUTATED         2        1         1         1       10
  DEL PEAK 15(8P23.1) WILD-TYPE       2        1         0         0       21
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 15(8P23.1) MUTATED          19         9        2         2
  DEL PEAK 15(8P23.1) WILD-TYPE        50        23        1         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 15(8P23.1) MUTATED            4          2        12         0
  DEL PEAK 15(8P23.1) WILD-TYPE          1          5        15         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 15(8P23.1) MUTATED           11         0         1
  DEL PEAK 15(8P23.1) WILD-TYPE         23         3         6
D43V44, multiclass
            clus
vv           DEL PEAK 15(8P23.1) MUTATED DEL PEAK 15(8P23.1) WILD-TYPE
  STAGE I                              2                             2
  STAGE IA                             1                             1
  STAGE IA1                            1                             0
  STAGE IA2                            1                             0
  STAGE IB                            10                            21
  STAGE IB1                           19                            50
  STAGE IB2                            9                            23
  STAGE II                             2                             1
  STAGE IIA                            2                             4
  STAGE IIA1                           4                             1
  STAGE IIA2                           2                             5
  STAGE IIB                           12                            15
  STAGE III                            0                             1
  STAGE IIIB                          11                            23
  STAGE IVA                            0                             3
  STAGE IVB                            1                             6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 16(10Q23.31) MUTATED    47  21
  DEL PEAK 16(10Q23.31) WILD-TYPE 136  29
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             68                             165 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             21                              29 
$`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       182.93       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 
       75.78        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-A2PM 
       14.96        13.48        12.59        26.27         6.64         0.59 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-FU-A2QG 
        1.18        23.70         2.24         0.10        20.35         0.92 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A40J TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.58         1.48         1.35         9.01        21.67        20.78 
TCGA-HM-A6W2 TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-A69B 
        9.44        66.81        78.71        36.36        20.48        10.06 
TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       30.31         0.07         5.49         2.96        13.35         3.39 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A94Y 
       12.16        61.28        20.22        19.96        53.52         4.73 
TCGA-VS-A954 TCGA-VS-A9U5 
       42.58        38.96 

$`DEL PEAK 16(10Q23.31) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
        5.46        67.46        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY 
       53.16         2.43        40.93         3.58        44.22        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A7CJ TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC 
      101.82        85.55        60.69        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         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        4.47         1.12        50.76        40.04        87.75        58.88 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
        1.35         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A97N 
        1.48        13.91        15.02        14.99        13.58         0.36 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       45.96         1.51         0.43         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RO 
       16.08         0.07         4.04         0.03         0.36         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.10         0.03         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       19.79         6.12         4.73         1.22        23.84         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        0.66         1.02         1.45         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-IR-A3L7 
        1.97         1.12        25.41         7.13        14.93       147.39 
TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      137.16       117.40        96.95        81.96        26.56        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        24.56        21.44        15.58         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
       21.11       195.85         7.99        11.28         0.89         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.82         0.20        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        0.07         4.34        15.58        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        3.88        11.67        93.99        10.03        34.52        29.03 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       14.07        32.15        46.03        23.28        11.51        49.55 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 
       39.78        31.27        16.64        23.24        44.88        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         182.93                          195.85 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         20.385                          14.890 
[1] "0.1 - 182.9 (20.4)" "0.0 - 195.8 (14.9)"
[1] "hr=" "1.4"
D44V2, continuous
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 16(10Q23.31) MUTATED   31 17     3
  DEL PEAK 16(10Q23.31) WILD-TYPE 90 33     8
D44V3, multiclass
       clus
vv      DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T1                               31                              90
  T2                               17                              33
  T3+T4                             3                               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   25 17
  DEL PEAK 16(10Q23.31) WILD-TYPE 86 30
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     25   17
  DEL PEAK 16(10Q23.31) WILD-TYPE   86   30
   clus
vv  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  0                            25                              86
  1                            17                              30
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 16(10Q23.31) MUTATED   22  3 28
  DEL PEAK 16(10Q23.31) WILD-TYPE 69  5 65
D44V5, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  M0                            22                              69
  M1                             3                               5
  MX                            28                              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  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                                 60
  DEL PEAK 16(10Q23.31) WILD-TYPE                              137
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 16(10Q23.31) MUTATED                                               1
  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                                              1
  DEL PEAK 16(10Q23.31) WILD-TYPE                                            5
D44V6, multiclass
                                               clus
vv                                              DEL PEAK 16(10Q23.31) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         60
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              1
                                               clus
vv                                              DEL PEAK 16(10Q23.31) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          137
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    13  58
  DEL PEAK 16(10Q23.31) WILD-TYPE  17 150
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     13   58
  DEL PEAK 16(10Q23.31) WILD-TYPE   17  150
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  NO                             13                              17
  YES                            58                             150
[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                          14
  DEL PEAK 16(10Q23.31) WILD-TYPE                        10
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 16(10Q23.31) MUTATED                                           0
  DEL PEAK 16(10Q23.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 16(10Q23.31) MUTATED      47
  DEL PEAK 16(10Q23.31) WILD-TYPE   122
D44V10, multiclass
                                           clus
vv                                          DEL PEAK 16(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                47
                                           clus
vv                                          DEL PEAK 16(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED     4  43
  DEL PEAK 16(10Q23.31) WILD-TYPE  12 106
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      4   43
  DEL PEAK 16(10Q23.31) WILD-TYPE   12  106
                        clus
vv                       DEL PEAK 16(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            43
                        clus
vv                       DEL PEAK 16(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             106
[1] 2 2
[1] FALSE
D44V12, continuous
D44V13, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   24 10
  DEL PEAK 16(10Q23.31) WILD-TYPE 47 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     24   10
  DEL PEAK 16(10Q23.31) WILD-TYPE   47   15
            clus
vv           DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  TUMOR FREE                            24                              47
  WITH TUMOR                            10                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 16(10Q23.31) MUTATED        6      2       1      0       0
  DEL PEAK 16(10Q23.31) WILD-TYPE     17      3       0     10       7
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 16(10Q23.31) MUTATED              58       4
  DEL PEAK 16(10Q23.31) WILD-TYPE           120      10
D44V14, multiclass
               clus
vv              DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  BRAZIL                                    6                              17
  CANADA                                    2                               3
  NIGERIA                                   1                               0
  RUSSIA                                    0                              10
  UKRAINE                                   0                               7
  UNITED STATES                            58                             120
  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 26 37  1  3
  DEL PEAK 16(10Q23.31) WILD-TYPE 14 80 60  0 11
D44V15, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  G1                             3                              14
  G2                            26                              80
  G3                            37                              60
  G4                             1                               0
  GX                             3                              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V16, continuous
D44V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 16(10Q23.31) MUTATED                                             9
  DEL PEAK 16(10Q23.31) WILD-TYPE                                          22
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 16(10Q23.31) MUTATED                                        4
  DEL PEAK 16(10Q23.31) WILD-TYPE                                      4
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 16(10Q23.31) MUTATED                                                 2
  DEL PEAK 16(10Q23.31) WILD-TYPE                                               0
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 16(10Q23.31) MUTATED               16                  24
  DEL PEAK 16(10Q23.31) WILD-TYPE             36                  88
D44V18, multiclass
                                                 clus
vv                                                DEL PEAK 16(10Q23.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             16
  LIFELONG NON-SMOKER                                                        24
                                                 clus
vv                                                DEL PEAK 16(10Q23.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               0
  CURRENT SMOKER                                                               36
  LIFELONG NON-SMOKER                                                          88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V19, continuous
D44V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 16(10Q23.31) MUTATED             7       22             6        3
  DEL PEAK 16(10Q23.31) WILD-TYPE          12       53             6        9
D44V21, multiclass
               clus
vv              DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  COMBINATION                               7                              12
  EXTERNAL                                 22                              53
  EXTERNAL BEAM                             6                               6
  INTERNAL                                  3                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    11             4
  DEL PEAK 16(10Q23.31) WILD-TYPE                  17            12
D44V23, multiclass
                     clus
vv                    DEL PEAK 16(10Q23.31) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                2
  PRIMARY TUMOR FIELD                            11
  REGIONAL SITE                                   4
                     clus
vv                    DEL PEAK 16(10Q23.31) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  0
  PRIMARY TUMOR FIELD                              17
  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"
D44V24, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   11  2
  DEL PEAK 16(10Q23.31) WILD-TYPE 23  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     11    2
  DEL PEAK 16(10Q23.31) WILD-TYPE   23    1
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CGY                            11                              23
  GY                              2                               1
[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                                   3
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 16(10Q23.31) MUTATED                         7
  DEL PEAK 16(10Q23.31) WILD-TYPE                      22
                                 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                         5
  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                                         7
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         5
                                     clus
vv                                    DEL PEAK 16(10Q23.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               3
  OTHER LOCATION, SPECIFY                                          22
  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                                                7
  DEL PEAK 16(10Q23.31) WILD-TYPE                                              9
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 16(10Q23.31) MUTATED                                                                                  25
  DEL PEAK 16(10Q23.31) WILD-TYPE                                                                                43
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 16(10Q23.31) MUTATED                                                                                             21
  DEL PEAK 16(10Q23.31) WILD-TYPE                                                                                           84
D44V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 16(10Q23.31) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            21
                                                                                              clus
vv                                                                                             DEL PEAK 16(10Q23.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                             9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         43
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V33, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   16 23
  DEL PEAK 16(10Q23.31) WILD-TYPE 52 47
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     16   23
  DEL PEAK 16(10Q23.31) WILD-TYPE   52   47
         clus
vv        DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  ABSENT                             16                              52
  PRESENT                            23                              47
[1] 2 2
[1] FALSE
D44V34, continuous
D44V35, continuous
D44V36, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   17 25
  DEL PEAK 16(10Q23.31) WILD-TYPE 26 69
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     17   25
  DEL PEAK 16(10Q23.31) WILD-TYPE   26   69
                                          clus
vv                                         DEL PEAK 16(10Q23.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            25
                                          clus
vv                                         DEL PEAK 16(10Q23.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              69
[1] 2 2
[1] FALSE
D44V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 16(10Q23.31) MUTATED              2          12         13
  DEL PEAK 16(10Q23.31) WILD-TYPE            8          37         44
D44V38, multiclass
              clus
vv             DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CURRENT USER                             2                               8
  FORMER USER                             12                              37
  NEVER USED                              13                              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V39, continuous
D44V40, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   22  5
  DEL PEAK 16(10Q23.31) WILD-TYPE 67 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     22    5
  DEL PEAK 16(10Q23.31) WILD-TYPE   67   11
         clus
vv        DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  ABSENT                             22                              67
  PRESENT                             5                              11
[1] 2 2
[1] FALSE
D44V41, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 16(10Q23.31) MUTATED     0    0   9   17    5  2   3    3    0   9
  DEL PEAK 16(10Q23.31) WILD-TYPE   1    1  21   48   19  2   5    4    9  13
                                 vv
clus                              T3 T3B T4 TIS TX
  DEL PEAK 16(10Q23.31) MUTATED    0   3  0   1  2
  DEL PEAK 16(10Q23.31) WILD-TYPE  1   5  2   0 12
D44V42, multiclass
      clus
vv     DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T1A                              0                               1
  T1A1                             0                               1
  T1B                              9                              21
  T1B1                            17                              48
  T1B2                             5                              19
  T2                               2                               2
  T2A                              3                               5
  T2A1                             3                               4
  T2A2                             0                               9
  T2B                              9                              13
  T3                               0                               1
  T3B                              3                               5
  T4                               0                               2
  TIS                              1                               0
  TX                               2                              12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 16(10Q23.31) MUTATED         1        0         0         1       12
  DEL PEAK 16(10Q23.31) WILD-TYPE       3        2         1         0       19
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 16(10Q23.31) MUTATED          17        10        0         3
  DEL PEAK 16(10Q23.31) WILD-TYPE        52        22        3         3
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 16(10Q23.31) MUTATED            2          1         9         0
  DEL PEAK 16(10Q23.31) WILD-TYPE          3          6        18         1
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 16(10Q23.31) MUTATED           11         1         2
  DEL PEAK 16(10Q23.31) WILD-TYPE         23         2         5
D44V44, multiclass
            clus
vv           DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                               0                               2
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                              12                              19
  STAGE IB1                             17                              52
  STAGE IB2                             10                              22
  STAGE II                               0                               3
  STAGE IIA                              3                               3
  STAGE IIA1                             2                               3
  STAGE IIA2                             1                               6
  STAGE IIB                              9                              18
  STAGE III                              0                               1
  STAGE IIIB                            11                              23
  STAGE IVA                              1                               2
  STAGE IVB                              2                               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 17(11P15.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(11P15.1) MUTATED    56  23
  DEL PEAK 17(11P15.1) WILD-TYPE 127  27
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            79                            154 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            23                             27 
$`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       182.93       154.32        15.48        60.69        94.95 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
        2.73        50.99        75.78        99.91        23.51        27.52 
TCGA-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         1.35        14.50         1.81        12.66         0.26 
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         6.12        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        26.56 
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         0.07         0.82 
TCGA-LP-A7HU TCGA-MY-A5BE TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73Q 
        0.20         0.07        13.35         3.39        17.56         5.88 
TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       19.59        12.16        10.03        20.22        14.07        19.96 
TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       46.03        49.55         4.73        42.08        39.35        38.96 
TCGA-WL-A834 
       18.05 

$`DEL PEAK 17(11P15.1) WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        23.67        11.44        68.84        36.56       144.16 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME 
      173.29        82.85        67.46        31.40        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       53.16         2.43        40.93         3.58        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35        38.43         0.82        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7CO 
       17.85        20.42       101.82       134.33        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XI 
       17.19        85.55         9.34        13.61        45.83         8.35 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        6.12        20.91         4.47         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       44.94        58.88         2.66        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       17.52         0.76         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A556 
       13.05         1.18        14.50         1.35        12.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 
        1.48        13.91        15.02        13.58        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       26.27         6.64         0.59         0.59         1.45         0.13 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.07         0.10         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70        19.79         4.73         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J 
        0.66         1.02         1.58         1.48         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.32         1.97         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LF 
       20.78        14.93         9.44       147.39       137.16        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VL 
       78.71        81.96        36.36        27.42         3.29        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        7.99         0.89         0.30        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       29.72         4.34         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         6.25        10.39         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL 
       11.67        93.99        61.28        34.52        29.03        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       32.15        23.28        11.51        39.78        31.27        16.64 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       23.24        44.88        42.58        43.82 

  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                        182.93                         195.85 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                         19.59                          14.91 
[1] "0.1 - 182.9 (19.6)" "0.0 - 195.8 (14.9)"
[1] "hr=" "1.4"
D45V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 17(11P15.1) MUTATED   37 18     5
  DEL PEAK 17(11P15.1) WILD-TYPE 84 32     6
D45V3, multiclass
       clus
vv      DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  T1                              37                             84
  T2                              18                             32
  T3+T4                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   32 16
  DEL PEAK 17(11P15.1) WILD-TYPE 79 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     32   16
  DEL PEAK 17(11P15.1) WILD-TYPE   79   31
   clus
vv  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  0                           32                             79
  1                           16                             31
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 17(11P15.1) MUTATED   32  2 31
  DEL PEAK 17(11P15.1) WILD-TYPE 59  6 62
D45V5, multiclass
    clus
vv   DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  M0                           32                             59
  M1                            2                              6
  MX                           31                             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(11P15.1) MUTATED               0                               76
  DEL PEAK 17(11P15.1) WILD-TYPE             5                              121
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 17(11P15.1) MUTATED                                               1
  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                                              1
  DEL PEAK 17(11P15.1) WILD-TYPE                                            5
D45V6, multiclass
                                               clus
vv                                              DEL PEAK 17(11P15.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        76
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK 17(11P15.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         121
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(11P15.1) MUTATED     8  74
  DEL PEAK 17(11P15.1) WILD-TYPE  22 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED      8   74
  DEL PEAK 17(11P15.1) WILD-TYPE   22  134
     clus
vv    DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  NO                             8                             22
  YES                           74                            134
[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                           8
  DEL PEAK 17(11P15.1) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 17(11P15.1) MUTATED                                           1
  DEL PEAK 17(11P15.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 17(11P15.1) MUTATED      56
  DEL PEAK 17(11P15.1) WILD-TYPE   113
D45V10, multiclass
                                           clus
vv                                          DEL PEAK 17(11P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               11
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               56
                                           clus
vv                                          DEL PEAK 17(11P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                  7
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED    4 54
  DEL PEAK 17(11P15.1) WILD-TYPE 12 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED      4   54
  DEL PEAK 17(11P15.1) WILD-TYPE   12   95
                        clus
vv                       DEL PEAK 17(11P15.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK 17(11P15.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                             95
[1] 2 2
[1] FALSE
D45V12, continuous
D45V13, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   21 14
  DEL PEAK 17(11P15.1) WILD-TYPE 50 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     21   14
  DEL PEAK 17(11P15.1) WILD-TYPE   50   11
            clus
vv           DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  TUMOR FREE                           21                             50
  WITH TUMOR                           14                             11
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 17(11P15.1) MUTATED       10      1       0      2       3
  DEL PEAK 17(11P15.1) WILD-TYPE     13      4       1      8       4
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 17(11P15.1) MUTATED              56      10
  DEL PEAK 17(11P15.1) WILD-TYPE           122       4
D45V14, multiclass
               clus
vv              DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  BRAZIL                                  10                             13
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  3                              4
  UNITED STATES                           56                            122
  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    2 32 40  0  6
  DEL PEAK 17(11P15.1) WILD-TYPE 15 74 57  1  8
D45V15, multiclass
    clus
vv   DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  G1                            2                             15
  G2                           32                             74
  G3                           40                             57
  G4                            0                              1
  GX                            6                              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V16, continuous
D45V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 17(11P15.1) MUTATED                                             9
  DEL PEAK 17(11P15.1) WILD-TYPE                                          22
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 17(11P15.1) MUTATED                                        3
  DEL PEAK 17(11P15.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 17(11P15.1) MUTATED                                                 0
  DEL PEAK 17(11P15.1) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 17(11P15.1) MUTATED               21                  43
  DEL PEAK 17(11P15.1) WILD-TYPE             31                  69
D45V18, multiclass
                                                 clus
vv                                                DEL PEAK 17(11P15.1) 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                                                            21
  LIFELONG NON-SMOKER                                                       43
                                                 clus
vv                                                DEL PEAK 17(11P15.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              31
  LIFELONG NON-SMOKER                                                         69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V19, continuous
D45V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 17(11P15.1) MUTATED             5       30             3        3
  DEL PEAK 17(11P15.1) WILD-TYPE          14       45             9        9
D45V21, multiclass
               clus
vv              DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  COMBINATION                              5                             14
  EXTERNAL                                30                             45
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    11             6
  DEL PEAK 17(11P15.1) WILD-TYPE                  17            10
D45V23, multiclass
                     clus
vv                    DEL PEAK 17(11P15.1) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                           11
  REGIONAL SITE                                  6
                     clus
vv                    DEL PEAK 17(11P15.1) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             17
  REGIONAL SITE                                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V24, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   10  2
  DEL PEAK 17(11P15.1) WILD-TYPE 24  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     10    2
  DEL PEAK 17(11P15.1) WILD-TYPE   24    1
     clus
vv    DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  CGY                           10                             24
  GY                             2                              1
[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                                     2
  DEL PEAK 17(11P15.1) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 17(11P15.1) MUTATED                         8
  DEL PEAK 17(11P15.1) WILD-TYPE                      21
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 17(11P15.1) MUTATED                         1
  DEL PEAK 17(11P15.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 17(11P15.1) MUTATED                         1
  DEL PEAK 17(11P15.1) WILD-TYPE                       6
D45V31, multiclass
                                     clus
vv                                    DEL PEAK 17(11P15.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        8
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 17(11P15.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                         21
  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                                                8
  DEL PEAK 17(11P15.1) WILD-TYPE                                              8
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 17(11P15.1) MUTATED                                                                                  28
  DEL PEAK 17(11P15.1) WILD-TYPE                                                                                40
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 17(11P15.1) MUTATED                                                                                             27
  DEL PEAK 17(11P15.1) WILD-TYPE                                                                                           78
D45V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 17(11P15.1) 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)                                      28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           27
                                                                                              clus
vv                                                                                             DEL PEAK 17(11P15.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D45V33, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   24 19
  DEL PEAK 17(11P15.1) WILD-TYPE 44 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     24   19
  DEL PEAK 17(11P15.1) WILD-TYPE   44   51
         clus
vv        DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  ABSENT                            24                             44
  PRESENT                           19                             51
[1] 2 2
[1] FALSE
D45V34, continuous
D45V35, continuous
D45V36, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   14 33
  DEL PEAK 17(11P15.1) WILD-TYPE 29 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     14   33
  DEL PEAK 17(11P15.1) WILD-TYPE   29   61
                                          clus
vv                                         DEL PEAK 17(11P15.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           33
                                          clus
vv                                         DEL PEAK 17(11P15.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             61
[1] 2 2
[1] FALSE
D45V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 17(11P15.1) MUTATED              2          13         26
  DEL PEAK 17(11P15.1) WILD-TYPE            8          36         31
D45V38, multiclass
              clus
vv             DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  CURRENT USER                            2                              8
  FORMER USER                            13                             36
  NEVER USED                             26                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V39, continuous
D45V40, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   30  5
  DEL PEAK 17(11P15.1) WILD-TYPE 59 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     30    5
  DEL PEAK 17(11P15.1) WILD-TYPE   59   11
         clus
vv        DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  ABSENT                            30                             59
  PRESENT                            5                             11
[1] 2 2
[1] FALSE
D45V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 17(11P15.1) MUTATED     1    0  10   21    5  2   1    2    5   8  0
  DEL PEAK 17(11P15.1) WILD-TYPE   0    1  20   44   19  2   7    5    4  14  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 17(11P15.1) MUTATED     4  1   0  7
  DEL PEAK 17(11P15.1) WILD-TYPE   4  1   1  7
D45V42, multiclass
      clus
vv     DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  T1A                             1                              0
  T1A1                            0                              1
  T1B                            10                             20
  T1B1                           21                             44
  T1B2                            5                             19
  T2                              2                              2
  T2A                             1                              7
  T2A1                            2                              5
  T2A2                            5                              4
  T2B                             8                             14
  T3                              0                              1
  T3B                             4                              4
  T4                              1                              1
  TIS                             0                              1
  TX                              7                              7
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 17(11P15.1) MUTATED         3        1         0         1       15
  DEL PEAK 17(11P15.1) WILD-TYPE       1        1         1         0       16
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 17(11P15.1) MUTATED          21         6        1         1
  DEL PEAK 17(11P15.1) WILD-TYPE        48        26        2         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 17(11P15.1) MUTATED            2          3        10         0
  DEL PEAK 17(11P15.1) WILD-TYPE          3          4        17         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 17(11P15.1) MUTATED           13         1         0
  DEL PEAK 17(11P15.1) WILD-TYPE         21         2         7
D45V44, multiclass
            clus
vv           DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             15                             16
  STAGE IB1                            21                             48
  STAGE IB2                             6                             26
  STAGE II                              1                              2
  STAGE IIA                             1                              5
  STAGE IIA1                            2                              3
  STAGE IIA2                            3                              4
  STAGE IIB                            10                             17
  STAGE III                             0                              1
  STAGE IIIB                           13                             21
  STAGE IVA                             1                              2
  STAGE IVB                             0                              7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 18(11Q23.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(11Q23.3) MUTATED   96 34
  DEL PEAK 18(11Q23.3) WILD-TYPE 87 16
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                           130                            103 
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                            34                             16 
$`DEL PEAK 18(11Q23.3) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 
      144.16       177.04       173.29        82.85        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       46.32        30.21        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        0.46         2.43        20.91        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL 
      100.14         0.82        52.01       182.93       154.32        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       20.35        17.19        60.69        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KK 
       45.83        75.78        99.91        23.51        27.52        50.76 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       87.75        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE 
       16.83         8.28        12.36         1.32        13.05         1.18 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZE 
        1.35        14.50         1.81         0.26        13.91        14.99 
TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG 
       14.96        13.48         0.36        12.59         6.64         1.51 
TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RM 
        0.59         0.13        16.08         0.03        23.70         2.24 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M 
        0.07         0.10        20.35         6.94        19.79         6.12 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LA 
        1.45         1.58         0.82         7.13        21.67       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VK 
       66.81       117.40        78.71        81.96        36.36        20.48 
TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06        21.11         7.99        11.28         0.07         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.20        13.87         0.03        29.72         0.07         4.34 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P 
        5.49         2.96        13.35         3.39        17.56        15.88 
TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
        5.88        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        29.03        20.22        14.07        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Z TCGA-VS-A952 
       32.15        46.03        11.51        49.55        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       42.58        42.08        39.35        38.96 

$`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        85.55        94.95         9.34 
TCGA-C5-A8XI TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
        8.35         6.12        20.91         4.47         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         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S 
        1.74         0.82         0.62        14.50         1.35        12.66 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2H0 
       12.82        14.89         1.48        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         4.73         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 
        0.66         1.02         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        26.56        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         5.13         6.71       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MU-A8JM TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       30.31         0.89         0.30         5.42        15.58        15.95 
TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EC 
       16.14        14.07         6.25        10.39        61.28        34.52 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A958 
       23.28        39.78        31.27        16.64         4.73        43.82 
TCGA-WL-A834 
       18.05 

  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 
                        182.93                         195.85 
  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE 
                         19.69                          14.50 
[1] "0.0 - 182.9 (19.7)" "0.0 - 195.8 (14.5)"
[1] "hr=" "1.2"
D46V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 18(11Q23.3) MUTATED   67 26     7
  DEL PEAK 18(11Q23.3) WILD-TYPE 54 24     4
D46V3, multiclass
       clus
vv      DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  T1                              67                             54
  T2                              26                             24
  T3+T4                            7                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   61 25
  DEL PEAK 18(11Q23.3) WILD-TYPE 50 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     61   25
  DEL PEAK 18(11Q23.3) WILD-TYPE   50   22
   clus
vv  DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  0                           61                             50
  1                           25                             22
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 18(11Q23.3) MUTATED   55  4 48
  DEL PEAK 18(11Q23.3) WILD-TYPE 36  4 45
D46V5, multiclass
    clus
vv   DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  M0                           55                             36
  M1                            4                              4
  MX                           48                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(11Q23.3) MUTATED               1                              118
  DEL PEAK 18(11Q23.3) WILD-TYPE             4                               79
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 18(11Q23.3) MUTATED                                               1
  DEL PEAK 18(11Q23.3) WILD-TYPE                                             4
                                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                                              2
  DEL PEAK 18(11Q23.3) WILD-TYPE                                            4
D46V6, multiclass
                                               clus
vv                                              DEL PEAK 18(11Q23.3) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       118
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              DEL PEAK 18(11Q23.3) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          79
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q23.3) MUTATED    20 112
  DEL PEAK 18(11Q23.3) WILD-TYPE  10  96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     20  112
  DEL PEAK 18(11Q23.3) WILD-TYPE   10   96
     clus
vv    DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  NO                            20                             10
  YES                          112                             96
[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                          18
  DEL PEAK 18(11Q23.3) WILD-TYPE                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 18(11Q23.3) MUTATED                                           1
  DEL PEAK 18(11Q23.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 18(11Q23.3) MUTATED      91
  DEL PEAK 18(11Q23.3) WILD-TYPE    78
D46V10, multiclass
                                           clus
vv                                          DEL PEAK 18(11Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               11
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               91
                                           clus
vv                                          DEL PEAK 18(11Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                  7
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED    6 81
  DEL PEAK 18(11Q23.3) WILD-TYPE 10 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED      6   81
  DEL PEAK 18(11Q23.3) WILD-TYPE   10   68
                        clus
vv                       DEL PEAK 18(11Q23.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK 18(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             68
[1] 2 2
[1] FALSE
D46V12, continuous
D46V13, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   40 18
  DEL PEAK 18(11Q23.3) WILD-TYPE 31  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     40   18
  DEL PEAK 18(11Q23.3) WILD-TYPE   31    7
            clus
vv           DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  TUMOR FREE                           40                             31
  WITH TUMOR                           18                              7
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 18(11Q23.3) MUTATED       16      1       1      4       3
  DEL PEAK 18(11Q23.3) WILD-TYPE      7      4       0      6       4
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 18(11Q23.3) MUTATED              98       9
  DEL PEAK 18(11Q23.3) WILD-TYPE            80       5
D46V14, multiclass
               clus
vv              DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  BRAZIL                                  16                              7
  CANADA                                   1                              4
  NIGERIA                                  1                              0
  RUSSIA                                   4                              6
  UKRAINE                                  3                              4
  UNITED STATES                           98                             80
  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    7 59 55  1  8
  DEL PEAK 18(11Q23.3) WILD-TYPE 10 47 42  0  6
D46V15, multiclass
    clus
vv   DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  G1                            7                             10
  G2                           59                             47
  G3                           55                             42
  G4                            1                              0
  GX                            8                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V16, continuous
D46V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 18(11Q23.3) MUTATED                                            20
  DEL PEAK 18(11Q23.3) WILD-TYPE                                          11
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 18(11Q23.3) MUTATED                                        6
  DEL PEAK 18(11Q23.3) WILD-TYPE                                      2
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 18(11Q23.3) MUTATED                                                 1
  DEL PEAK 18(11Q23.3) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 18(11Q23.3) MUTATED               23                  64
  DEL PEAK 18(11Q23.3) WILD-TYPE             29                  48
D46V18, multiclass
                                                 clus
vv                                                DEL PEAK 18(11Q23.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            23
  LIFELONG NON-SMOKER                                                       64
                                                 clus
vv                                                DEL PEAK 18(11Q23.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              29
  LIFELONG NON-SMOKER                                                         48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V19, continuous
D46V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 18(11Q23.3) MUTATED            15       40             6        7
  DEL PEAK 18(11Q23.3) WILD-TYPE           4       35             6        5
D46V21, multiclass
               clus
vv              DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  COMBINATION                             15                              4
  EXTERNAL                                40                             35
  EXTERNAL BEAM                            6                              6
  INTERNAL                                 7                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    17            10
  DEL PEAK 18(11Q23.3) WILD-TYPE                  11             6
D46V23, multiclass
                     clus
vv                    DEL PEAK 18(11Q23.3) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                           17
  REGIONAL SITE                                 10
                     clus
vv                    DEL PEAK 18(11Q23.3) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             11
  REGIONAL SITE                                    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"
D46V24, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   21  3
  DEL PEAK 18(11Q23.3) WILD-TYPE 13  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     21    3
  DEL PEAK 18(11Q23.3) WILD-TYPE   13    0
     clus
vv    DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  CGY                           21                             13
  GY                             3                              0
[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                                   2
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 18(11Q23.3) MUTATED                        17
  DEL PEAK 18(11Q23.3) WILD-TYPE                      12
                                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                         4
  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                                       17
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        4
                                     clus
vv                                    DEL PEAK 18(11Q23.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  OTHER LOCATION, SPECIFY                                         12
  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                                               11
  DEL PEAK 18(11Q23.3) WILD-TYPE                                              5
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 18(11Q23.3) MUTATED                                                                                  45
  DEL PEAK 18(11Q23.3) WILD-TYPE                                                                                23
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 18(11Q23.3) MUTATED                                                                                             50
  DEL PEAK 18(11Q23.3) WILD-TYPE                                                                                           55
D46V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 18(11Q23.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           50
                                                                                              clus
vv                                                                                             DEL PEAK 18(11Q23.3) 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)                                        23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V33, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   33 43
  DEL PEAK 18(11Q23.3) WILD-TYPE 35 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     33   43
  DEL PEAK 18(11Q23.3) WILD-TYPE   35   27
         clus
vv        DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  ABSENT                            33                             35
  PRESENT                           43                             27
[1] 2 2
[1] FALSE
D46V34, continuous
D46V35, continuous
D46V36, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   26 51
  DEL PEAK 18(11Q23.3) WILD-TYPE 17 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     26   51
  DEL PEAK 18(11Q23.3) WILD-TYPE   17   43
                                          clus
vv                                         DEL PEAK 18(11Q23.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           51
                                          clus
vv                                         DEL PEAK 18(11Q23.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             43
[1] 2 2
[1] FALSE
D46V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 18(11Q23.3) MUTATED              3          26         36
  DEL PEAK 18(11Q23.3) WILD-TYPE            7          23         21
D46V38, multiclass
              clus
vv             DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  CURRENT USER                            3                              7
  FORMER USER                            26                             23
  NEVER USED                             36                             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"
D46V39, continuous
D46V40, binary
                                cls
clus                              0  1
  DEL PEAK 18(11Q23.3) MUTATED   47 11
  DEL PEAK 18(11Q23.3) WILD-TYPE 42  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.3) MUTATED     47   11
  DEL PEAK 18(11Q23.3) WILD-TYPE   42    5
         clus
vv        DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  ABSENT                            47                             42
  PRESENT                           11                              5
[1] 2 2
[1] FALSE
D46V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 18(11Q23.3) MUTATED     1    1  20   38    7  4   2    4    4  12  0
  DEL PEAK 18(11Q23.3) WILD-TYPE   0    0  10   27   17  0   6    3    5  10  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 18(11Q23.3) MUTATED     6  1   1  8
  DEL PEAK 18(11Q23.3) WILD-TYPE   2  1   0  6
D46V42, multiclass
      clus
vv     DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  T1A                             1                              0
  T1A1                            1                              0
  T1B                            20                             10
  T1B1                           38                             27
  T1B2                            7                             17
  T2                              4                              0
  T2A                             2                              6
  T2A1                            4                              3
  T2A2                            4                              5
  T2B                            12                             10
  T3                              0                              1
  T3B                             6                              2
  T4                              1                              1
  TIS                             1                              0
  TX                              8                              6
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 18(11Q23.3) MUTATED         3        1         1         1       25
  DEL PEAK 18(11Q23.3) WILD-TYPE       1        1         0         0        6
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 18(11Q23.3) MUTATED          37        11        2         1
  DEL PEAK 18(11Q23.3) WILD-TYPE        32        21        1         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 18(11Q23.3) MUTATED            4          4        18         0
  DEL PEAK 18(11Q23.3) WILD-TYPE          1          3         9         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 18(11Q23.3) MUTATED           17         2         2
  DEL PEAK 18(11Q23.3) WILD-TYPE         17         1         5
D46V44, multiclass
            clus
vv           DEL PEAK 18(11Q23.3) MUTATED DEL PEAK 18(11Q23.3) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                              1                              1
  STAGE IA1                             1                              0
  STAGE IA2                             1                              0
  STAGE IB                             25                              6
  STAGE IB1                            37                             32
  STAGE IB2                            11                             21
  STAGE II                              2                              1
  STAGE IIA                             1                              5
  STAGE IIA1                            4                              1
  STAGE IIA2                            4                              3
  STAGE IIB                            18                              9
  STAGE III                             0                              1
  STAGE IIIB                           17                             17
  STAGE IVA                             2                              1
  STAGE IVB                             2                              5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 19(11Q25) MUTATION ANALYSIS
D47V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 19(11Q25) MUTATED   94 35
  DEL PEAK 19(11Q25) WILD-TYPE 89 15
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                         129                          104 
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                          35                           15 
$`DEL PEAK 19(11Q25) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85         5.46        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       31.40        46.32        30.21        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-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         0.82        52.01       182.93       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        60.69        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        75.78        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-A7WH TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR 
       22.98        16.83        17.52         8.28        12.36         1.32 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E 
       13.05         1.18         1.35        14.50         1.81         0.26 
TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       13.91        14.99        14.96        13.48         0.36        12.59 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD 
        6.64         1.51         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 
       23.70         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         6.12         1.45         1.58         0.82         7.13 
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-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX 
       36.36        20.48        21.11         7.99        11.28         0.07 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82         0.20        13.87         0.03        29.72         0.07 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW 
        4.34         5.49         2.96        13.35         3.39        17.56 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       15.88         5.88        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       12.16        10.03        29.03        20.22        14.07        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Z 
       53.52        32.15        46.03        11.51        49.55        23.24 
TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A9U5 
       44.88        42.08        38.96 

$`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        85.55        94.95         9.34         8.35 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL 
        6.12        20.91         4.47         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         0.76         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 
        0.62        14.50         1.35        12.66        12.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PL 
        1.48        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         4.73 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-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        26.56        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        10.06         5.13         6.71       195.85        30.31 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MU-A8JM TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        0.89         0.30         5.42        15.58        15.95        16.14 
TCGA-Q1-A73O TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8QA 
       14.07         6.25        10.39        61.28        34.52        23.28 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A954 TCGA-VS-A958 
       39.78        31.27        16.64         4.73        42.58        43.82 
TCGA-VS-A959 TCGA-WL-A834 
       39.35        18.05 

  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 
                      182.93                       195.85 
  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE 
                       18.74                        14.60 
[1] "0.0 - 182.9 (18.7)" "0.0 - 195.8 (14.6)"
[1] "hr=" "1.4"
D47V2, continuous
                              vv
clus                           T1 T2 T3+T4
  DEL PEAK 19(11Q25) MUTATED   67 25     6
  DEL PEAK 19(11Q25) WILD-TYPE 54 25     5
D47V3, multiclass
       clus
vv      DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  T1                            67                           54
  T2                            25                           25
  T3+T4                          6                            5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   62 25
  DEL PEAK 19(11Q25) WILD-TYPE 49 22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     62   25
  DEL PEAK 19(11Q25) WILD-TYPE   49   22
   clus
vv  DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  0                         62                           49
  1                         25                           22
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  DEL PEAK 19(11Q25) MUTATED   55  4 46
  DEL PEAK 19(11Q25) WILD-TYPE 36  4 47
D47V5, multiclass
    clus
vv   DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  M0                         55                           36
  M1                          4                            4
  MX                         46                           47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(11Q25) MUTATED               1                              117
  DEL PEAK 19(11Q25) WILD-TYPE             4                               80
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 19(11Q25) MUTATED                                               1
  DEL PEAK 19(11Q25) WILD-TYPE                                             4
                              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                                              2
  DEL PEAK 19(11Q25) WILD-TYPE                                            4
D47V6, multiclass
                                               clus
vv                                              DEL PEAK 19(11Q25) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                     117
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           2
                                               clus
vv                                              DEL PEAK 19(11Q25) WILD-TYPE
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        80
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                              cls
clus                             0   1
  DEL PEAK 19(11Q25) MUTATED    21 110
  DEL PEAK 19(11Q25) WILD-TYPE   9  98
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     21  110
  DEL PEAK 19(11Q25) WILD-TYPE    9   98
     clus
vv    DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  NO                          21                            9
  YES                        110                           98
[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                          18
  DEL PEAK 19(11Q25) WILD-TYPE                         6
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(11Q25) MUTATED                                           1    92
  DEL PEAK 19(11Q25) WILD-TYPE                                         0    77
D47V10, multiclass
                                           clus
vv                                          DEL PEAK 19(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   3
  ASIAN                                                             11
  BLACK OR AFRICAN AMERICAN                                         18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             92
                                           clus
vv                                          DEL PEAK 19(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED    5 83
  DEL PEAK 19(11Q25) WILD-TYPE 11 66
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED      5   83
  DEL PEAK 19(11Q25) WILD-TYPE   11   66
                        clus
vv                       DEL PEAK 19(11Q25) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         83
                        clus
vv                       DEL PEAK 19(11Q25) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                           66
[1] 2 2
[1] FALSE
D47V12, continuous
D47V13, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   41 19
  DEL PEAK 19(11Q25) WILD-TYPE 30  6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     41   19
  DEL PEAK 19(11Q25) WILD-TYPE   30    6
            clus
vv           DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  TUMOR FREE                         41                           30
  WITH TUMOR                         19                            6
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 19(11Q25) MUTATED       14      1       1      4       3
  DEL PEAK 19(11Q25) WILD-TYPE      9      4       0      6       4
                              vv
clus                           UNITED STATES VIETNAM
  DEL PEAK 19(11Q25) MUTATED              99       9
  DEL PEAK 19(11Q25) WILD-TYPE            79       5
D47V14, multiclass
               clus
vv              DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  BRAZIL                                14                            9
  CANADA                                 1                            4
  NIGERIA                                1                            0
  RUSSIA                                 4                            6
  UKRAINE                                3                            4
  UNITED STATES                         99                           79
  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    7 59 55  1  7
  DEL PEAK 19(11Q25) WILD-TYPE 10 47 42  0  7
D47V15, multiclass
    clus
vv   DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  G1                          7                           10
  G2                         59                           47
  G3                         55                           42
  G4                          1                            0
  GX                          7                            7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V16, continuous
D47V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 19(11Q25) MUTATED                                            20
  DEL PEAK 19(11Q25) WILD-TYPE                                          11
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 19(11Q25) MUTATED                                        6
  DEL PEAK 19(11Q25) WILD-TYPE                                      2
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 19(11Q25) MUTATED                                                 1
  DEL PEAK 19(11Q25) WILD-TYPE                                               1
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 19(11Q25) MUTATED               24                  62
  DEL PEAK 19(11Q25) WILD-TYPE             28                  50
D47V18, multiclass
                                                 clus
vv                                                DEL PEAK 19(11Q25) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          1
  CURRENT SMOKER                                                          24
  LIFELONG NON-SMOKER                                                     62
                                                 clus
vv                                                DEL PEAK 19(11Q25) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            28
  LIFELONG NON-SMOKER                                                       50
[1] 5 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       39             6        7
  DEL PEAK 19(11Q25) WILD-TYPE           3       36             6        5
D47V21, multiclass
               clus
vv              DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  COMBINATION                           16                            3
  EXTERNAL                              39                           36
  EXTERNAL BEAM                          6                            6
  INTERNAL                               7                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    17             8
  DEL PEAK 19(11Q25) WILD-TYPE                  11             8
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                         17                           11
  REGIONAL SITE                                8                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V24, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   19  3
  DEL PEAK 19(11Q25) WILD-TYPE 15  0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     19    3
  DEL PEAK 19(11Q25) WILD-TYPE   15    0
     clus
vv    DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  CGY                         19                           15
  GY                           3                            0
[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                                   2
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 19(11Q25) MUTATED                        17                       1
  DEL PEAK 19(11Q25) WILD-TYPE                      12                       0
                              vv
clus                           POSITIVE VAGINAL MARGIN
  DEL PEAK 19(11Q25) MUTATED                         4
  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                                     17
  POSITIVE BLADDER MARGIN                                      1
  POSITIVE VAGINAL MARGIN                                      4
                                     clus
vv                                    DEL PEAK 19(11Q25) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       12
  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                                               11
  DEL PEAK 19(11Q25) WILD-TYPE                                              5
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 19(11Q25) MUTATED                                                                                  43
  DEL PEAK 19(11Q25) WILD-TYPE                                                                                25
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 19(11Q25) MUTATED                                                                                             51
  DEL PEAK 19(11Q25) WILD-TYPE                                                                                           54
D47V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 19(11Q25) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    43
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         51
                                                                                              clus
vv                                                                                             DEL PEAK 19(11Q25) 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)                                      25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V33, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   33 44
  DEL PEAK 19(11Q25) WILD-TYPE 35 26
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     33   44
  DEL PEAK 19(11Q25) WILD-TYPE   35   26
         clus
vv        DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  ABSENT                          33                           35
  PRESENT                         44                           26
[1] 2 2
[1] FALSE
D47V34, continuous
D47V35, continuous
D47V36, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   26 52
  DEL PEAK 19(11Q25) WILD-TYPE 17 42
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     26   52
  DEL PEAK 19(11Q25) WILD-TYPE   17   42
                                          clus
vv                                         DEL PEAK 19(11Q25) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         52
                                          clus
vv                                         DEL PEAK 19(11Q25) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           42
[1] 2 2
[1] FALSE
D47V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  DEL PEAK 19(11Q25) MUTATED              3          27         34
  DEL PEAK 19(11Q25) WILD-TYPE            7          22         23
D47V38, multiclass
              clus
vv             DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  CURRENT USER                          3                            7
  FORMER USER                          27                           22
  NEVER USED                           34                           23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V39, continuous
D47V40, binary
                              cls
clus                            0  1
  DEL PEAK 19(11Q25) MUTATED   47 11
  DEL PEAK 19(11Q25) WILD-TYPE 42  5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(11Q25) MUTATED     47   11
  DEL PEAK 19(11Q25) WILD-TYPE   42    5
         clus
vv        DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  ABSENT                          47                           42
  PRESENT                         11                            5
[1] 2 2
[1] FALSE
D47V41, continuous
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 19(11Q25) MUTATED     1    1  20   39    6  4   2    4    4  11  0
  DEL PEAK 19(11Q25) WILD-TYPE   0    0  10   26   18  0   6    3    5  11  1
                              vv
clus                           T3B T4 TIS TX
  DEL PEAK 19(11Q25) MUTATED     5  1   1  8
  DEL PEAK 19(11Q25) WILD-TYPE   3  1   0  6
D47V42, multiclass
      clus
vv     DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  T1A                           1                            0
  T1A1                          1                            0
  T1B                          20                           10
  T1B1                         39                           26
  T1B2                          6                           18
  T2                            4                            0
  T2A                           2                            6
  T2A1                          4                            3
  T2A2                          4                            5
  T2B                          11                           11
  T3                            0                            1
  T3B                           5                            3
  T4                            1                            1
  TIS                           1                            0
  TX                            8                            6
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 19(11Q25) MUTATED         3        1         1         1       25
  DEL PEAK 19(11Q25) WILD-TYPE       1        1         0         0        6
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 19(11Q25) MUTATED          38        11        2         1
  DEL PEAK 19(11Q25) WILD-TYPE        31        21        1         5
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 19(11Q25) MUTATED            4          4        17         0
  DEL PEAK 19(11Q25) WILD-TYPE          1          3        10         1
                              vv
clus                           STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 19(11Q25) MUTATED           16         2         2
  DEL PEAK 19(11Q25) WILD-TYPE         18         1         5
D47V44, multiclass
            clus
vv           DEL PEAK 19(11Q25) MUTATED DEL PEAK 19(11Q25) WILD-TYPE
  STAGE I                             3                            1
  STAGE IA                            1                            1
  STAGE IA1                           1                            0
  STAGE IA2                           1                            0
  STAGE IB                           25                            6
  STAGE IB1                          38                           31
  STAGE IB2                          11                           21
  STAGE II                            2                            1
  STAGE IIA                           1                            5
  STAGE IIA1                          4                            1
  STAGE IIA2                          4                            3
  STAGE IIB                          17                           10
  STAGE III                           0                            1
  STAGE IIIB                         16                           18
  STAGE IVA                           2                            1
  STAGE IVB                           2                            5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 20(13Q12.11) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(13Q12.11) MUTATED    62  16
  DEL PEAK 20(13Q12.11) WILD-TYPE 121  34
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                             78                             155 
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                             16                              34 
$`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       182.93       154.32       134.33 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XK 
      147.35        85.55        60.69        94.95         9.34        99.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT 
        4.47        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 
        1.18        12.66        15.02         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA 
       26.27         0.43         0.59         0.59         1.45        16.08 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-EX-A69M TCGA-FU-A23L 
        4.04         0.36         2.24        20.35         6.12        23.84 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.45         1.58         1.97        25.41         7.13        21.67 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-AAVH TCGA-JX-A3PZ 
        9.44       147.39        78.71        20.48         6.71        21.11 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MY-A913 TCGA-Q1-A5R3 
       30.31        11.28         0.89         0.07         5.49        15.95 
TCGA-Q1-A6DT TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
        3.39         6.25        19.59        12.16        10.03        34.52 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q9 TCGA-VS-A8QM TCGA-VS-A957 TCGA-WL-A834 
       20.22        14.07        46.03        31.27        42.08        18.05 

$`DEL PEAK 20(13Q12.11) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BQ TCGA-C5-A1M5 
       23.67        11.44        36.56       177.04        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       46.32        30.21        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14         0.82        52.01        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A7X8 
      101.82        15.48        20.35        17.19        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99        45.83         8.35        75.78        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        6.12        20.91         1.12        50.76        44.94        40.04 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88        36.76         2.66        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         0.76         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
        0.62        13.05        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        1.81        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2PG 
       14.99        14.96        13.58        13.48         6.64         1.51 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN 
        0.13         0.07         0.03         1.18        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.10         0.10         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70        19.79         4.73         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        0.66         1.02         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA 
        1.32         1.12         9.01        20.78        14.93       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81       117.40        96.95        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        10.06 
TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
        5.13       195.85         7.99         0.30         0.82         0.20 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        2.96        15.58        13.35        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       15.88         5.88        10.39         3.88        11.67        93.99 
TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA 
       61.28        29.03        19.96        53.52        32.15        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       11.51        49.55        39.78        16.64         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       44.88        42.58        43.82        39.35        38.96 

  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                         182.93                          195.85 
  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE 
                         20.285                          14.890 
[1] "0.1 - 182.9 (20.3)" "0.0 - 195.8 (14.9)"
[1] "hr=" "1.7"
D48V2, continuous
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 20(13Q12.11) MUTATED   36 13     5
  DEL PEAK 20(13Q12.11) WILD-TYPE 85 37     6
D48V3, multiclass
       clus
vv      DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  T1                               36                              85
  T2                               13                              37
  T3+T4                             5                               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   31 19
  DEL PEAK 20(13Q12.11) WILD-TYPE 80 28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     31   19
  DEL PEAK 20(13Q12.11) WILD-TYPE   80   28
   clus
vv  DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  0                            31                              80
  1                            19                              28
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 20(13Q12.11) MUTATED   29  4 27
  DEL PEAK 20(13Q12.11) WILD-TYPE 62  4 66
D48V5, multiclass
    clus
vv   DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  M0                            29                              62
  M1                             4                               4
  MX                            27                              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  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                                 77
  DEL PEAK 20(13Q12.11) WILD-TYPE                              120
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 20(13Q12.11) MUTATED                                               0
  DEL PEAK 20(13Q12.11) WILD-TYPE                                             5
                                 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                                            6
D48V6, multiclass
                                               clus
vv                                              DEL PEAK 20(13Q12.11) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         77
  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                                          120
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(13Q12.11) MUTATED    14  68
  DEL PEAK 20(13Q12.11) WILD-TYPE  16 140
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     14   68
  DEL PEAK 20(13Q12.11) WILD-TYPE   16  140
     clus
vv    DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  NO                             14                              16
  YES                            68                             140
[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                          11
  DEL PEAK 20(13Q12.11) WILD-TYPE                        13
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 20(13Q12.11) MUTATED                                           0
  DEL PEAK 20(13Q12.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 20(13Q12.11) MUTATED      59
  DEL PEAK 20(13Q12.11) WILD-TYPE   110
D48V10, multiclass
                                           clus
vv                                          DEL PEAK 20(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                59
                                           clus
vv                                          DEL PEAK 20(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  11
  BLACK OR AFRICAN AMERICAN                                              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 110
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED    3 50
  DEL PEAK 20(13Q12.11) WILD-TYPE 13 99
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED      3   50
  DEL PEAK 20(13Q12.11) WILD-TYPE   13   99
                        clus
vv                       DEL PEAK 20(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            50
                        clus
vv                       DEL PEAK 20(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                              99
[1] 2 2
[1] FALSE
D48V12, continuous
D48V13, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   26  9
  DEL PEAK 20(13Q12.11) WILD-TYPE 45 16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     26    9
  DEL PEAK 20(13Q12.11) WILD-TYPE   45   16
            clus
vv           DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  TUMOR FREE                            26                              45
  WITH TUMOR                             9                              16
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 20(13Q12.11) MUTATED        7      1       0      2       2
  DEL PEAK 20(13Q12.11) WILD-TYPE     16      4       1      8       5
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 20(13Q12.11) MUTATED              65       5
  DEL PEAK 20(13Q12.11) WILD-TYPE           113       9
D48V14, multiclass
               clus
vv              DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  BRAZIL                                    7                              16
  CANADA                                    1                               4
  NIGERIA                                   0                               1
  RUSSIA                                    2                               8
  UKRAINE                                   2                               5
  UNITED STATES                            65                             113
  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    3 32 40  1  5
  DEL PEAK 20(13Q12.11) WILD-TYPE 14 74 57  0  9
D48V15, multiclass
    clus
vv   DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  G1                             3                              14
  G2                            32                              74
  G3                            40                              57
  G4                             1                               0
  GX                             5                               9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                                          21
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 20(13Q12.11) MUTATED                                        4
  DEL PEAK 20(13Q12.11) WILD-TYPE                                      4
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 20(13Q12.11) MUTATED                                                 2
  DEL PEAK 20(13Q12.11) WILD-TYPE                                               0
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 20(13Q12.11) MUTATED               19                  30
  DEL PEAK 20(13Q12.11) WILD-TYPE             33                  82
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                             2
  CURRENT SMOKER                                                             19
  LIFELONG NON-SMOKER                                                        30
                                                 clus
vv                                                DEL PEAK 20(13Q12.11) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               0
  CURRENT SMOKER                                                               33
  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"
D48V19, continuous
D48V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 20(13Q12.11) MUTATED             9       24             4        3
  DEL PEAK 20(13Q12.11) WILD-TYPE          10       51             8        9
D48V21, multiclass
               clus
vv              DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  COMBINATION                               9                              10
  EXTERNAL                                 24                              51
  EXTERNAL BEAM                             4                               8
  INTERNAL                                  3                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    12             5
  DEL PEAK 20(13Q12.11) WILD-TYPE                  16            11
D48V23, multiclass
                     clus
vv                    DEL PEAK 20(13Q12.11) MUTATED
  DISTANT RECURRENCE                              1
  LOCAL RECURRENCE                                1
  PRIMARY TUMOR FIELD                            12
  REGIONAL SITE                                   5
                     clus
vv                    DEL PEAK 20(13Q12.11) WILD-TYPE
  DISTANT RECURRENCE                                1
  LOCAL RECURRENCE                                  1
  PRIMARY TUMOR FIELD                              16
  REGIONAL SITE                                    11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V24, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   11  2
  DEL PEAK 20(13Q12.11) WILD-TYPE 23  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     11    2
  DEL PEAK 20(13Q12.11) WILD-TYPE   23    1
     clus
vv    DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  CGY                            11                              23
  GY                              2                               1
[1] 2 2
[1] FALSE
D48V25, continuous
D48V26, continuous
D48V27, continuous
D48V28, continuous
D48V29, continuous
D48V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                     1
  DEL PEAK 20(13Q12.11) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 20(13Q12.11) MUTATED                         7
  DEL PEAK 20(13Q12.11) WILD-TYPE                      22
                                 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                       4
D48V31, multiclass
                                     clus
vv                                    DEL PEAK 20(13Q12.11) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         7
  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                                          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 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                                                5
  DEL PEAK 20(13Q12.11) WILD-TYPE                                             11
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 20(13Q12.11) MUTATED                                                                                  21
  DEL PEAK 20(13Q12.11) WILD-TYPE                                                                                47
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 20(13Q12.11) MUTATED                                                                                             36
  DEL PEAK 20(13Q12.11) WILD-TYPE                                                                                           69
D48V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 20(13Q12.11) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            36
                                                                                              clus
vv                                                                                             DEL PEAK 20(13Q12.11) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         47
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V33, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   18 25
  DEL PEAK 20(13Q12.11) WILD-TYPE 50 45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     18   25
  DEL PEAK 20(13Q12.11) WILD-TYPE   50   45
         clus
vv        DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  ABSENT                             18                              50
  PRESENT                            25                              45
[1] 2 2
[1] FALSE
D48V34, continuous
D48V35, continuous
D48V36, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   14 37
  DEL PEAK 20(13Q12.11) WILD-TYPE 29 57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     14   37
  DEL PEAK 20(13Q12.11) WILD-TYPE   29   57
                                          clus
vv                                         DEL PEAK 20(13Q12.11) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            37
                                          clus
vv                                         DEL PEAK 20(13Q12.11) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              57
[1] 2 2
[1] FALSE
D48V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 20(13Q12.11) MUTATED              2          15         18
  DEL PEAK 20(13Q12.11) WILD-TYPE            8          34         39
D48V38, multiclass
              clus
vv             DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  CURRENT USER                             2                               8
  FORMER USER                             15                              34
  NEVER USED                              18                              39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V39, continuous
D48V40, binary
                                 cls
clus                               0  1
  DEL PEAK 20(13Q12.11) MUTATED   22  7
  DEL PEAK 20(13Q12.11) WILD-TYPE 67  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.11) MUTATED     22    7
  DEL PEAK 20(13Q12.11) WILD-TYPE   67    9
         clus
vv        DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  ABSENT                             22                              67
  PRESENT                             7                               9
[1] 2 2
[1] FALSE
D48V41, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 20(13Q12.11) MUTATED     0    0  12   16    8  3   1    2    3   4
  DEL PEAK 20(13Q12.11) WILD-TYPE   1    1  18   49   16  1   7    5    6  18
                                 vv
clus                              T3 T3B T4 TIS TX
  DEL PEAK 20(13Q12.11) MUTATED    0   5  0   1  6
  DEL PEAK 20(13Q12.11) WILD-TYPE  1   3  2   0  8
D48V42, multiclass
      clus
vv     DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  T1A                              0                               1
  T1A1                             0                               1
  T1B                             12                              18
  T1B1                            16                              49
  T1B2                             8                              16
  T2                               3                               1
  T2A                              1                               7
  T2A1                             2                               5
  T2A2                             3                               6
  T2B                              4                              18
  T3                               0                               1
  T3B                              5                               3
  T4                               0                               2
  TIS                              1                               0
  TX                               6                               8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 20(13Q12.11) MUTATED         2        1         0         1       17
  DEL PEAK 20(13Q12.11) WILD-TYPE       2        1         1         0       14
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 20(13Q12.11) MUTATED          15        11        0         2
  DEL PEAK 20(13Q12.11) WILD-TYPE        54        21        3         4
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 20(13Q12.11) MUTATED            2          1         8         0
  DEL PEAK 20(13Q12.11) WILD-TYPE          3          6        19         1
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 20(13Q12.11) MUTATED           16         1         2
  DEL PEAK 20(13Q12.11) WILD-TYPE         18         2         5
D48V44, multiclass
            clus
vv           DEL PEAK 20(13Q12.11) MUTATED DEL PEAK 20(13Q12.11) WILD-TYPE
  STAGE I                                2                               2
  STAGE IA                               1                               1
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                              17                              14
  STAGE IB1                             15                              54
  STAGE IB2                             11                              21
  STAGE II                               0                               3
  STAGE IIA                              2                               4
  STAGE IIA1                             2                               3
  STAGE IIA2                             1                               6
  STAGE IIB                              8                              19
  STAGE III                              0                               1
  STAGE IIIB                            16                              18
  STAGE IVA                              1                               2
  STAGE IVB                              2                               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 21(13Q14.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(13Q14.2) MUTATED    75  17
  DEL PEAK 21(13Q14.2) WILD-TYPE 108  33
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            92                            141 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            17                             33 
$`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       182.93       154.32       134.33 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XI 
      147.35        85.55        60.69        94.95         9.34         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DR-A0ZL 
       75.78        99.91        20.91         4.47        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         1.18 
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-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RD 
        1.51         0.43         0.59         1.45        16.08         0.03 
TCGA-EK-A2RE TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI 
        0.36         0.10        20.35         6.12        23.84         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.58         1.48         1.97        25.41         7.13        21.67 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A852 
       14.93         9.44       147.39        78.71        20.48         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
        6.71        21.11        30.31        11.28         0.89         0.07 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
        0.07         5.49         3.39         5.88         6.25        19.59 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       12.16        10.03        34.52        20.22        14.07        19.96 
TCGA-VS-A8EL TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A954 TCGA-VS-A957 
       53.52        49.55        31.27         4.73        42.58        42.08 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

$`DEL PEAK 21(13Q14.2) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1BQ 
       23.67        11.44        36.56       177.04         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI 
       67.46        46.32        30.21        35.01        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14         0.82        52.01        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A7X8 
      101.82        15.48        20.35        17.19        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-DG-A2KH 
       50.99        45.83        23.51        27.52         6.12         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       50.76        44.94        40.04        58.88        36.76         2.66 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18        17.52         8.28         0.76         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        1.32         0.82         0.62        14.50         1.35         1.35 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IP 
       13.91        15.02        14.99        14.96        13.58         6.64 
TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.59         0.13         0.07         4.04         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
        2.24         0.10         0.07         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70        19.79         4.73         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        2.17         0.66         1.02         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-IR-A3LA TCGA-IR-A3LB 
        1.32         1.12         9.01        20.78       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        81.96        26.56        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3Q0 
        3.29        24.56        21.44        15.58        10.06       195.85 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        7.99         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         4.34         2.96        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73S 
       15.95        16.14        17.56        14.07        15.88        10.39 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8Q8 
        3.88        11.67        93.99        61.28        29.03        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Z 
       46.03        23.28        11.51        39.78        16.64        23.24 
TCGA-VS-A952 TCGA-VS-A958 TCGA-VS-A959 
       44.88        43.82        39.35 

  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 
                        182.93                         195.85 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                        20.285                         14.890 
[1] "0.0 - 182.9 (20.3)" "0.0 - 195.8 (14.9)"
[1] "hr=" "1.9"
D49V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 21(13Q14.2) MUTATED   44 18     7
  DEL PEAK 21(13Q14.2) WILD-TYPE 77 32     4
D49V3, multiclass
       clus
vv      DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  T1                              44                             77
  T2                              18                             32
  T3+T4                            7                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   37 22
  DEL PEAK 21(13Q14.2) WILD-TYPE 74 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     37   22
  DEL PEAK 21(13Q14.2) WILD-TYPE   74   25
   clus
vv  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  0                           37                             74
  1                           22                             25
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 21(13Q14.2) MUTATED   34  5 35
  DEL PEAK 21(13Q14.2) WILD-TYPE 57  3 58
D49V5, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  M0                           34                             57
  M1                            5                              3
  MX                           35                             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(13Q14.2) MUTATED               2                               90
  DEL PEAK 21(13Q14.2) WILD-TYPE             3                              107
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 21(13Q14.2) MUTATED                                               0
  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                                              0
  DEL PEAK 21(13Q14.2) WILD-TYPE                                            6
D49V6, multiclass
                                               clus
vv                                              DEL PEAK 21(13Q14.2) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        90
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              DEL PEAK 21(13Q14.2) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         107
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    14  82
  DEL PEAK 21(13Q14.2) WILD-TYPE  16 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     14   82
  DEL PEAK 21(13Q14.2) WILD-TYPE   16  126
     clus
vv    DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  NO                            14                             16
  YES                           82                            126
[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                          15
  DEL PEAK 21(13Q14.2) WILD-TYPE                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 21(13Q14.2) MUTATED                                           1
  DEL PEAK 21(13Q14.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 21(13Q14.2) MUTATED      64
  DEL PEAK 21(13Q14.2) WILD-TYPE   105
D49V10, multiclass
                                           clus
vv                                          DEL PEAK 21(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                           15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               64
                                           clus
vv                                          DEL PEAK 21(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 10
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D49V11, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED    4 55
  DEL PEAK 21(13Q14.2) WILD-TYPE 12 94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED      4   55
  DEL PEAK 21(13Q14.2) WILD-TYPE   12   94
                        clus
vv                       DEL PEAK 21(13Q14.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       DEL PEAK 21(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                             94
[1] 2 2
[1] FALSE
D49V12, continuous
D49V13, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   29  8
  DEL PEAK 21(13Q14.2) WILD-TYPE 42 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     29    8
  DEL PEAK 21(13Q14.2) WILD-TYPE   42   17
            clus
vv           DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  TUMOR FREE                           29                             42
  WITH TUMOR                            8                             17
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 21(13Q14.2) MUTATED       12      1       0      2       1
  DEL PEAK 21(13Q14.2) WILD-TYPE     11      4       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 21(13Q14.2) MUTATED              74       6
  DEL PEAK 21(13Q14.2) WILD-TYPE           104       8
D49V14, multiclass
               clus
vv              DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  BRAZIL                                  12                             11
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  1                              6
  UNITED STATES                           74                            104
  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    4 34 48  1  7
  DEL PEAK 21(13Q14.2) WILD-TYPE 13 72 49  0  7
D49V15, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  G1                            4                             13
  G2                           34                             72
  G3                           48                             49
  G4                            1                              0
  GX                            7                              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V16, continuous
D49V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 21(13Q14.2) MUTATED                                            13
  DEL PEAK 21(13Q14.2) WILD-TYPE                                          18
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 21(13Q14.2) MUTATED                                        6
  DEL PEAK 21(13Q14.2) WILD-TYPE                                      2
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 21(13Q14.2) MUTATED                                                 2
  DEL PEAK 21(13Q14.2) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 21(13Q14.2) MUTATED               22                  36
  DEL PEAK 21(13Q14.2) WILD-TYPE             30                  76
D49V18, multiclass
                                                 clus
vv                                                DEL PEAK 21(13Q14.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            22
  LIFELONG NON-SMOKER                                                       36
                                                 clus
vv                                                DEL PEAK 21(13Q14.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                              30
  LIFELONG NON-SMOKER                                                         76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V19, continuous
D49V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 21(13Q14.2) MUTATED             8       32             5        4
  DEL PEAK 21(13Q14.2) WILD-TYPE          11       43             7        8
D49V21, multiclass
               clus
vv              DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  COMBINATION                              8                             11
  EXTERNAL                                32                             43
  EXTERNAL BEAM                            5                              7
  INTERNAL                                 4                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    15             8
  DEL PEAK 21(13Q14.2) WILD-TYPE                  13             8
D49V23, multiclass
                     clus
vv                    DEL PEAK 21(13Q14.2) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                           15
  REGIONAL SITE                                  8
                     clus
vv                    DEL PEAK 21(13Q14.2) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             13
  REGIONAL SITE                                    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"
D49V24, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   15  2
  DEL PEAK 21(13Q14.2) WILD-TYPE 19  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     15    2
  DEL PEAK 21(13Q14.2) WILD-TYPE   19    1
     clus
vv    DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  CGY                           15                             19
  GY                             2                              1
[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                                     1
  DEL PEAK 21(13Q14.2) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 21(13Q14.2) MUTATED                        11
  DEL PEAK 21(13Q14.2) WILD-TYPE                      18
                                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                         3
  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                            1
  OTHER LOCATION, SPECIFY                                       11
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        3
                                     clus
vv                                    DEL PEAK 21(13Q14.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         18
  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                                                7
  DEL PEAK 21(13Q14.2) WILD-TYPE                                              9
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 21(13Q14.2) MUTATED                                                                                  26
  DEL PEAK 21(13Q14.2) WILD-TYPE                                                                                42
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 21(13Q14.2) MUTATED                                                                                             43
  DEL PEAK 21(13Q14.2) WILD-TYPE                                                                                           62
D49V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 21(13Q14.2) 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)                                      26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           43
                                                                                              clus
vv                                                                                             DEL PEAK 21(13Q14.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        42
  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"
D49V33, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   21 27
  DEL PEAK 21(13Q14.2) WILD-TYPE 47 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     21   27
  DEL PEAK 21(13Q14.2) WILD-TYPE   47   43
         clus
vv        DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  ABSENT                            21                             47
  PRESENT                           27                             43
[1] 2 2
[1] FALSE
D49V34, continuous
D49V35, continuous
D49V36, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   17 41
  DEL PEAK 21(13Q14.2) WILD-TYPE 26 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     17   41
  DEL PEAK 21(13Q14.2) WILD-TYPE   26   53
                                          clus
vv                                         DEL PEAK 21(13Q14.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           41
                                          clus
vv                                         DEL PEAK 21(13Q14.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             53
[1] 2 2
[1] FALSE
D49V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 21(13Q14.2) MUTATED              3          19         18
  DEL PEAK 21(13Q14.2) WILD-TYPE            7          30         39
D49V38, multiclass
              clus
vv             DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  CURRENT USER                            3                              7
  FORMER USER                            19                             30
  NEVER USED                             18                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V39, continuous
D49V40, binary
                                cls
clus                              0  1
  DEL PEAK 21(13Q14.2) MUTATED   24  8
  DEL PEAK 21(13Q14.2) WILD-TYPE 65  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     24    8
  DEL PEAK 21(13Q14.2) WILD-TYPE   65    8
         clus
vv        DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  ABSENT                            24                             65
  PRESENT                            8                              8
[1] 2 2
[1] FALSE
D49V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 21(13Q14.2) MUTATED     0    0  12   21   11  3   1    3    2   9  0
  DEL PEAK 21(13Q14.2) WILD-TYPE   1    1  18   44   13  1   7    4    7  13  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 21(13Q14.2) MUTATED     7  0   1  6
  DEL PEAK 21(13Q14.2) WILD-TYPE   1  2   0  8
D49V42, multiclass
      clus
vv     DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                            12                             18
  T1B1                           21                             44
  T1B2                           11                             13
  T2                              3                              1
  T2A                             1                              7
  T2A1                            3                              4
  T2A2                            2                              7
  T2B                             9                             13
  T3                              0                              1
  T3B                             7                              1
  T4                              0                              2
  TIS                             1                              0
  TX                              6                              8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 21(13Q14.2) MUTATED         3        1         0         1       17
  DEL PEAK 21(13Q14.2) WILD-TYPE       1        1         1         0       14
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 21(13Q14.2) MUTATED          17        12        0         2
  DEL PEAK 21(13Q14.2) WILD-TYPE        52        20        3         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 21(13Q14.2) MUTATED            3          1        14         0
  DEL PEAK 21(13Q14.2) WILD-TYPE          2          6        13         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 21(13Q14.2) MUTATED           19         1         2
  DEL PEAK 21(13Q14.2) WILD-TYPE         15         2         5
D49V44, multiclass
            clus
vv           DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  STAGE I                               3                              1
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             17                             14
  STAGE IB1                            17                             52
  STAGE IB2                            12                             20
  STAGE II                              0                              3
  STAGE IIA                             2                              4
  STAGE IIA1                            3                              2
  STAGE IIA2                            1                              6
  STAGE IIB                            14                             13
  STAGE III                             0                              1
  STAGE IIIB                           19                             15
  STAGE IVA                             1                              2
  STAGE IVB                             2                              5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 22(14Q32.31) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 22(14Q32.31) MUTATED    31   7
  DEL PEAK 22(14Q32.31) WILD-TYPE 152  43
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                             38                             195 
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                              7                              43 
$`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         1.74 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A78R TCGA-EK-A2PG TCGA-EK-A2PM 
       14.50         1.35         1.81        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         4.73        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         0.20 
TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A73R TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A8QH 
       29.72        13.35         6.25        12.16        53.52        39.78 
TCGA-VS-A94Y TCGA-VS-A959 
        4.73        39.35 

$`DEL PEAK 22(14Q32.31) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MH 
       67.46        31.40        46.32        30.21        35.01        38.99 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       35.61         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.18        73.45        78.35       100.14         0.82        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       182.93       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34        13.61         2.73        50.99         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       99.91        23.51         6.12        20.91         4.47         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28         0.76        12.36         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A44S 
        0.62        13.05         1.18         1.35        14.50        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         0.26        14.89         1.48        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
       26.27         6.64         0.43         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN 
        0.07         4.04         0.03         0.36        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70        19.79         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        2.17         0.66         1.02         1.45         1.58         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41         7.13        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
      147.39        66.81       117.40        96.95        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       15.58        10.06         5.13         6.71       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        7.99         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42         0.07         4.34         5.49         2.96        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        5.88        10.39        19.59         3.88        11.67        93.99 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       61.28        10.03        34.52        29.03        20.22        14.07 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        32.15        46.03        23.28        11.51        49.55 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       31.27        16.64        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        38.96        18.05 

  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                           0.20                            0.03 
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                         137.16                          195.85 
  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE 
                          13.99                           15.95 
[1] "0.2 - 137.2 (14.0)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.1"
D50V2, continuous
                                 vv
clus                               T1  T2 T3+T4
  DEL PEAK 22(14Q32.31) MUTATED    18  12     1
  DEL PEAK 22(14Q32.31) WILD-TYPE 103  38    10
D50V3, multiclass
       clus
vv      DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  T1                               18                             103
  T2                               12                              38
  T3+T4                             1                              10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED   21  6
  DEL PEAK 22(14Q32.31) WILD-TYPE 90 41
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     21    6
  DEL PEAK 22(14Q32.31) WILD-TYPE   90   41
   clus
vv  DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  0                            21                              90
  1                             6                              41
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 22(14Q32.31) MUTATED   20  0 14
  DEL PEAK 22(14Q32.31) WILD-TYPE 71  8 79
D50V5, multiclass
    clus
vv   DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  M0                            20                              71
  M1                             0                               8
  MX                            14                              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"
                                 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                                 30
  DEL PEAK 22(14Q32.31) WILD-TYPE                              167
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 22(14Q32.31) MUTATED                                               2
  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                                              1
  DEL PEAK 22(14Q32.31) WILD-TYPE                                            5
D50V6, multiclass
                                               clus
vv                                              DEL PEAK 22(14Q32.31) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              1
                                               clus
vv                                              DEL PEAK 22(14Q32.31) WILD-TYPE
  ADENOSQUAMOUS                                                               5
  CERVICAL SQUAMOUS CELL CARCINOMA                                          167
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                 cls
clus                                0   1
  DEL PEAK 22(14Q32.31) MUTATED     2  38
  DEL PEAK 22(14Q32.31) WILD-TYPE  28 170
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED      2   38
  DEL PEAK 22(14Q32.31) WILD-TYPE   28  170
     clus
vv    DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  NO                              2                              28
  YES                            38                             170
[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                        21
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 22(14Q32.31) MUTATED                                           0
  DEL PEAK 22(14Q32.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 22(14Q32.31) MUTATED      30
  DEL PEAK 22(14Q32.31) WILD-TYPE   139
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                                                                30
                                           clus
vv                                          DEL PEAK 22(14Q32.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 139
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, binary
                                 cls
clus                                0   1
  DEL PEAK 22(14Q32.31) MUTATED     3  21
  DEL PEAK 22(14Q32.31) WILD-TYPE  13 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED      3   21
  DEL PEAK 22(14Q32.31) WILD-TYPE   13  128
                        clus
vv                       DEL PEAK 22(14Q32.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            21
                        clus
vv                       DEL PEAK 22(14Q32.31) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             128
[1] 2 2
[1] FALSE
D50V12, continuous
D50V13, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED   15  0
  DEL PEAK 22(14Q32.31) WILD-TYPE 56 25
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     15    0
  DEL PEAK 22(14Q32.31) WILD-TYPE   56   25
            clus
vv           DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  TUMOR FREE                            15                              56
  WITH TUMOR                             0                              25
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 22(14Q32.31) MUTATED        4      1       0      2       2
  DEL PEAK 22(14Q32.31) WILD-TYPE     19      4       1      8       5
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 22(14Q32.31) MUTATED              27       4
  DEL PEAK 22(14Q32.31) WILD-TYPE           151      10
D50V14, multiclass
               clus
vv              DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  BRAZIL                                    4                              19
  CANADA                                    1                               4
  NIGERIA                                   0                               1
  RUSSIA                                    2                               8
  UKRAINE                                   2                               5
  UNITED STATES                            27                             151
  VIETNAM                                   4                              10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 22(14Q32.31) MUTATED    3 12 21  1  2
  DEL PEAK 22(14Q32.31) WILD-TYPE 14 94 76  0 12
D50V15, multiclass
    clus
vv   DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  G1                             3                              14
  G2                            12                              94
  G3                            21                              76
  G4                             1                               0
  GX                             2                              12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V16, continuous
D50V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 22(14Q32.31) MUTATED                                             6
  DEL PEAK 22(14Q32.31) WILD-TYPE                                          25
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 22(14Q32.31) MUTATED                                        0
  DEL PEAK 22(14Q32.31) WILD-TYPE                                      8
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 22(14Q32.31) MUTATED                                                 0
  DEL PEAK 22(14Q32.31) WILD-TYPE                                               2
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 22(14Q32.31) MUTATED                3                  23
  DEL PEAK 22(14Q32.31) WILD-TYPE             49                  89
D50V18, multiclass
                                                 clus
vv                                                DEL PEAK 22(14Q32.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                              3
  LIFELONG NON-SMOKER                                                        23
                                                 clus
vv                                                DEL PEAK 22(14Q32.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               2
  CURRENT SMOKER                                                               49
  LIFELONG NON-SMOKER                                                          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"
D50V19, continuous
D50V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 22(14Q32.31) MUTATED             2       15             0        0
  DEL PEAK 22(14Q32.31) WILD-TYPE          17       60            12       12
D50V21, multiclass
               clus
vv              DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  COMBINATION                               2                              17
  EXTERNAL                                 15                              60
  EXTERNAL BEAM                             0                              12
  INTERNAL                                  0                              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     6             1
  DEL PEAK 22(14Q32.31) WILD-TYPE                  22            15
D50V23, multiclass
                     clus
vv                    DEL PEAK 22(14Q32.31) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                0
  PRIMARY TUMOR FIELD                             6
  REGIONAL SITE                                   1
                     clus
vv                    DEL PEAK 22(14Q32.31) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  2
  PRIMARY TUMOR FIELD                              22
  REGIONAL SITE                                    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"
D50V24, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED    7  0
  DEL PEAK 22(14Q32.31) WILD-TYPE 27  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED      7    0
  DEL PEAK 22(14Q32.31) WILD-TYPE   27    3
     clus
vv    DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  CGY                             7                              27
  GY                              0                               3
[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                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 22(14Q32.31) MUTATED                         6
  DEL PEAK 22(14Q32.31) WILD-TYPE                      23
                                 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                       5
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                               5
  OTHER LOCATION, SPECIFY                                          23
  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 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                                             15
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 22(14Q32.31) MUTATED                                                                                  15
  DEL PEAK 22(14Q32.31) WILD-TYPE                                                                                53
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 22(14Q32.31) MUTATED                                                                                             15
  DEL PEAK 22(14Q32.31) WILD-TYPE                                                                                           90
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)                                       15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            15
                                                                                              clus
vv                                                                                             DEL PEAK 22(14Q32.31) 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)                                         53
  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"
D50V33, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED   10 14
  DEL PEAK 22(14Q32.31) WILD-TYPE 58 56
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     10   14
  DEL PEAK 22(14Q32.31) WILD-TYPE   58   56
         clus
vv        DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  ABSENT                             10                              58
  PRESENT                            14                              56
[1] 2 2
[1] FALSE
D50V34, continuous
D50V35, continuous
D50V36, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED    7 13
  DEL PEAK 22(14Q32.31) WILD-TYPE 36 81
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED      7   13
  DEL PEAK 22(14Q32.31) WILD-TYPE   36   81
                                          clus
vv                                         DEL PEAK 22(14Q32.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            13
                                          clus
vv                                         DEL PEAK 22(14Q32.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              81
[1] 2 2
[1] FALSE
D50V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 22(14Q32.31) MUTATED              2           8          7
  DEL PEAK 22(14Q32.31) WILD-TYPE            8          41         50
D50V38, multiclass
              clus
vv             DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  CURRENT USER                             2                               8
  FORMER USER                              8                              41
  NEVER USED                               7                              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V39, continuous
D50V40, binary
                                 cls
clus                               0  1
  DEL PEAK 22(14Q32.31) MUTATED   16  3
  DEL PEAK 22(14Q32.31) WILD-TYPE 73 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(14Q32.31) MUTATED     16    3
  DEL PEAK 22(14Q32.31) WILD-TYPE   73   13
         clus
vv        DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  ABSENT                             16                              73
  PRESENT                             3                              13
[1] 2 2
[1] FALSE
D50V41, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 22(14Q32.31) MUTATED     0    0   4   10    4  3   2    3    0   4
  DEL PEAK 22(14Q32.31) WILD-TYPE   1    1  26   55   20  1   6    4    9  18
                                 vv
clus                              T3 T3B T4 TIS TX
  DEL PEAK 22(14Q32.31) MUTATED    0   1  0   0  3
  DEL PEAK 22(14Q32.31) WILD-TYPE  1   7  2   1 11
D50V42, multiclass
      clus
vv     DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  T1A                              0                               1
  T1A1                             0                               1
  T1B                              4                              26
  T1B1                            10                              55
  T1B2                             4                              20
  T2                               3                               1
  T2A                              2                               6
  T2A1                             3                               4
  T2A2                             0                               9
  T2B                              4                              18
  T3                               0                               1
  T3B                              1                               7
  T4                               0                               2
  TIS                              0                               1
  TX                               3                              11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        2         1         1       26
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 22(14Q32.31) MUTATED          13         5        2         1
  DEL PEAK 22(14Q32.31) WILD-TYPE        56        27        1         5
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 22(14Q32.31) MUTATED            2          0         5         0
  DEL PEAK 22(14Q32.31) WILD-TYPE          3          7        22         1
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 22(14Q32.31) MUTATED            4         0         0
  DEL PEAK 22(14Q32.31) WILD-TYPE         30         3         7
D50V44, multiclass
            clus
vv           DEL PEAK 22(14Q32.31) MUTATED DEL PEAK 22(14Q32.31) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                               0                               2
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               5                              26
  STAGE IB1                             13                              56
  STAGE IB2                              5                              27
  STAGE II                               2                               1
  STAGE IIA                              1                               5
  STAGE IIA1                             2                               3
  STAGE IIA2                             0                               7
  STAGE IIB                              5                              22
  STAGE III                              0                               1
  STAGE IIIB                             4                              30
  STAGE IVA                              0                               3
  STAGE IVB                              0                               7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 23(15Q21.1) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(15Q21.1) MUTATED    39  11
  DEL PEAK 23(15Q21.1) WILD-TYPE 144  39
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            50                            183 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            11                             39 
$`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       182.93       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         1.81        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-MU-A8JM 
       78.71        26.56        10.06        30.31         0.07         5.42 
TCGA-MY-A5BD TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       29.72         5.49         2.96        15.58        13.35        15.95 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Z TCGA-VS-A954 
       14.07        19.96        49.55        39.78        23.24        42.58 
TCGA-VS-A957 TCGA-VS-A9U5 
       42.08        38.96 

$`DEL PEAK 23(15Q21.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        30.21        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       35.61         0.46         2.43         3.58        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       83.05        78.35       100.14        38.43         0.82        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       17.85        20.42       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        85.55        60.69        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YR 
        2.73        50.99        45.83         8.35        75.78        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL 
        6.12        20.91         4.47         1.12        58.88        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       40.04        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       22.98        16.83        16.18         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         1.35         1.35        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91        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-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK 
        4.04         0.03         0.36        23.70         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         4.73         1.22         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
       20.78        14.93       147.39       117.40        96.95        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-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58         5.13         6.71        21.11       195.85         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       11.28         0.89         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        0.03         0.07         4.34         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
        3.88        11.67        93.99        12.16        61.28        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       34.52        29.03        20.22        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 
       23.28        11.51        31.27        16.64         4.73        44.88 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                        182.93                         195.85 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                        22.455                         14.930 
[1] "0.1 - 182.9 (22.5)" "0.0 - 195.8 (14.9)"
[1] "hr=" "1.2"
D51V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 23(15Q21.1) MUTATED   22 11     3
  DEL PEAK 23(15Q21.1) WILD-TYPE 99 39     8
D51V3, multiclass
       clus
vv      DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  T1                              22                             99
  T2                              11                             39
  T3+T4                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   24  6
  DEL PEAK 23(15Q21.1) WILD-TYPE 87 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     24    6
  DEL PEAK 23(15Q21.1) WILD-TYPE   87   41
   clus
vv  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  0                           24                             87
  1                            6                             41
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 23(15Q21.1) MUTATED   16  3 21
  DEL PEAK 23(15Q21.1) WILD-TYPE 75  5 72
D51V5, multiclass
    clus
vv   DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  M0                           16                             75
  M1                            3                              5
  MX                           21                             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"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(15Q21.1) MUTATED               1                               40
  DEL PEAK 23(15Q21.1) WILD-TYPE             4                              157
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 23(15Q21.1) MUTATED                                               0
  DEL PEAK 23(15Q21.1) WILD-TYPE                                             5
                                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                                              2
  DEL PEAK 23(15Q21.1) WILD-TYPE                                            4
D51V6, multiclass
                                               clus
vv                                              DEL PEAK 23(15Q21.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        40
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              DEL PEAK 23(15Q21.1) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         157
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q21.1) MUTATED     6  45
  DEL PEAK 23(15Q21.1) WILD-TYPE  24 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED      6   45
  DEL PEAK 23(15Q21.1) WILD-TYPE   24  163
     clus
vv    DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  NO                             6                             24
  YES                           45                            163
[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                           8
  DEL PEAK 23(15Q21.1) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 23(15Q21.1) MUTATED                                           1
  DEL PEAK 23(15Q21.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 23(15Q21.1) MUTATED      36
  DEL PEAK 23(15Q21.1) WILD-TYPE   133
D51V10, multiclass
                                           clus
vv                                          DEL PEAK 23(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               36
                                           clus
vv                                          DEL PEAK 23(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             16
  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"
D51V11, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q21.1) MUTATED     3  29
  DEL PEAK 23(15Q21.1) WILD-TYPE  13 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED      3   29
  DEL PEAK 23(15Q21.1) WILD-TYPE   13  120
                        clus
vv                       DEL PEAK 23(15Q21.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK 23(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            120
[1] 2 2
[1] FALSE
D51V12, continuous
D51V13, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   18  6
  DEL PEAK 23(15Q21.1) WILD-TYPE 53 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     18    6
  DEL PEAK 23(15Q21.1) WILD-TYPE   53   19
            clus
vv           DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  TUMOR FREE                           18                             53
  WITH TUMOR                            6                             19
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 23(15Q21.1) MUTATED        8      1       1      1       1
  DEL PEAK 23(15Q21.1) WILD-TYPE     15      4       0      9       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 23(15Q21.1) MUTATED              37       2
  DEL PEAK 23(15Q21.1) WILD-TYPE           141      12
D51V14, multiclass
               clus
vv              DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  BRAZIL                                   8                             15
  CANADA                                   1                              4
  NIGERIA                                  1                              0
  RUSSIA                                   1                              9
  UKRAINE                                  1                              6
  UNITED STATES                           37                            141
  VIETNAM                                  2                             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 23(15Q21.1) MUTATED    1 16 31  1  2
  DEL PEAK 23(15Q21.1) WILD-TYPE 16 90 66  0 12
D51V15, multiclass
    clus
vv   DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  G1                            1                             16
  G2                           16                             90
  G3                           31                             66
  G4                            1                              0
  GX                            2                             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V16, continuous
D51V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 23(15Q21.1) MUTATED                                             6
  DEL PEAK 23(15Q21.1) WILD-TYPE                                          25
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 23(15Q21.1) MUTATED                                        2
  DEL PEAK 23(15Q21.1) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 23(15Q21.1) MUTATED                                                 1
  DEL PEAK 23(15Q21.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 23(15Q21.1) MUTATED                7                  24
  DEL PEAK 23(15Q21.1) WILD-TYPE             45                  88
D51V18, multiclass
                                                 clus
vv                                                DEL PEAK 23(15Q21.1) 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                                                       24
                                                 clus
vv                                                DEL PEAK 23(15Q21.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              45
  LIFELONG NON-SMOKER                                                         88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V19, continuous
D51V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 23(15Q21.1) MUTATED             4       21             2        1
  DEL PEAK 23(15Q21.1) WILD-TYPE          15       54            10       11
D51V21, multiclass
               clus
vv              DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                21                             54
  EXTERNAL BEAM                            2                             10
  INTERNAL                                 1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     9             3
  DEL PEAK 23(15Q21.1) WILD-TYPE                  19            13
D51V23, multiclass
                     clus
vv                    DEL PEAK 23(15Q21.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            9
  REGIONAL SITE                                  3
                     clus
vv                    DEL PEAK 23(15Q21.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             19
  REGIONAL SITE                                   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"
D51V24, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   11  1
  DEL PEAK 23(15Q21.1) WILD-TYPE 23  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     11    1
  DEL PEAK 23(15Q21.1) WILD-TYPE   23    2
     clus
vv    DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  CGY                           11                             23
  GY                             1                              2
[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                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 23(15Q21.1) MUTATED                         4
  DEL PEAK 23(15Q21.1) WILD-TYPE                      25
                                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                       6
D51V31, multiclass
                                     clus
vv                                    DEL PEAK 23(15Q21.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        4
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 23(15Q21.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  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)
  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                                                2
  DEL PEAK 23(15Q21.1) WILD-TYPE                                             14
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 23(15Q21.1) MUTATED                                                                                  20
  DEL PEAK 23(15Q21.1) WILD-TYPE                                                                                48
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 23(15Q21.1) MUTATED                                                                                             20
  DEL PEAK 23(15Q21.1) WILD-TYPE                                                                                           85
D51V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 23(15Q21.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           20
                                                                                              clus
vv                                                                                             DEL PEAK 23(15Q21.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D51V33, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED    9 12
  DEL PEAK 23(15Q21.1) WILD-TYPE 59 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED      9   12
  DEL PEAK 23(15Q21.1) WILD-TYPE   59   58
         clus
vv        DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  ABSENT                             9                             59
  PRESENT                           12                             58
[1] 2 2
[1] FALSE
D51V34, continuous
D51V35, continuous
D51V36, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED    8 15
  DEL PEAK 23(15Q21.1) WILD-TYPE 35 79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED      8   15
  DEL PEAK 23(15Q21.1) WILD-TYPE   35   79
                                          clus
vv                                         DEL PEAK 23(15Q21.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           15
                                          clus
vv                                         DEL PEAK 23(15Q21.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             79
[1] 2 2
[1] FALSE
D51V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 23(15Q21.1) MUTATED              1          11         14
  DEL PEAK 23(15Q21.1) WILD-TYPE            9          38         43
D51V38, multiclass
              clus
vv             DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  CURRENT USER                            1                              9
  FORMER USER                            11                             38
  NEVER USED                             14                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V39, continuous
D51V40, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   13  3
  DEL PEAK 23(15Q21.1) WILD-TYPE 76 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     13    3
  DEL PEAK 23(15Q21.1) WILD-TYPE   76   13
         clus
vv        DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  ABSENT                            13                             76
  PRESENT                            3                             13
[1] 2 2
[1] FALSE
D51V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 23(15Q21.1) MUTATED     0    0   4   15    3  0   1    4    0   6  0
  DEL PEAK 23(15Q21.1) WILD-TYPE   1    1  26   50   21  4   7    3    9  16  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 23(15Q21.1) MUTATED     3  0   1  4
  DEL PEAK 23(15Q21.1) WILD-TYPE   5  2   0 10
D51V42, multiclass
      clus
vv     DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             4                             26
  T1B1                           15                             50
  T1B2                            3                             21
  T2                              0                              4
  T2A                             1                              7
  T2A1                            4                              3
  T2A2                            0                              9
  T2B                             6                             16
  T3                              0                              1
  T3B                             3                              5
  T4                              0                              2
  TIS                             1                              0
  TX                              4                             10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 23(15Q21.1) MUTATED         0        0         0         1        6
  DEL PEAK 23(15Q21.1) WILD-TYPE       4        2         1         0       25
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 23(15Q21.1) MUTATED          16         4        0         1
  DEL PEAK 23(15Q21.1) WILD-TYPE        53        28        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 23(15Q21.1) MUTATED            3          0        10         0
  DEL PEAK 23(15Q21.1) WILD-TYPE          2          7        17         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 23(15Q21.1) MUTATED            6         0         1
  DEL PEAK 23(15Q21.1) WILD-TYPE         28         3         6
D51V44, multiclass
            clus
vv           DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              6                             25
  STAGE IB1                            16                             53
  STAGE IB2                             4                             28
  STAGE II                              0                              3
  STAGE IIA                             1                              5
  STAGE IIA1                            3                              2
  STAGE IIA2                            0                              7
  STAGE IIB                            10                             17
  STAGE III                             0                              1
  STAGE IIIB                            6                             28
  STAGE IVA                             0                              3
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 24(16Q11.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(16Q11.2) MUTATED    32   9
  DEL PEAK 24(16Q11.2) WILD-TYPE 151  41
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                            41                            192 
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                             9                             41 
$`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       182.93 
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         1.32 
TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EX-A1H6 TCGA-FU-A3TX TCGA-FU-A40J 
        1.81         1.51         1.18         7.92         1.48         1.35 
TCGA-FU-A770 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JX-A5QV 
        1.12       137.16        66.81        96.95        26.56         7.99 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A6DT TCGA-Q1-A73P 
        0.30         0.20         4.34         5.49         3.39        15.88 
TCGA-UC-A7PD TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A952 
       11.67        34.52        19.96        32.15        44.88 

$`DEL PEAK 24(16Q11.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       31.40        46.32        53.16        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ 
        2.43        40.93         3.58        73.45        78.35       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
        0.82        52.01        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48        20.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI 
       94.95         9.34        13.61         2.73        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        4.47         1.12        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS 
       22.98        16.18         8.28         0.76         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       14.50        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
        0.36        12.59        45.96        26.27         6.64         0.43 
TCGA-EK-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-A2RM TCGA-EK-A2RN 
        4.04         0.03         0.36        23.70         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 
        0.07         0.10         0.10         0.03        20.35         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         6.12         4.73         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-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 
        7.13        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        78.71        81.96        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
        6.71        21.11       195.85        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        0.07         2.96        15.58        13.35        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       17.56        14.07         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
        3.88        93.99        12.16        61.28        10.03        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       20.22        14.07        53.52        46.03        23.28        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       49.55        39.78        31.27        16.64         4.73        23.24 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                          0.20                           0.03 
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                        182.93                         195.85 
  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE 
                        19.960                         15.005 
[1] "0.2 - 182.9 (20.0)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1.2"
D52V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 24(16Q11.2) MUTATED   27  8     2
  DEL PEAK 24(16Q11.2) WILD-TYPE 94 42     9
D52V3, multiclass
       clus
vv      DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  T1                              27                             94
  T2                               8                             42
  T3+T4                            2                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED   30  6
  DEL PEAK 24(16Q11.2) WILD-TYPE 81 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     30    6
  DEL PEAK 24(16Q11.2) WILD-TYPE   81   41
   clus
vv  DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  0                           30                             81
  1                            6                             41
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 24(16Q11.2) MUTATED   20  2 17
  DEL PEAK 24(16Q11.2) WILD-TYPE 71  6 76
D52V5, multiclass
    clus
vv   DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  M0                           20                             71
  M1                            2                              6
  MX                           17                             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(16Q11.2) MUTATED               0                               28
  DEL PEAK 24(16Q11.2) WILD-TYPE             5                              169
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 24(16Q11.2) MUTATED                                               4
  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                                              1
  DEL PEAK 24(16Q11.2) WILD-TYPE                                            5
D52V6, multiclass
                                               clus
vv                                              DEL PEAK 24(16Q11.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK 24(16Q11.2) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         169
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q11.2) MUTATED     6  38
  DEL PEAK 24(16Q11.2) WILD-TYPE  24 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED      6   38
  DEL PEAK 24(16Q11.2) WILD-TYPE   24  170
     clus
vv    DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  NO                             6                             24
  YES                           38                            170
[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                        22
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 24(16Q11.2) MUTATED                                           0
  DEL PEAK 24(16Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 24(16Q11.2) MUTATED      37
  DEL PEAK 24(16Q11.2) WILD-TYPE   132
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                                                               37
                                           clus
vv                                          DEL PEAK 24(16Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                132
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q11.2) MUTATED     2  29
  DEL PEAK 24(16Q11.2) WILD-TYPE  14 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED      2   29
  DEL PEAK 24(16Q11.2) WILD-TYPE   14  120
                        clus
vv                       DEL PEAK 24(16Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK 24(16Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            120
[1] 2 2
[1] FALSE
D52V12, continuous
D52V13, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED   14  4
  DEL PEAK 24(16Q11.2) WILD-TYPE 57 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     14    4
  DEL PEAK 24(16Q11.2) WILD-TYPE   57   21
            clus
vv           DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  TUMOR FREE                           14                             57
  WITH TUMOR                            4                             21
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 24(16Q11.2) MUTATED        4      0       0      2       1
  DEL PEAK 24(16Q11.2) WILD-TYPE     19      5       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 24(16Q11.2) MUTATED              34       3
  DEL PEAK 24(16Q11.2) WILD-TYPE           144      11
D52V14, multiclass
               clus
vv              DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  BRAZIL                                   4                             19
  CANADA                                   0                              5
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  1                              6
  UNITED STATES                           34                            144
  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 20 17  0  1
  DEL PEAK 24(16Q11.2) WILD-TYPE 12 86 80  1 13
D52V15, multiclass
    clus
vv   DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  G1                            5                             12
  G2                           20                             86
  G3                           17                             80
  G4                            0                              1
  GX                            1                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V16, continuous
D52V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 24(16Q11.2) MUTATED                                             4
  DEL PEAK 24(16Q11.2) WILD-TYPE                                          27
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 24(16Q11.2) MUTATED                                        2
  DEL PEAK 24(16Q11.2) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 24(16Q11.2) MUTATED                                                 1
  DEL PEAK 24(16Q11.2) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 24(16Q11.2) MUTATED                7                  25
  DEL PEAK 24(16Q11.2) WILD-TYPE             45                  87
D52V18, multiclass
                                                 clus
vv                                                DEL PEAK 24(16Q11.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             7
  LIFELONG NON-SMOKER                                                       25
                                                 clus
vv                                                DEL PEAK 24(16Q11.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              45
  LIFELONG NON-SMOKER                                                         87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V19, continuous
D52V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 24(16Q11.2) MUTATED             3       10             3        4
  DEL PEAK 24(16Q11.2) WILD-TYPE          16       65             9        8
D52V21, multiclass
               clus
vv              DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  COMBINATION                              3                             16
  EXTERNAL                                10                             65
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 4                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     3             3
  DEL PEAK 24(16Q11.2) WILD-TYPE                  25            13
D52V23, multiclass
                     clus
vv                    DEL PEAK 24(16Q11.2) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            3
  REGIONAL SITE                                  3
                     clus
vv                    DEL PEAK 24(16Q11.2) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             25
  REGIONAL SITE                                   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"
D52V24, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED    5  1
  DEL PEAK 24(16Q11.2) WILD-TYPE 29  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED      5    1
  DEL PEAK 24(16Q11.2) WILD-TYPE   29    2
     clus
vv    DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  CGY                            5                             29
  GY                             1                              2
[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                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 24(16Q11.2) MUTATED                         9
  DEL PEAK 24(16Q11.2) WILD-TYPE                      20
                                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                       6
D52V31, multiclass
                                     clus
vv                                    DEL PEAK 24(16Q11.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        9
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 24(16Q11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                         20
  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 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                                                1
  DEL PEAK 24(16Q11.2) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 24(16Q11.2) MUTATED                                                                                  18
  DEL PEAK 24(16Q11.2) WILD-TYPE                                                                                50
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 24(16Q11.2) MUTATED                                                                                             16
  DEL PEAK 24(16Q11.2) WILD-TYPE                                                                                           89
D52V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 24(16Q11.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           16
                                                                                              clus
vv                                                                                             DEL PEAK 24(16Q11.2) 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)                                        50
  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"
D52V33, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED   16 12
  DEL PEAK 24(16Q11.2) WILD-TYPE 52 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     16   12
  DEL PEAK 24(16Q11.2) WILD-TYPE   52   58
         clus
vv        DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  ABSENT                            16                             52
  PRESENT                           12                             58
[1] 2 2
[1] FALSE
D52V34, continuous
D52V35, continuous
D52V36, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED    9  8
  DEL PEAK 24(16Q11.2) WILD-TYPE 34 86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED      9    8
  DEL PEAK 24(16Q11.2) WILD-TYPE   34   86
                                          clus
vv                                         DEL PEAK 24(16Q11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            8
                                          clus
vv                                         DEL PEAK 24(16Q11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             86
[1] 2 2
[1] FALSE
D52V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 24(16Q11.2) MUTATED              2          10         14
  DEL PEAK 24(16Q11.2) WILD-TYPE            8          39         43
D52V38, multiclass
              clus
vv             DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  CURRENT USER                            2                              8
  FORMER USER                            10                             39
  NEVER USED                             14                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V39, continuous
D52V40, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q11.2) MUTATED   22  1
  DEL PEAK 24(16Q11.2) WILD-TYPE 67 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q11.2) MUTATED     22    1
  DEL PEAK 24(16Q11.2) WILD-TYPE   67   15
         clus
vv        DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  ABSENT                            22                             67
  PRESENT                            1                             15
[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                             11 
                    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-MU-A51Y 
"DEL PEAK 24(16Q11.2) WILD-TYPE" "DEL PEAK 24(16Q11.2) WILD-TYPE" 
                    TCGA-MU-A8JM 
"DEL PEAK 24(16Q11.2) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 24(16Q11.2) MUTATED     0    0  10   12    5  2   2    1    2   1  0
  DEL PEAK 24(16Q11.2) WILD-TYPE   1    1  20   53   19  2   6    6    7  21  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 24(16Q11.2) MUTATED     2  0   1  1
  DEL PEAK 24(16Q11.2) WILD-TYPE   6  2   0 13
D52V42, multiclass
      clus
vv     DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                            10                             20
  T1B1                           12                             53
  T1B2                            5                             19
  T2                              2                              2
  T2A                             2                              6
  T2A1                            1                              6
  T2A2                            2                              7
  T2B                             1                             21
  T3                              0                              1
  T3B                             2                              6
  T4                              0                              2
  TIS                             1                              0
  TX                              1                             13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       3        2         1         1       24
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 24(16Q11.2) MUTATED          17         7        2         2
  DEL PEAK 24(16Q11.2) WILD-TYPE        52        25        1         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 24(16Q11.2) MUTATED            0          1         1         0
  DEL PEAK 24(16Q11.2) WILD-TYPE          5          6        26         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 24(16Q11.2) MUTATED            5         0         0
  DEL PEAK 24(16Q11.2) WILD-TYPE         29         3         7
D52V44, multiclass
            clus
vv           DEL PEAK 24(16Q11.2) MUTATED DEL PEAK 24(16Q11.2) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              7                             24
  STAGE IB1                            17                             52
  STAGE IB2                             7                             25
  STAGE II                              2                              1
  STAGE IIA                             2                              4
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             1                             26
  STAGE III                             0                              1
  STAGE IIIB                            5                             29
  STAGE IVA                             0                              3
  STAGE IVB                             0                              7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 25(16Q23.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(16Q23.1) MUTATED    34   8
  DEL PEAK 25(16Q23.1) WILD-TYPE 149  42
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            42                            191 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                             8                             42 
$`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       182.93 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A8XH TCGA-DG-A2KJ TCGA-DS-A3LQ TCGA-DS-A7WH 
      147.35        60.69        45.83        58.88        22.98        17.52 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A3GN 
        1.81        14.89         0.59         1.45         1.18         0.03 
TCGA-EX-A1H6 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A3EO TCGA-FU-A3TQ TCGA-FU-A3TX 
        7.92         6.12         4.73         2.17         1.58         1.48 
TCGA-FU-A40J TCGA-FU-A770 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JX-A5QV 
        1.35         1.12       137.16        66.81        96.95         7.99 
TCGA-LP-A7HU TCGA-MY-A5BF TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A94Y 
        0.20         4.34        34.52        19.96        32.15         4.73 

$`DEL PEAK 25(16Q23.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        46.32        30.21        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LY 
        0.46         2.43        40.93         3.58        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
      100.14         0.82        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
      134.33        15.48        20.35        17.19        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34        13.61         2.73        50.99         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-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-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99       118.65        16.83        16.18 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50        12.66        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       12.59        45.96        26.27         6.64         1.51         0.43 
TCGA-EK-A2R7 TCGA-EK-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-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A23K 
        0.10        20.35         6.94        14.70        19.79         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB 
       23.84         0.92         0.66         1.02         1.45         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        3.52         1.32         1.97         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC 
       21.67        20.78        14.93         9.44       147.39       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
        6.71        21.11       195.85        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.07         0.30         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         5.49         2.96        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        12.16        61.28        10.03        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       14.07        53.52        46.03        23.28        11.51        49.55 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       39.78        31.27        16.64        23.24        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.08        43.82        39.35        38.96        18.05 

  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 
                        182.93                         195.85 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                        20.435                         15.480 
[1] "0.0 - 182.9 (20.4)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.5"
D53V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 25(16Q23.1) MUTATED   24 10     3
  DEL PEAK 25(16Q23.1) WILD-TYPE 97 40     8
D53V3, multiclass
       clus
vv      DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  T1                              24                             97
  T2                              10                             40
  T3+T4                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED   25  9
  DEL PEAK 25(16Q23.1) WILD-TYPE 86 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     25    9
  DEL PEAK 25(16Q23.1) WILD-TYPE   86   38
   clus
vv  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  0                           25                             86
  1                            9                             38
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 25(16Q23.1) MUTATED   21  1 15
  DEL PEAK 25(16Q23.1) WILD-TYPE 70  7 78
D53V5, multiclass
    clus
vv   DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  M0                           21                             70
  M1                            1                              7
  MX                           15                             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(16Q23.1) MUTATED               0                               30
  DEL PEAK 25(16Q23.1) WILD-TYPE             5                              167
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 25(16Q23.1) MUTATED                                               3
  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                                              0
  DEL PEAK 25(16Q23.1) WILD-TYPE                                            6
D53V6, multiclass
                                               clus
vv                                              DEL PEAK 25(16Q23.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              DEL PEAK 25(16Q23.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         167
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       12
  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"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED     7  38
  DEL PEAK 25(16Q23.1) WILD-TYPE  23 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      7   38
  DEL PEAK 25(16Q23.1) WILD-TYPE   23  170
     clus
vv    DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  NO                             7                             23
  YES                           38                            170
[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                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 25(16Q23.1) MUTATED                                           0
  DEL PEAK 25(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 25(16Q23.1) MUTATED      40
  DEL PEAK 25(16Q23.1) WILD-TYPE   129
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                                                               40
                                           clus
vv                                          DEL PEAK 25(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D53V11, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED     1  29
  DEL PEAK 25(16Q23.1) WILD-TYPE  15 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      1   29
  DEL PEAK 25(16Q23.1) WILD-TYPE   15  120
                        clus
vv                       DEL PEAK 25(16Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK 25(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            120
[1] 2 2
[1] FALSE
D53V12, continuous
D53V13, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED   14  2
  DEL PEAK 25(16Q23.1) WILD-TYPE 57 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     14    2
  DEL PEAK 25(16Q23.1) WILD-TYPE   57   23
            clus
vv           DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  TUMOR FREE                           14                             57
  WITH TUMOR                            2                             23
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 25(16Q23.1) MUTATED        4      1       0      1       1
  DEL PEAK 25(16Q23.1) WILD-TYPE     19      4       1      9       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 25(16Q23.1) MUTATED              36       2
  DEL PEAK 25(16Q23.1) WILD-TYPE           142      12
D53V14, multiclass
               clus
vv              DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  BRAZIL                                   4                             19
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   1                              9
  UKRAINE                                  1                              6
  UNITED STATES                           36                            142
  VIETNAM                                  2                             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 25(16Q23.1) MUTATED    4 17 22  0  1
  DEL PEAK 25(16Q23.1) WILD-TYPE 13 89 75  1 13
D53V15, multiclass
    clus
vv   DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  G1                            4                             13
  G2                           17                             89
  G3                           22                             75
  G4                            0                              1
  GX                            1                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V16, continuous
D53V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 25(16Q23.1) MUTATED                                             6
  DEL PEAK 25(16Q23.1) WILD-TYPE                                          25
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 25(16Q23.1) MUTATED                                        3
  DEL PEAK 25(16Q23.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 25(16Q23.1) MUTATED                                                 0
  DEL PEAK 25(16Q23.1) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 25(16Q23.1) MUTATED                9                  19
  DEL PEAK 25(16Q23.1) WILD-TYPE             43                  93
D53V18, multiclass
                                                 clus
vv                                                DEL PEAK 25(16Q23.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             9
  LIFELONG NON-SMOKER                                                       19
                                                 clus
vv                                                DEL PEAK 25(16Q23.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              43
  LIFELONG NON-SMOKER                                                         93
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V19, continuous
D53V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 25(16Q23.1) MUTATED             4       11             3        3
  DEL PEAK 25(16Q23.1) WILD-TYPE          15       64             9        9
D53V21, multiclass
               clus
vv              DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  COMBINATION                              4                             15
  EXTERNAL                                11                             64
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     2             4
  DEL PEAK 25(16Q23.1) WILD-TYPE                  26            12
D53V23, multiclass
                     clus
vv                    DEL PEAK 25(16Q23.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            2
  REGIONAL SITE                                  4
                     clus
vv                    DEL PEAK 25(16Q23.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             26
  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"
D53V24, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED    5  0
  DEL PEAK 25(16Q23.1) WILD-TYPE 29  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      5    0
  DEL PEAK 25(16Q23.1) WILD-TYPE   29    3
     clus
vv    DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  CGY                            5                             29
  GY                             0                              3
[1] 2 2
[1] FALSE
D53V25, continuous
D53V26, continuous
D53V27, continuous
D53V28, continuous
D53V29, continuous
D53V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 25(16Q23.1) MUTATED                         8
  DEL PEAK 25(16Q23.1) WILD-TYPE                      21
                                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                       5
D53V31, multiclass
                                     clus
vv                                    DEL PEAK 25(16Q23.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        8
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 25(16Q23.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         21
  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 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                                                1
  DEL PEAK 25(16Q23.1) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 25(16Q23.1) MUTATED                                                                                  15
  DEL PEAK 25(16Q23.1) WILD-TYPE                                                                                53
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 25(16Q23.1) MUTATED                                                                                             17
  DEL PEAK 25(16Q23.1) WILD-TYPE                                                                                           88
D53V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 25(16Q23.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           17
                                                                                              clus
vv                                                                                             DEL PEAK 25(16Q23.1) 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)                                        53
  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"
D53V33, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED   14 12
  DEL PEAK 25(16Q23.1) WILD-TYPE 54 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     14   12
  DEL PEAK 25(16Q23.1) WILD-TYPE   54   58
         clus
vv        DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  ABSENT                            14                             54
  PRESENT                           12                             58
[1] 2 2
[1] FALSE
D53V34, continuous
D53V35, continuous
D53V36, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED    9 10
  DEL PEAK 25(16Q23.1) WILD-TYPE 34 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      9   10
  DEL PEAK 25(16Q23.1) WILD-TYPE   34   84
                                          clus
vv                                         DEL PEAK 25(16Q23.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           10
                                          clus
vv                                         DEL PEAK 25(16Q23.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             84
[1] 2 2
[1] FALSE
D53V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 25(16Q23.1) MUTATED              3          12         10
  DEL PEAK 25(16Q23.1) WILD-TYPE            7          37         47
D53V38, multiclass
              clus
vv             DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  CURRENT USER                            3                              7
  FORMER USER                            12                             37
  NEVER USED                             10                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V39, continuous
D53V40, binary
                                cls
clus                              0  1
  DEL PEAK 25(16Q23.1) MUTATED   20  2
  DEL PEAK 25(16Q23.1) WILD-TYPE 69 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     20    2
  DEL PEAK 25(16Q23.1) WILD-TYPE   69   14
         clus
vv        DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  ABSENT                            20                             69
  PRESENT                            2                             14
[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                             12 
                    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-MU-A51Y 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-MY-A913 
"DEL PEAK 25(16Q23.1) WILD-TYPE" "DEL PEAK 25(16Q23.1) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 25(16Q23.1) MUTATED     0    0   6   12    6  2   0    2    2   4  0
  DEL PEAK 25(16Q23.1) WILD-TYPE   1    1  24   53   18  2   8    5    7  18  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 25(16Q23.1) MUTATED     3  0   0  1
  DEL PEAK 25(16Q23.1) WILD-TYPE   5  2   1 13
D53V42, multiclass
      clus
vv     DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             6                             24
  T1B1                           12                             53
  T1B2                            6                             18
  T2                              2                              2
  T2A                             0                              8
  T2A1                            2                              5
  T2A2                            2                              7
  T2B                             4                             18
  T3                              0                              1
  T3B                             3                              5
  T4                              0                              2
  TIS                             0                              1
  TX                              1                             13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 25(16Q23.1) MUTATED         0        0         0         0        5
  DEL PEAK 25(16Q23.1) WILD-TYPE       4        2         1         1       26
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 25(16Q23.1) MUTATED          15         8        1         1
  DEL PEAK 25(16Q23.1) WILD-TYPE        54        24        2         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 25(16Q23.1) MUTATED            0          1         5         0
  DEL PEAK 25(16Q23.1) WILD-TYPE          5          6        22         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 25(16Q23.1) MUTATED            9         0         0
  DEL PEAK 25(16Q23.1) WILD-TYPE         25         3         7
D53V44, multiclass
            clus
vv           DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              5                             26
  STAGE IB1                            15                             54
  STAGE IB2                             8                             24
  STAGE II                              1                              2
  STAGE IIA                             1                              5
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             5                             22
  STAGE III                             0                              1
  STAGE IIIB                            9                             25
  STAGE IVA                             0                              3
  STAGE IVB                             0                              7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 26(17P12) MUTATION ANALYSIS
D54V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(17P12) MUTATED    61  23
  DEL PEAK 26(17P12) WILD-TYPE 122  27
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                          84                          149 
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                          23                           27 
$`DEL PEAK 26(17P12) MUTATED`
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN 
       23.67        68.84        18.74       144.16       173.29         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX 
       19.86        67.46        38.99        40.93        73.18        83.05 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X3 
       38.43        52.01        15.48       147.35        17.19         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8YQ 
       13.61         2.73        50.99        45.83        75.78        23.51 
TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ 
       20.91        58.88        87.75         2.66       118.65        22.98 
TCGA-EA-A1QT TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.36        14.50        12.66        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R8 
       13.48         0.36        45.96         1.51         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN 
        0.13        16.08         0.03         1.18         2.24         0.10 
TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A3EO TCGA-FU-A3NI 
        0.10        20.35         6.94         6.12         2.17         1.45 
TCGA-GH-A9DA TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A69B 
        9.01        66.81        78.71        26.56        24.56        10.06 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       11.28         0.89         0.03         2.96        13.35         3.39 
TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
        5.88        10.39         3.88        12.16        61.28        10.03 
TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       34.52        14.07        19.96        11.51        49.55        39.78 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
        4.73        23.24        42.58        42.08        43.82        39.35 

$`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         0.82        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM 
       20.42       182.93       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 
       85.55        60.69        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 
        6.12         4.47         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         0.76         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05         1.18        14.50         1.35         1.35         1.81 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         0.26        14.89         1.48        13.91        15.02 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2RB 
       12.59        26.27         6.64         0.43         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
        4.04         0.36        23.70         0.07         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        7.92        14.70        19.79         4.73         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.92         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        7.13        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      137.16       117.40        96.95        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        21.44        20.48        15.58         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 
       21.11       195.85        30.31         7.99         0.07         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82         0.20        13.87         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         5.49        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-A7PF 
       14.07        15.88         6.25        19.59        11.67        93.99 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       29.03        20.22        53.52        32.15        46.03        23.28 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A9U5 TCGA-WL-A834 
       31.27        16.64        44.88        38.96        18.05 

  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                       195.85 
  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE 
                      15.235                       15.950 
[1] "0.0 - 173.3 (15.2)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.5"
D54V2, continuous
                              vv
clus                           T1 T2 T3+T4
  DEL PEAK 26(17P12) MUTATED   36 18     6
  DEL PEAK 26(17P12) WILD-TYPE 85 32     5
D54V3, multiclass
       clus
vv      DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  T1                            36                           85
  T2                            18                           32
  T3+T4                          6                            5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   31 15
  DEL PEAK 26(17P12) WILD-TYPE 80 32
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     31   15
  DEL PEAK 26(17P12) WILD-TYPE   80   32
   clus
vv  DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  0                         31                           80
  1                         15                           32
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  DEL PEAK 26(17P12) MUTATED   30  2 33
  DEL PEAK 26(17P12) WILD-TYPE 61  6 60
D54V5, multiclass
    clus
vv   DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  M0                         30                           61
  M1                          2                            6
  MX                         33                           60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(17P12) MUTATED               1                               77
  DEL PEAK 26(17P12) WILD-TYPE             4                              120
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 26(17P12) MUTATED                                               0
  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                                              2
  DEL PEAK 26(17P12) WILD-TYPE                                            4
D54V6, multiclass
                                               clus
vv                                              DEL PEAK 26(17P12) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      77
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           2
                                               clus
vv                                              DEL PEAK 26(17P12) WILD-TYPE
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       120
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                              cls
clus                             0   1
  DEL PEAK 26(17P12) MUTATED    14  72
  DEL PEAK 26(17P12) WILD-TYPE  16 136
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     14   72
  DEL PEAK 26(17P12) WILD-TYPE   16  136
     clus
vv    DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  NO                          14                           16
  YES                         72                          136
[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                           6
  DEL PEAK 26(17P12) WILD-TYPE                        18
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 26(17P12) MUTATED                                           1    64
  DEL PEAK 26(17P12) WILD-TYPE                                         0   105
D54V10, multiclass
                                           clus
vv                                          DEL PEAK 26(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              8
  BLACK OR AFRICAN AMERICAN                                          6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             64
                                           clus
vv                                          DEL PEAK 26(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              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"
D54V11, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED    4 52
  DEL PEAK 26(17P12) WILD-TYPE 12 97
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED      4   52
  DEL PEAK 26(17P12) WILD-TYPE   12   97
                        clus
vv                       DEL PEAK 26(17P12) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         52
                        clus
vv                       DEL PEAK 26(17P12) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                           97
[1] 2 2
[1] FALSE
D54V12, continuous
D54V13, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   24 10
  DEL PEAK 26(17P12) WILD-TYPE 47 15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     24   10
  DEL PEAK 26(17P12) WILD-TYPE   47   15
            clus
vv           DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  TUMOR FREE                         24                           47
  WITH TUMOR                         10                           15
[1] 2 2
[1] FALSE
                              vv
clus                           BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 26(17P12) MUTATED       13      1       1      1       2
  DEL PEAK 26(17P12) WILD-TYPE     10      4       0      9       5
                              vv
clus                           UNITED STATES VIETNAM
  DEL PEAK 26(17P12) MUTATED              61       7
  DEL PEAK 26(17P12) WILD-TYPE           117       7
D54V14, multiclass
               clus
vv              DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  BRAZIL                                13                           10
  CANADA                                 1                            4
  NIGERIA                                1                            0
  RUSSIA                                 1                            9
  UKRAINE                                2                            5
  UNITED STATES                         61                          117
  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 37 35  1  7
  DEL PEAK 26(17P12) WILD-TYPE 13 69 62  0  7
D54V15, multiclass
    clus
vv   DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  G1                          4                           13
  G2                         37                           69
  G3                         35                           62
  G4                          1                            0
  GX                          7                            7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V16, continuous
D54V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 26(17P12) MUTATED                                            12
  DEL PEAK 26(17P12) WILD-TYPE                                          19
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 26(17P12) MUTATED                                        6
  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                                               2
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 26(17P12) MUTATED               20                  31
  DEL PEAK 26(17P12) WILD-TYPE             32                  81
D54V18, multiclass
                                                 clus
vv                                                DEL PEAK 26(17P12) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          0
  CURRENT SMOKER                                                          20
  LIFELONG NON-SMOKER                                                     31
                                                 clus
vv                                                DEL PEAK 26(17P12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            2
  CURRENT SMOKER                                                            32
  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"
D54V19, continuous
D54V20, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 26(17P12) MUTATED            10       33             4        4
  DEL PEAK 26(17P12) WILD-TYPE           9       42             8        8
D54V21, multiclass
               clus
vv              DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  COMBINATION                           10                            9
  EXTERNAL                              33                           42
  EXTERNAL BEAM                          4                            8
  INTERNAL                               4                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    11            10
  DEL PEAK 26(17P12) WILD-TYPE                  17             6
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                         11                           17
  REGIONAL SITE                               10                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V24, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   15  1
  DEL PEAK 26(17P12) WILD-TYPE 19  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     15    1
  DEL PEAK 26(17P12) WILD-TYPE   19    2
     clus
vv    DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  CGY                         15                           19
  GY                           1                            2
[1] 2 2
[1] FALSE
D54V25, continuous
D54V26, continuous
D54V27, continuous
D54V28, continuous
D54V29, continuous
D54V30, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   3
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 26(17P12) MUTATED                        12                       0
  DEL PEAK 26(17P12) WILD-TYPE                      17                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  DEL PEAK 26(17P12) MUTATED                         3
  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                                     12
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      3
                                     clus
vv                                    DEL PEAK 26(17P12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  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)
  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                                                7
  DEL PEAK 26(17P12) WILD-TYPE                                              9
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 26(17P12) MUTATED                                                                                  27
  DEL PEAK 26(17P12) WILD-TYPE                                                                                41
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 26(17P12) MUTATED                                                                                             33
  DEL PEAK 26(17P12) WILD-TYPE                                                                                           72
D54V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 26(17P12) 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)                         33
                                                                                              clus
vv                                                                                             DEL PEAK 26(17P12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           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"
D54V33, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   20 22
  DEL PEAK 26(17P12) WILD-TYPE 48 48
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     20   22
  DEL PEAK 26(17P12) WILD-TYPE   48   48
         clus
vv        DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  ABSENT                          20                           48
  PRESENT                         22                           48
[1] 2 2
[1] FALSE
D54V34, continuous
D54V35, continuous
D54V36, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   19 34
  DEL PEAK 26(17P12) WILD-TYPE 24 60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     19   34
  DEL PEAK 26(17P12) WILD-TYPE   24   60
                                          clus
vv                                         DEL PEAK 26(17P12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         34
                                          clus
vv                                         DEL PEAK 26(17P12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           60
[1] 2 2
[1] FALSE
D54V37, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  DEL PEAK 26(17P12) MUTATED              3          16         20
  DEL PEAK 26(17P12) WILD-TYPE            7          33         37
D54V38, multiclass
              clus
vv             DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  CURRENT USER                          3                            7
  FORMER USER                          16                           33
  NEVER USED                           20                           37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V39, continuous
D54V40, binary
                              cls
clus                            0  1
  DEL PEAK 26(17P12) MUTATED   28  5
  DEL PEAK 26(17P12) WILD-TYPE 61 11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(17P12) MUTATED     28    5
  DEL PEAK 26(17P12) WILD-TYPE   61   11
         clus
vv        DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  ABSENT                          28                           61
  PRESENT                          5                           11
[1] 2 2
[1] FALSE
D54V41, continuous
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 26(17P12) MUTATED     0    1  10   18    7  2   1    3    2  10  0
  DEL PEAK 26(17P12) WILD-TYPE   1    0  20   47   17  2   7    4    7  12  1
                              vv
clus                           T3B T4 TIS TX
  DEL PEAK 26(17P12) MUTATED     6  0   0  7
  DEL PEAK 26(17P12) WILD-TYPE   2  2   1  7
D54V42, multiclass
      clus
vv     DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  T1A                           0                            1
  T1A1                          1                            0
  T1B                          10                           20
  T1B1                         18                           47
  T1B2                          7                           17
  T2                            2                            2
  T2A                           1                            7
  T2A1                          3                            4
  T2A2                          2                            7
  T2B                          10                           12
  T3                            0                            1
  T3B                           6                            2
  T4                            0                            2
  TIS                           0                            1
  TX                            7                            7
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V43, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 26(17P12) MUTATED         2        1         1         1       11
  DEL PEAK 26(17P12) WILD-TYPE       2        1         0         0       20
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 26(17P12) MUTATED          21         9        0         1
  DEL PEAK 26(17P12) WILD-TYPE        48        23        3         5
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 26(17P12) MUTATED            3          1        17         0
  DEL PEAK 26(17P12) WILD-TYPE          2          6        10         1
                              vv
clus                           STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 26(17P12) MUTATED           14         1         1
  DEL PEAK 26(17P12) WILD-TYPE         20         2         6
D54V44, multiclass
            clus
vv           DEL PEAK 26(17P12) MUTATED DEL PEAK 26(17P12) WILD-TYPE
  STAGE I                             2                            2
  STAGE IA                            1                            1
  STAGE IA1                           1                            0
  STAGE IA2                           1                            0
  STAGE IB                           11                           20
  STAGE IB1                          21                           48
  STAGE IB2                           9                           23
  STAGE II                            0                            3
  STAGE IIA                           1                            5
  STAGE IIA1                          3                            2
  STAGE IIA2                          1                            6
  STAGE IIB                          17                           10
  STAGE III                           0                            1
  STAGE IIIB                         14                           20
  STAGE IVA                           1                            2
  STAGE IVB                           1                            6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK 27(17Q25.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(17Q25.3) MUTATED    29   9
  DEL PEAK 27(17Q25.3) WILD-TYPE 154  41
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                            38                            195 
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                             9                             41 
$`DEL PEAK 27(17Q25.3) MUTATED`
TCGA-C5-A1BN TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A7UC TCGA-C5-A7UH 
        5.46        38.99        40.93        73.18        17.19        60.69 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT 
       13.61         2.73        75.78        36.76       118.65        12.36 
TCGA-EA-A3HR TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.32         0.36         6.64         1.51         0.59         1.45 
TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-FU-A3HY TCGA-FU-A3NI 
        0.03         1.18         0.10         0.10         0.66         1.45 
TCGA-FU-A3TQ TCGA-GH-A9DA TCGA-HM-A4S6 TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VL 
        1.58         9.01        14.93        26.56        24.56        15.58 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-Q1-A73O TCGA-VS-A8EB TCGA-VS-A8QC 
        0.07         0.82        13.87        14.07        10.03        11.51 
TCGA-VS-A954 TCGA-WL-A834 
       42.58        18.05 

$`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 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      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 
       85.55        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         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-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         0.76         1.74         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R9 
       12.59        45.96        26.27         0.43         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
       16.08         0.07         4.04         0.36        23.70         2.24 
TCGA-EK-A2RO TCGA-EK-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-A23L 
       14.70        19.79         6.12         4.73         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.92         2.17         1.02         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
        1.35         1.32         1.97         1.12        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       21.67        20.78         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        21.44        20.48        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       195.85        30.31         7.99        11.28         0.89 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.30         0.20         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        4.34         5.49         2.96        15.58        13.35        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
        3.39        16.14        17.56        15.88         5.88         6.25 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       10.39        19.59         3.88        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       61.28        34.52        29.03        20.22        14.07        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       53.52        32.15        46.03        23.28        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 
       31.27        16.64         4.73        23.24        44.88        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       43.82        39.35        38.96 

  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 
                        118.65                         195.85 
  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE 
                         10.77                          17.52 
[1] "0.0 - 118.7 (10.8)" "0.0 - 195.8 (17.5)"
[1] "hr=" "1.8"
D55V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 27(17Q25.3) MUTATED   23  6     2
  DEL PEAK 27(17Q25.3) WILD-TYPE 98 44     9
D55V3, multiclass
       clus
vv      DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  T1                              23                             98
  T2                               6                             44
  T3+T4                            2                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED   17 10
  DEL PEAK 27(17Q25.3) WILD-TYPE 94 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     17   10
  DEL PEAK 27(17Q25.3) WILD-TYPE   94   37
   clus
vv  DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  0                           17                             94
  1                           10                             37
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 27(17Q25.3) MUTATED   13  1 17
  DEL PEAK 27(17Q25.3) WILD-TYPE 78  7 76
D55V5, multiclass
    clus
vv   DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  M0                           13                             78
  M1                            1                              7
  MX                           17                             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(17Q25.3) MUTATED               0                               39
  DEL PEAK 27(17Q25.3) WILD-TYPE             5                              158
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 27(17Q25.3) MUTATED                                               0
  DEL PEAK 27(17Q25.3) WILD-TYPE                                             5
                                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                                              1
  DEL PEAK 27(17Q25.3) WILD-TYPE                                            5
D55V6, multiclass
                                               clus
vv                                              DEL PEAK 27(17Q25.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        39
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK 27(17Q25.3) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         158
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(17Q25.3) MUTATED     5  35
  DEL PEAK 27(17Q25.3) WILD-TYPE  25 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED      5   35
  DEL PEAK 27(17Q25.3) WILD-TYPE   25  173
     clus
vv    DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  NO                             5                             25
  YES                           35                            173
[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                           2
  DEL PEAK 27(17Q25.3) WILD-TYPE                        22
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(17Q25.3) MUTATED                                           1
  DEL PEAK 27(17Q25.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 27(17Q25.3) MUTATED      29
  DEL PEAK 27(17Q25.3) WILD-TYPE   140
D55V10, multiclass
                                           clus
vv                                          DEL PEAK 27(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               29
                                           clus
vv                                          DEL PEAK 27(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D55V11, binary
                                cls
clus                               0   1
  DEL PEAK 27(17Q25.3) MUTATED     3  27
  DEL PEAK 27(17Q25.3) WILD-TYPE  13 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED      3   27
  DEL PEAK 27(17Q25.3) WILD-TYPE   13  122
                        clus
vv                       DEL PEAK 27(17Q25.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       DEL PEAK 27(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            122
[1] 2 2
[1] FALSE
D55V12, continuous
D55V13, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED    7  4
  DEL PEAK 27(17Q25.3) WILD-TYPE 64 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED      7    4
  DEL PEAK 27(17Q25.3) WILD-TYPE   64   21
            clus
vv           DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  TUMOR FREE                            7                             64
  WITH TUMOR                            4                             21
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 27(17Q25.3) MUTATED        3      0       0      2       1
  DEL PEAK 27(17Q25.3) WILD-TYPE     20      5       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 27(17Q25.3) MUTATED              31       3
  DEL PEAK 27(17Q25.3) WILD-TYPE           147      11
D55V14, multiclass
               clus
vv              DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  BRAZIL                                   3                             20
  CANADA                                   0                              5
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  1                              6
  UNITED STATES                           31                            147
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 27(17Q25.3) MUTATED    1 15 21  0  2
  DEL PEAK 27(17Q25.3) WILD-TYPE 16 91 76  1 12
D55V15, multiclass
    clus
vv   DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  G1                            1                             16
  G2                           15                             91
  G3                           21                             76
  G4                            0                              1
  GX                            2                             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V16, continuous
D55V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 27(17Q25.3) MUTATED                                             2
  DEL PEAK 27(17Q25.3) WILD-TYPE                                          29
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 27(17Q25.3) MUTATED                                        2
  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                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 27(17Q25.3) MUTATED               11                  14
  DEL PEAK 27(17Q25.3) WILD-TYPE             41                  98
D55V18, multiclass
                                                 clus
vv                                                DEL PEAK 27(17Q25.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            11
  LIFELONG NON-SMOKER                                                       14
                                                 clus
vv                                                DEL PEAK 27(17Q25.3) 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                                                              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"
D55V19, continuous
D55V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 27(17Q25.3) MUTATED             3       11             3        1
  DEL PEAK 27(17Q25.3) WILD-TYPE          16       64             9       11
D55V21, multiclass
               clus
vv              DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  COMBINATION                              3                             16
  EXTERNAL                                11                             64
  EXTERNAL BEAM                            3                              9
  INTERNAL                                 1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     3             3
  DEL PEAK 27(17Q25.3) WILD-TYPE                  25            13
D55V23, multiclass
                     clus
vv                    DEL PEAK 27(17Q25.3) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            3
  REGIONAL SITE                                  3
                     clus
vv                    DEL PEAK 27(17Q25.3) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             25
  REGIONAL SITE                                   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"
D55V24, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED    3  0
  DEL PEAK 27(17Q25.3) WILD-TYPE 31  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED      3    0
  DEL PEAK 27(17Q25.3) WILD-TYPE   31    3
     clus
vv    DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  CGY                            3                             31
  GY                             0                              3
[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                                     1
  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                      23
                                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                         1
  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                            1
  OTHER LOCATION, SPECIFY                                        6
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 27(17Q25.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         23
  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                                                2
  DEL PEAK 27(17Q25.3) WILD-TYPE                                             14
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 27(17Q25.3) MUTATED                                                                                  10
  DEL PEAK 27(17Q25.3) WILD-TYPE                                                                                58
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 27(17Q25.3) MUTATED                                                                                             18
  DEL PEAK 27(17Q25.3) WILD-TYPE                                                                                           87
D55V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 27(17Q25.3) 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)                                      10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           18
                                                                                              clus
vv                                                                                             DEL PEAK 27(17Q25.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        58
  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"
D55V33, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED   12 11
  DEL PEAK 27(17Q25.3) WILD-TYPE 56 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     12   11
  DEL PEAK 27(17Q25.3) WILD-TYPE   56   59
         clus
vv        DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  ABSENT                            12                             56
  PRESENT                           11                             59
[1] 2 2
[1] FALSE
D55V34, continuous
D55V35, continuous
D55V36, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED   10 17
  DEL PEAK 27(17Q25.3) WILD-TYPE 33 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     10   17
  DEL PEAK 27(17Q25.3) WILD-TYPE   33   77
                                          clus
vv                                         DEL PEAK 27(17Q25.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           17
                                          clus
vv                                         DEL PEAK 27(17Q25.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             77
[1] 2 2
[1] FALSE
D55V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 27(17Q25.3) MUTATED              2           7          9
  DEL PEAK 27(17Q25.3) WILD-TYPE            8          42         48
D55V38, multiclass
              clus
vv             DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  CURRENT USER                            2                              8
  FORMER USER                             7                             42
  NEVER USED                              9                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V39, continuous
D55V40, binary
                                cls
clus                              0  1
  DEL PEAK 27(17Q25.3) MUTATED   13  1
  DEL PEAK 27(17Q25.3) WILD-TYPE 76 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17Q25.3) MUTATED     13    1
  DEL PEAK 27(17Q25.3) WILD-TYPE   76   15
         clus
vv        DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  ABSENT                            13                             76
  PRESENT                            1                             15
[1] 2 2
[1] FALSE
D55V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 27(17Q25.3) MUTATED     1    0   5    9    8  0   2    1    0   3  0
  DEL PEAK 27(17Q25.3) WILD-TYPE   0    1  25   56   16  4   6    6    9  19  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 27(17Q25.3) MUTATED     2  0   0  2
  DEL PEAK 27(17Q25.3) WILD-TYPE   6  2   1 12
D55V42, multiclass
      clus
vv     DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  T1A                             1                              0
  T1A1                            0                              1
  T1B                             5                             25
  T1B1                            9                             56
  T1B2                            8                             16
  T2                              0                              4
  T2A                             2                              6
  T2A1                            1                              6
  T2A2                            0                              9
  T2B                             3                             19
  T3                              0                              1
  T3B                             2                              6
  T4                              0                              2
  TIS                             0                              1
  TX                              2                             12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 27(17Q25.3) MUTATED         0        1         0         1        8
  DEL PEAK 27(17Q25.3) WILD-TYPE       4        1         1         0       23
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 27(17Q25.3) MUTATED           8         8        1         0
  DEL PEAK 27(17Q25.3) WILD-TYPE        61        24        2         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 27(17Q25.3) MUTATED            1          0         1         0
  DEL PEAK 27(17Q25.3) WILD-TYPE          4          7        26         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 27(17Q25.3) MUTATED            7         1         1
  DEL PEAK 27(17Q25.3) WILD-TYPE         27         2         6
D55V44, multiclass
            clus
vv           DEL PEAK 27(17Q25.3) MUTATED DEL PEAK 27(17Q25.3) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              8                             23
  STAGE IB1                             8                             61
  STAGE IB2                             8                             24
  STAGE II                              1                              2
  STAGE IIA                             0                              6
  STAGE IIA1                            1                              4
  STAGE IIA2                            0                              7
  STAGE IIB                             1                             26
  STAGE III                             0                              1
  STAGE IIIB                            7                             27
  STAGE IVA                             1                              2
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 28(18Q21.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(18Q21.2) MUTATED    45  19
  DEL PEAK 28(18Q21.2) WILD-TYPE 138  31
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            64                            169 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            19                             31 
$`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         0.82 
TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH 
      154.32        17.19        60.69        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         0.76        12.36 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
        1.81        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        23.70         2.24         7.92         6.94 
TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LH 
        2.17         1.12        21.67       137.16        66.81        78.71 
TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX 
       81.96        24.56        10.06        21.11         0.89         0.07 
TCGA-LP-A7HU TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73P TCGA-RA-A741 
        0.20        15.58        13.35         3.39        15.88         3.88 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 
       11.67        10.03        14.07        19.96        53.52        46.03 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A959 
       23.28        39.78        44.88        39.35 

$`DEL PEAK 28(18Q21.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH 
       19.86        67.46        46.32        30.21        53.16        38.99 
TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A3HD 
        2.43         3.58        44.22        83.05       100.14        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       15.48        20.35       147.35        85.55        94.95         9.34 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
       50.99         8.35        75.78        23.51        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91         4.47         1.12        58.88        50.76        44.94 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52         8.28         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50        12.66        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A2RO 
        4.04         0.03         0.36         1.18         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.10         0.03        20.35        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY 
        6.12         4.73         1.22        23.84         0.92         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.35         1.32         1.97         9.01        25.41         7.13 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF 
       20.78        14.93         9.44       147.39       117.40        96.95 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        27.42         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       15.58         5.13         6.71       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       11.28         0.30         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 
       29.72         0.07         4.34         5.49         2.96        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        17.56        14.07         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
       19.59        93.99        12.16        61.28        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X 
       20.22        32.15        11.51        49.55        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 
        4.73        23.24        42.58        42.08        43.82        38.96 
TCGA-WL-A834 
       18.05 

  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                        154.32                         195.85 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                         21.01                          14.99 
[1] "0.1 - 154.3 (21.0)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1.3"
D56V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 28(18Q21.2) MUTATED   31 11     3
  DEL PEAK 28(18Q21.2) WILD-TYPE 90 39     8
D56V3, multiclass
       clus
vv      DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  T1                              31                             90
  T2                              11                             39
  T3+T4                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   29  9
  DEL PEAK 28(18Q21.2) WILD-TYPE 82 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     29    9
  DEL PEAK 28(18Q21.2) WILD-TYPE   82   38
   clus
vv  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  0                           29                             82
  1                            9                             38
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 28(18Q21.2) MUTATED   25  3 21
  DEL PEAK 28(18Q21.2) WILD-TYPE 66  5 72
D56V5, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  M0                           25                             66
  M1                            3                              5
  MX                           21                             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"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(18Q21.2) MUTATED               0                               45
  DEL PEAK 28(18Q21.2) WILD-TYPE             5                              152
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 28(18Q21.2) MUTATED                                               1
  DEL PEAK 28(18Q21.2) WILD-TYPE                                             4
                                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                                              4
  DEL PEAK 28(18Q21.2) WILD-TYPE                                            2
D56V6, multiclass
                                               clus
vv                                              DEL PEAK 28(18Q21.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        45
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              DEL PEAK 28(18Q21.2) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         152
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    10  56
  DEL PEAK 28(18Q21.2) WILD-TYPE  20 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     10   56
  DEL PEAK 28(18Q21.2) WILD-TYPE   20  152
     clus
vv    DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  NO                            10                             20
  YES                           56                            152
[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                        15
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 28(18Q21.2) MUTATED                                           0
  DEL PEAK 28(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 28(18Q21.2) MUTATED      48
  DEL PEAK 28(18Q21.2) WILD-TYPE   121
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                                                               48
                                           clus
vv                                          DEL PEAK 28(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                121
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED     3  37
  DEL PEAK 28(18Q21.2) WILD-TYPE  13 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED      3   37
  DEL PEAK 28(18Q21.2) WILD-TYPE   13  112
                        clus
vv                       DEL PEAK 28(18Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       DEL PEAK 28(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            112
[1] 2 2
[1] FALSE
D56V12, continuous
D56V13, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   20  9
  DEL PEAK 28(18Q21.2) WILD-TYPE 51 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     20    9
  DEL PEAK 28(18Q21.2) WILD-TYPE   51   16
            clus
vv           DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  TUMOR FREE                           20                             51
  WITH TUMOR                            9                             16
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 28(18Q21.2) MUTATED        9      1       0      3       1
  DEL PEAK 28(18Q21.2) WILD-TYPE     14      4       1      7       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 28(18Q21.2) MUTATED              49       3
  DEL PEAK 28(18Q21.2) WILD-TYPE           129      11
D56V14, multiclass
               clus
vv              DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  BRAZIL                                   9                             14
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   3                              7
  UKRAINE                                  1                              6
  UNITED STATES                           49                            129
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 28(18Q21.2) MUTATED    4 25 29  1  6
  DEL PEAK 28(18Q21.2) WILD-TYPE 13 81 68  0  8
D56V15, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  G1                            4                             13
  G2                           25                             81
  G3                           29                             68
  G4                            1                              0
  GX                            6                              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V16, continuous
D56V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 28(18Q21.2) MUTATED                                             5
  DEL PEAK 28(18Q21.2) WILD-TYPE                                          26
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 28(18Q21.2) MUTATED                                        1
  DEL PEAK 28(18Q21.2) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 28(18Q21.2) MUTATED                                                 0
  DEL PEAK 28(18Q21.2) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 28(18Q21.2) MUTATED               12                  35
  DEL PEAK 28(18Q21.2) WILD-TYPE             40                  77
D56V18, multiclass
                                                 clus
vv                                                DEL PEAK 28(18Q21.2) 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                                                            12
  LIFELONG NON-SMOKER                                                       35
                                                 clus
vv                                                DEL PEAK 28(18Q21.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              40
  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"
D56V19, continuous
D56V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 28(18Q21.2) MUTATED             5       20             5        2
  DEL PEAK 28(18Q21.2) WILD-TYPE          14       55             7       10
D56V21, multiclass
               clus
vv              DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  COMBINATION                              5                             14
  EXTERNAL                                20                             55
  EXTERNAL BEAM                            5                              7
  INTERNAL                                 2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     8             2
  DEL PEAK 28(18Q21.2) WILD-TYPE                  20            14
D56V23, multiclass
                     clus
vv                    DEL PEAK 28(18Q21.2) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            8
  REGIONAL SITE                                  2
                     clus
vv                    DEL PEAK 28(18Q21.2) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             20
  REGIONAL SITE                                   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"
D56V24, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED    8  0
  DEL PEAK 28(18Q21.2) WILD-TYPE 26  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED      8    0
  DEL PEAK 28(18Q21.2) WILD-TYPE   26    3
     clus
vv    DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  CGY                            8                             26
  GY                             0                              3
[1] 2 2
[1] FALSE
D56V25, continuous
D56V26, continuous
D56V27, continuous
D56V28, continuous
D56V29, continuous
D56V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 28(18Q21.2) MUTATED                        11
  DEL PEAK 28(18Q21.2) WILD-TYPE                      18
                                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                         3
  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                                       11
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        3
                                     clus
vv                                    DEL PEAK 28(18Q21.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         18
  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                                                5
  DEL PEAK 28(18Q21.2) WILD-TYPE                                             11
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 28(18Q21.2) MUTATED                                                                                  22
  DEL PEAK 28(18Q21.2) WILD-TYPE                                                                                46
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 28(18Q21.2) MUTATED                                                                                             27
  DEL PEAK 28(18Q21.2) WILD-TYPE                                                                                           78
D56V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 28(18Q21.2) 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)                                      22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           27
                                                                                              clus
vv                                                                                             DEL PEAK 28(18Q21.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        46
  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"
D56V33, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   22 11
  DEL PEAK 28(18Q21.2) WILD-TYPE 46 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     22   11
  DEL PEAK 28(18Q21.2) WILD-TYPE   46   59
         clus
vv        DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  ABSENT                            22                             46
  PRESENT                           11                             59
[1] 2 2
[1] FALSE
D56V34, continuous
D56V35, continuous
D56V36, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   11 18
  DEL PEAK 28(18Q21.2) WILD-TYPE 32 76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     11   18
  DEL PEAK 28(18Q21.2) WILD-TYPE   32   76
                                          clus
vv                                         DEL PEAK 28(18Q21.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           18
                                          clus
vv                                         DEL PEAK 28(18Q21.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             76
[1] 2 2
[1] FALSE
D56V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 28(18Q21.2) MUTATED              4          19         16
  DEL PEAK 28(18Q21.2) WILD-TYPE            6          30         41
D56V38, multiclass
              clus
vv             DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  CURRENT USER                            4                              6
  FORMER USER                            19                             30
  NEVER USED                             16                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V39, continuous
D56V40, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   27  1
  DEL PEAK 28(18Q21.2) WILD-TYPE 62 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     27    1
  DEL PEAK 28(18Q21.2) WILD-TYPE   62   15
         clus
vv        DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  ABSENT                            27                             62
  PRESENT                            1                             15
[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                             11 
                    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-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 28(18Q21.2) WILD-TYPE" "DEL PEAK 28(18Q21.2) WILD-TYPE" 
                    TCGA-MY-A913 
"DEL PEAK 28(18Q21.2) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 28(18Q21.2) MUTATED     0    0   9   20    2  1   1    2    1   6  0
  DEL PEAK 28(18Q21.2) WILD-TYPE   1    1  21   45   22  3   7    5    8  16  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 28(18Q21.2) MUTATED     3  0   0  4
  DEL PEAK 28(18Q21.2) WILD-TYPE   5  2   1 10
D56V42, multiclass
      clus
vv     DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             9                             21
  T1B1                           20                             45
  T1B2                            2                             22
  T2                              1                              3
  T2A                             1                              7
  T2A1                            2                              5
  T2A2                            1                              8
  T2B                             6                             16
  T3                              0                              1
  T3B                             3                              5
  T4                              0                              2
  TIS                             0                              1
  TX                              4                             10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 28(18Q21.2) MUTATED         1        1         0         0       10
  DEL PEAK 28(18Q21.2) WILD-TYPE       3        1         1         1       21
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 28(18Q21.2) MUTATED          25         4        1         1
  DEL PEAK 28(18Q21.2) WILD-TYPE        44        28        2         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 28(18Q21.2) MUTATED            2          0        11         0
  DEL PEAK 28(18Q21.2) WILD-TYPE          3          7        16         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 28(18Q21.2) MUTATED            5         0         2
  DEL PEAK 28(18Q21.2) WILD-TYPE         29         3         5
D56V44, multiclass
            clus
vv           DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             10                             21
  STAGE IB1                            25                             44
  STAGE IB2                             4                             28
  STAGE II                              1                              2
  STAGE IIA                             1                              5
  STAGE IIA1                            2                              3
  STAGE IIA2                            0                              7
  STAGE IIB                            11                             16
  STAGE III                             0                              1
  STAGE IIIB                            5                             29
  STAGE IVA                             0                              3
  STAGE IVB                             2                              5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 29(19P13.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(19P13.3) MUTATED    56  23
  DEL PEAK 29(19P13.3) WILD-TYPE 127  27
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            79                            154 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            23                             27 
$`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         4.47       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         1.35        14.50         1.81 
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-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
        0.43         0.59         1.45        16.08         1.18         2.24 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A5XV 
        0.10         0.10         0.03        19.79        23.84         1.97 
TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-JW-A5VI TCGA-JW-A5VK 
        9.01         7.13        14.93       117.40        24.56        20.48 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 
       21.11         7.99         0.07         5.49         2.96        15.95 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EJ TCGA-VS-A8Q8 
       10.39         3.88        12.16        10.03        19.96        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A957 
       46.03        23.28        49.55        16.64         4.73        42.08 
TCGA-VS-A959 
       39.35 

$`DEL PEAK 29(19P13.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        57.04        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1MH 
      173.29        82.85        19.86        67.46        46.32        38.99 
TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
        2.43         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14        38.43         0.82        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7UC 
      182.93       154.32       101.82       134.33        20.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YT 
       85.55        60.69        94.95         8.35        75.78         6.12 
TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91         1.12        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WF 
       87.75        58.88        36.76         2.66        22.98        16.18 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        0.76         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
        1.18         1.35        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
        1.48        15.02        13.48        12.59        45.96        26.27 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.51         0.59         0.13         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.36        23.70         0.07         0.10        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70         6.12         4.73         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.35         1.32         1.12        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       21.67        20.78         9.44       147.39       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        26.56        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        21.44        15.58        10.06         5.13         6.71 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 
      195.85        30.31        11.28         0.89         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.20        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34        15.58        13.35         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD 
       14.07        15.88         5.88         6.25        19.59        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       93.99        61.28        34.52        29.03        20.22        14.07 
TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A952 
       53.52        11.51        39.78        31.27        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        43.82        38.96        18.05 

  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                         195.85 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                         14.99                          16.16 
[1] "0.0 - 147.3 (15.0)" "0.0 - 195.8 (16.2)"
[1] "hr=" "2.1"
D57V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 29(19P13.3) MUTATED   42 13     3
  DEL PEAK 29(19P13.3) WILD-TYPE 79 37     8
D57V3, multiclass
       clus
vv      DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  T1                              42                             79
  T2                              13                             37
  T3+T4                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   37 14
  DEL PEAK 29(19P13.3) WILD-TYPE 74 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     37   14
  DEL PEAK 29(19P13.3) WILD-TYPE   74   33
   clus
vv  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  0                           37                             74
  1                           14                             33
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 29(19P13.3) MUTATED   27  3 32
  DEL PEAK 29(19P13.3) WILD-TYPE 64  5 61
D57V5, multiclass
    clus
vv   DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  M0                           27                             64
  M1                            3                              5
  MX                           32                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(19P13.3) MUTATED               2                               74
  DEL PEAK 29(19P13.3) WILD-TYPE             3                              123
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 29(19P13.3) MUTATED                                               0
  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                                              1
  DEL PEAK 29(19P13.3) WILD-TYPE                                            5
D57V6, multiclass
                                               clus
vv                                              DEL PEAK 29(19P13.3) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        74
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK 29(19P13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    12  70
  DEL PEAK 29(19P13.3) WILD-TYPE  18 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     12   70
  DEL PEAK 29(19P13.3) WILD-TYPE   18  138
     clus
vv    DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  NO                            12                             18
  YES                           70                            138
[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                           7
  DEL PEAK 29(19P13.3) WILD-TYPE                        17
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(19P13.3) MUTATED                                           1
  DEL PEAK 29(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 29(19P13.3) MUTATED      64
  DEL PEAK 29(19P13.3) WILD-TYPE   105
D57V10, multiclass
                                           clus
vv                                          DEL PEAK 29(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               64
                                           clus
vv                                          DEL PEAK 29(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D57V11, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED    4 53
  DEL PEAK 29(19P13.3) WILD-TYPE 12 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED      4   53
  DEL PEAK 29(19P13.3) WILD-TYPE   12   96
                        clus
vv                       DEL PEAK 29(19P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       DEL PEAK 29(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                             96
[1] 2 2
[1] FALSE
D57V12, continuous
D57V13, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   24 11
  DEL PEAK 29(19P13.3) WILD-TYPE 47 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     24   11
  DEL PEAK 29(19P13.3) WILD-TYPE   47   14
            clus
vv           DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  TUMOR FREE                           24                             47
  WITH TUMOR                           11                             14
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 29(19P13.3) MUTATED       10      0       1      2       4
  DEL PEAK 29(19P13.3) WILD-TYPE     13      5       0      8       3
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 29(19P13.3) MUTATED              60       5
  DEL PEAK 29(19P13.3) WILD-TYPE           118       9
D57V14, multiclass
               clus
vv              DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  BRAZIL                                  10                             13
  CANADA                                   0                              5
  NIGERIA                                  1                              0
  RUSSIA                                   2                              8
  UKRAINE                                  4                              3
  UNITED STATES                           60                            118
  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 33 40  0  4
  DEL PEAK 29(19P13.3) WILD-TYPE 14 73 57  1 10
D57V15, multiclass
    clus
vv   DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  G1                            3                             14
  G2                           33                             73
  G3                           40                             57
  G4                            0                              1
  GX                            4                             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V16, continuous
D57V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 29(19P13.3) MUTATED                                             9
  DEL PEAK 29(19P13.3) WILD-TYPE                                          22
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 29(19P13.3) MUTATED                                        3
  DEL PEAK 29(19P13.3) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 29(19P13.3) MUTATED                                                 1
  DEL PEAK 29(19P13.3) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 29(19P13.3) MUTATED               16                  38
  DEL PEAK 29(19P13.3) WILD-TYPE             36                  74
D57V18, multiclass
                                                 clus
vv                                                DEL PEAK 29(19P13.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            16
  LIFELONG NON-SMOKER                                                       38
                                                 clus
vv                                                DEL PEAK 29(19P13.3) 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                                                              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"
D57V19, continuous
D57V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 29(19P13.3) MUTATED             8       30             4        5
  DEL PEAK 29(19P13.3) WILD-TYPE          11       45             8        7
D57V21, multiclass
               clus
vv              DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  COMBINATION                              8                             11
  EXTERNAL                                30                             45
  EXTERNAL BEAM                            4                              8
  INTERNAL                                 5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    11             7
  DEL PEAK 29(19P13.3) WILD-TYPE                  17             9
D57V23, multiclass
                     clus
vv                    DEL PEAK 29(19P13.3) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                           11
  REGIONAL SITE                                  7
                     clus
vv                    DEL PEAK 29(19P13.3) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             17
  REGIONAL SITE                                    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"
D57V24, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   14  2
  DEL PEAK 29(19P13.3) WILD-TYPE 20  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     14    2
  DEL PEAK 29(19P13.3) WILD-TYPE   20    1
     clus
vv    DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  CGY                           14                             20
  GY                             2                              1
[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                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 29(19P13.3) MUTATED                        13
  DEL PEAK 29(19P13.3) WILD-TYPE                      16
                                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                         1
  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                                        1
                                     clus
vv                                    DEL PEAK 29(19P13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                         16
  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                                                6
  DEL PEAK 29(19P13.3) WILD-TYPE                                             10
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 29(19P13.3) MUTATED                                                                                  17
  DEL PEAK 29(19P13.3) WILD-TYPE                                                                                51
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 29(19P13.3) MUTATED                                                                                             34
  DEL PEAK 29(19P13.3) WILD-TYPE                                                                                           71
D57V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 29(19P13.3) 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)                           34
                                                                                              clus
vv                                                                                             DEL PEAK 29(19P13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V33, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   19 24
  DEL PEAK 29(19P13.3) WILD-TYPE 49 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     19   24
  DEL PEAK 29(19P13.3) WILD-TYPE   49   46
         clus
vv        DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  ABSENT                            19                             49
  PRESENT                           24                             46
[1] 2 2
[1] FALSE
D57V34, continuous
D57V35, continuous
D57V36, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   15 31
  DEL PEAK 29(19P13.3) WILD-TYPE 28 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     15   31
  DEL PEAK 29(19P13.3) WILD-TYPE   28   63
                                          clus
vv                                         DEL PEAK 29(19P13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           31
                                          clus
vv                                         DEL PEAK 29(19P13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             63
[1] 2 2
[1] FALSE
D57V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 29(19P13.3) MUTATED              3          19         15
  DEL PEAK 29(19P13.3) WILD-TYPE            7          30         42
D57V38, multiclass
              clus
vv             DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  CURRENT USER                            3                              7
  FORMER USER                            19                             30
  NEVER USED                             15                             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V39, continuous
D57V40, binary
                                cls
clus                              0  1
  DEL PEAK 29(19P13.3) MUTATED   27  5
  DEL PEAK 29(19P13.3) WILD-TYPE 62 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     27    5
  DEL PEAK 29(19P13.3) WILD-TYPE   62   11
         clus
vv        DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  ABSENT                            27                             62
  PRESENT                            5                             11
[1] 2 2
[1] FALSE
D57V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 29(19P13.3) MUTATED     0    0   9   23   10  0   1    2    2   8  0
  DEL PEAK 29(19P13.3) WILD-TYPE   1    1  21   42   14  4   7    5    7  14  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 29(19P13.3) MUTATED     3  0   1  5
  DEL PEAK 29(19P13.3) WILD-TYPE   5  2   0  9
D57V42, multiclass
      clus
vv     DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             9                             21
  T1B1                           23                             42
  T1B2                           10                             14
  T2                              0                              4
  T2A                             1                              7
  T2A1                            2                              5
  T2A2                            2                              7
  T2B                             8                             14
  T3                              0                              1
  T3B                             3                              5
  T4                              0                              2
  TIS                             1                              0
  TX                              5                              9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 29(19P13.3) MUTATED         0        0         0         0       10
  DEL PEAK 29(19P13.3) WILD-TYPE       4        2         1         1       21
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 29(19P13.3) MUTATED          29        12        0         2
  DEL PEAK 29(19P13.3) WILD-TYPE        40        20        3         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 29(19P13.3) MUTATED            2          2        11         0
  DEL PEAK 29(19P13.3) WILD-TYPE          3          5        16         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 29(19P13.3) MUTATED           11         0         1
  DEL PEAK 29(19P13.3) WILD-TYPE         23         3         6
D57V44, multiclass
            clus
vv           DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              0                              2
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             10                             21
  STAGE IB1                            29                             40
  STAGE IB2                            12                             20
  STAGE II                              0                              3
  STAGE IIA                             2                              4
  STAGE IIA1                            2                              3
  STAGE IIA2                            2                              5
  STAGE IIB                            11                             16
  STAGE III                             0                              1
  STAGE IIIB                           11                             23
  STAGE IVA                             0                              3
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 30(19Q13.33) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 30(19Q13.33) MUTATED    23   8
  DEL PEAK 30(19Q13.33) WILD-TYPE 160  42
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                             31                             202 
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                              8                              42 
$`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         1.32 
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 
       29.72         3.39        20.22        19.96        46.03        39.78 
TCGA-VS-A957 
       42.08 

$`DEL PEAK 30(19Q13.33) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MF 
       19.86        67.46        31.40        46.32        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         2.43        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC 
      154.32       101.82       134.33        15.48       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
       85.55        60.69         9.34        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        75.78        99.91        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        4.47         1.12        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS 
       16.18        17.52         8.28         0.76         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       14.50         1.81        12.66        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        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-A2PL 
        0.36        12.59        45.96        26.27         1.51         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.03         0.36         1.18        23.70         2.24         0.10 
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-A23L 
       14.70        19.79         6.12         4.73         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17         0.66         1.02         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-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         7.13        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK TCGA-IR-A3LL 
      147.39       137.16        66.81        96.95        26.56        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        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        6.71        21.11       195.85         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42         0.07         4.34         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       13.35        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       14.07        53.52        32.15        23.28        11.51        49.55 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       31.27        16.64         4.73        23.24        44.88        42.58 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

  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                          195.85 
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                         20.910                          15.005 
[1] "0.1 - 118.7 (20.9)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1.1"
D58V2, continuous
                                 vv
clus                               T1  T2 T3+T4
  DEL PEAK 30(19Q13.33) MUTATED    15   7     2
  DEL PEAK 30(19Q13.33) WILD-TYPE 106  43     9
D58V3, multiclass
       clus
vv      DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  T1                               15                             106
  T2                                7                              43
  T3+T4                             2                               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED   14  5
  DEL PEAK 30(19Q13.33) WILD-TYPE 97 42
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED     14    5
  DEL PEAK 30(19Q13.33) WILD-TYPE   97   42
   clus
vv  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  0                            14                              97
  1                             5                              42
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 30(19Q13.33) MUTATED   11  2 13
  DEL PEAK 30(19Q13.33) WILD-TYPE 80  6 80
D58V5, multiclass
    clus
vv   DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  M0                            11                              80
  M1                             2                               6
  MX                            13                              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  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                                 23
  DEL PEAK 30(19Q13.33) WILD-TYPE                              174
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 30(19Q13.33) MUTATED                                               1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                             4
                                 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                                              2
  DEL PEAK 30(19Q13.33) WILD-TYPE                                            4
D58V6, multiclass
                                               clus
vv                                              DEL PEAK 30(19Q13.33) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         23
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              2
                                               clus
vv                                              DEL PEAK 30(19Q13.33) WILD-TYPE
  ADENOSQUAMOUS                                                               5
  CERVICAL SQUAMOUS CELL CARCINOMA                                          174
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 30(19Q13.33) MUTATED     4  27
  DEL PEAK 30(19Q13.33) WILD-TYPE  26 181
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      4   27
  DEL PEAK 30(19Q13.33) WILD-TYPE   26  181
     clus
vv    DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  NO                              4                              26
  YES                            27                             181
[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                           3
  DEL PEAK 30(19Q13.33) WILD-TYPE                        21
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(19Q13.33) MUTATED                                           1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 30(19Q13.33) MUTATED      23
  DEL PEAK 30(19Q13.33) WILD-TYPE   146
D58V10, multiclass
                                           clus
vv                                          DEL PEAK 30(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 1
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                23
                                           clus
vv                                          DEL PEAK 30(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  17
  BLACK OR AFRICAN AMERICAN                                              21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 146
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                                 cls
clus                                0   1
  DEL PEAK 30(19Q13.33) MUTATED     3  14
  DEL PEAK 30(19Q13.33) WILD-TYPE  13 135
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      3   14
  DEL PEAK 30(19Q13.33) WILD-TYPE   13  135
                        clus
vv                       DEL PEAK 30(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            14
                        clus
vv                       DEL PEAK 30(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             135
[1] 2 2
[1] FALSE
D58V12, continuous
D58V13, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED   11  4
  DEL PEAK 30(19Q13.33) WILD-TYPE 60 21
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED     11    4
  DEL PEAK 30(19Q13.33) WILD-TYPE   60   21
            clus
vv           DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  TUMOR FREE                            11                              60
  WITH TUMOR                             4                              21
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 30(19Q13.33) MUTATED        5      1       0      3       0
  DEL PEAK 30(19Q13.33) WILD-TYPE     18      4       1      7       7
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 30(19Q13.33) MUTATED              22       0
  DEL PEAK 30(19Q13.33) WILD-TYPE           156      14
D58V14, multiclass
               clus
vv              DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  BRAZIL                                    5                              18
  CANADA                                    1                               4
  NIGERIA                                   0                               1
  RUSSIA                                    3                               7
  UKRAINE                                   0                               7
  UNITED STATES                            22                             156
  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 13 15  1  1
  DEL PEAK 30(19Q13.33) WILD-TYPE 16 93 82  0 13
D58V15, multiclass
    clus
vv   DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  G1                             1                              16
  G2                            13                              93
  G3                            15                              82
  G4                             1                               0
  GX                             1                              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V16, continuous
[1] "Remove cluster labels:"        "DEL PEAK 30(19Q13.33) MUTATED"
clus
  DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE 
                              2                              32 
                     TCGA-BI-A0VR                      TCGA-C5-A1BJ 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A1BL                      TCGA-C5-A1BQ 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A1ME                      TCGA-C5-A1MF 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A1MH                      TCGA-C5-A2M2 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A3HD                      TCGA-C5-A7CO 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A8XH                      TCGA-C5-A907 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-DG-A2KK                      TCGA-DS-A3LQ 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-EK-A2RA                      TCGA-EX-A69M 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-FU-A2QG                      TCGA-FU-A3TX 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-FU-A3WB                      TCGA-HM-A3JK 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-HM-A4S6                      TCGA-IR-A3L7 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-IR-A3LB                      TCGA-JX-A3Q0 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-MU-A5YI                      TCGA-MU-A8JM 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-Q1-A6DW                      TCGA-Q1-A73S 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-RA-A741                      TCGA-VS-A8QF 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
                     TCGA-VS-A94Z                      TCGA-WL-A834 
"DEL PEAK 30(19Q13.33) WILD-TYPE" "DEL PEAK 30(19Q13.33) WILD-TYPE" 
D58V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 30(19Q13.33) MUTATED                                             2
  DEL PEAK 30(19Q13.33) WILD-TYPE                                          29
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 30(19Q13.33) MUTATED                                        1
  DEL PEAK 30(19Q13.33) WILD-TYPE                                      7
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 30(19Q13.33) MUTATED                                                 0
  DEL PEAK 30(19Q13.33) WILD-TYPE                                               2
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 30(19Q13.33) MUTATED                9                  15
  DEL PEAK 30(19Q13.33) WILD-TYPE             43                  97
D58V18, multiclass
                                                 clus
vv                                                DEL PEAK 30(19Q13.33) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                              9
  LIFELONG NON-SMOKER                                                        15
                                                 clus
vv                                                DEL PEAK 30(19Q13.33) 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                                                               43
  LIFELONG NON-SMOKER                                                          97
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V19, continuous
D58V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 30(19Q13.33) MUTATED             1       13             3        0
  DEL PEAK 30(19Q13.33) WILD-TYPE          18       62             9       12
D58V21, multiclass
               clus
vv              DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  COMBINATION                               1                              18
  EXTERNAL                                 13                              62
  EXTERNAL BEAM                             3                               9
  INTERNAL                                  0                              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     5             2
  DEL PEAK 30(19Q13.33) WILD-TYPE                  23            14
D58V23, multiclass
                     clus
vv                    DEL PEAK 30(19Q13.33) MUTATED
  DISTANT RECURRENCE                              0
  LOCAL RECURRENCE                                0
  PRIMARY TUMOR FIELD                             5
  REGIONAL SITE                                   2
                     clus
vv                    DEL PEAK 30(19Q13.33) WILD-TYPE
  DISTANT RECURRENCE                                2
  LOCAL RECURRENCE                                  2
  PRIMARY TUMOR FIELD                              23
  REGIONAL SITE                                    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"
D58V24, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED    7  0
  DEL PEAK 30(19Q13.33) WILD-TYPE 27  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      7    0
  DEL PEAK 30(19Q13.33) WILD-TYPE   27    3
     clus
vv    DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  CGY                             7                              27
  GY                              0                               3
[1] 2 2
[1] FALSE
D58V25, continuous
D58V26, continuous
D58V27, continuous
D58V28, continuous
D58V29, continuous
D58V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 30(19Q13.33) MUTATED                         5
  DEL PEAK 30(19Q13.33) WILD-TYPE                      24
                                 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                         1
  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                                         5
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         1
                                     clus
vv                                    DEL PEAK 30(19Q13.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                          24
  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                                                2
  DEL PEAK 30(19Q13.33) WILD-TYPE                                             14
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 30(19Q13.33) MUTATED                                                                                  12
  DEL PEAK 30(19Q13.33) WILD-TYPE                                                                                56
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 30(19Q13.33) MUTATED                                                                                              9
  DEL PEAK 30(19Q13.33) WILD-TYPE                                                                                           96
D58V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 30(19Q13.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             9
                                                                                              clus
vv                                                                                             DEL PEAK 30(19Q13.33) 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)                                         56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V33, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED    8  7
  DEL PEAK 30(19Q13.33) WILD-TYPE 60 63
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      8    7
  DEL PEAK 30(19Q13.33) WILD-TYPE   60   63
         clus
vv        DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  ABSENT                              8                              60
  PRESENT                             7                              63
[1] 2 2
[1] FALSE
D58V34, continuous
D58V35, continuous
D58V36, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED    4  9
  DEL PEAK 30(19Q13.33) WILD-TYPE 39 85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED      4    9
  DEL PEAK 30(19Q13.33) WILD-TYPE   39   85
                                          clus
vv                                         DEL PEAK 30(19Q13.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             9
                                          clus
vv                                         DEL PEAK 30(19Q13.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              85
[1] 2 2
[1] FALSE
D58V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 30(19Q13.33) MUTATED              1           5          8
  DEL PEAK 30(19Q13.33) WILD-TYPE            9          44         49
D58V38, multiclass
              clus
vv             DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  CURRENT USER                             1                               9
  FORMER USER                              5                              44
  NEVER USED                               8                              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V39, continuous
D58V40, binary
                                 cls
clus                               0  1
  DEL PEAK 30(19Q13.33) MUTATED   14  1
  DEL PEAK 30(19Q13.33) WILD-TYPE 75 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(19Q13.33) MUTATED     14    1
  DEL PEAK 30(19Q13.33) WILD-TYPE   75   15
         clus
vv        DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  ABSENT                             14                              75
  PRESENT                             1                              15
[1] 2 2
[1] FALSE
D58V41, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 30(19Q13.33) MUTATED     0    0   4    9    2  0   2    1    0   4
  DEL PEAK 30(19Q13.33) WILD-TYPE   1    1  26   56   22  4   6    6    9  18
                                 vv
clus                              T3 T3B T4 TIS TX
  DEL PEAK 30(19Q13.33) MUTATED    0   2  0   0  3
  DEL PEAK 30(19Q13.33) WILD-TYPE  1   6  2   1 11
D58V42, multiclass
      clus
vv     DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  T1A                              0                               1
  T1A1                             0                               1
  T1B                              4                              26
  T1B1                             9                              56
  T1B2                             2                              22
  T2                               0                               4
  T2A                              2                               6
  T2A1                             1                               6
  T2A2                             0                               9
  T2B                              4                              18
  T3                               0                               1
  T3B                              2                               6
  T4                               0                               2
  TIS                              0                               1
  TX                               3                              11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 30(19Q13.33) MUTATED         1        0         0         0        2
  DEL PEAK 30(19Q13.33) WILD-TYPE       3        2         1         1       29
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 30(19Q13.33) MUTATED          16         3        1         0
  DEL PEAK 30(19Q13.33) WILD-TYPE        53        29        2         6
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 30(19Q13.33) MUTATED            1          0         4         0
  DEL PEAK 30(19Q13.33) WILD-TYPE          4          7        23         1
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 30(19Q13.33) MUTATED            2         0         1
  DEL PEAK 30(19Q13.33) WILD-TYPE         32         3         6
D58V44, multiclass
            clus
vv           DEL PEAK 30(19Q13.33) MUTATED DEL PEAK 30(19Q13.33) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                               0                               2
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               2                              29
  STAGE IB1                             16                              53
  STAGE IB2                              3                              29
  STAGE II                               1                               2
  STAGE IIA                              0                               6
  STAGE IIA1                             1                               4
  STAGE IIA2                             0                               7
  STAGE IIB                              4                              23
  STAGE III                              0                               1
  STAGE IIIB                             2                              32
  STAGE IVA                              0                               3
  STAGE IVB                              1                               6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK 31(20P12.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(20P12.1) MUTATED    19  10
  DEL PEAK 31(20P12.1) WILD-TYPE 164  40
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            29                            204 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            10                             40 
$`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         1.35         0.26        45.96 
TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A770 TCGA-GH-A9DA TCGA-IR-A3LB 
        7.92         2.17         0.66         1.12         9.01        66.81 
TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX TCGA-MU-A5YI 
       26.56        24.56        21.11         7.99         0.07         0.03 
TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8Q9 TCGA-VS-A94Y 
        5.49         3.88        11.67        46.03         4.73 

$`DEL PEAK 31(20P12.1) WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        23.67        11.44        18.74        36.56       144.16 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      173.29        82.85         5.46        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       30.21        35.01        53.16        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        2.43        20.91        40.93         3.58        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       182.93       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
       85.55        60.69        94.95         9.34         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35        75.78        99.91        23.51        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91         4.47         1.12        58.88        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50         1.35        14.50         1.81        12.66        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48         0.36        12.59        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       23.70         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03        20.35         6.94        14.70        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A3NI 
        4.73         1.22        23.84         0.92         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
        9.44       147.39       137.16       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
       81.96        36.36        27.42         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       15.58        10.06         5.13         6.71       195.85        30.31 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       11.28         0.89         0.30         0.82         0.20        13.87 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       13.35        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PF 
       15.88         5.88         6.25        10.39        19.59        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC 
       14.07        19.96        53.52        32.15        23.28        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       49.55        39.78        31.27        16.64        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                        177.04                         195.85 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                        12.360                         16.015 
[1] "0.0 - 177.0 (12.4)" "0.0 - 195.8 (16.0)"
[1] "hr=" "1.9"
D59V2, continuous
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 31(20P12.1) MUTATED    18   5     1
  DEL PEAK 31(20P12.1) WILD-TYPE 103  45    10
D59V3, multiclass
       clus
vv      DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  T1                              18                            103
  T2                               5                             45
  T3+T4                            1                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED   16  6
  DEL PEAK 31(20P12.1) WILD-TYPE 95 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     16    6
  DEL PEAK 31(20P12.1) WILD-TYPE   95   41
   clus
vv  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  0                           16                             95
  1                            6                             41
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 31(20P12.1) MUTATED   13  1 12
  DEL PEAK 31(20P12.1) WILD-TYPE 78  7 81
D59V5, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  M0                           13                             78
  M1                            1                              7
  MX                           12                             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(20P12.1) MUTATED               0                               26
  DEL PEAK 31(20P12.1) WILD-TYPE             5                              171
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 31(20P12.1) MUTATED                                               1
  DEL PEAK 31(20P12.1) WILD-TYPE                                             4
                                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                                              0
  DEL PEAK 31(20P12.1) WILD-TYPE                                            6
D59V6, multiclass
                                               clus
vv                                              DEL PEAK 31(20P12.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        26
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              DEL PEAK 31(20P12.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         171
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED     3  28
  DEL PEAK 31(20P12.1) WILD-TYPE  27 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      3   28
  DEL PEAK 31(20P12.1) WILD-TYPE   27  180
     clus
vv    DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  NO                             3                             27
  YES                           28                            180
[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                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(20P12.1) MUTATED                                           0
  DEL PEAK 31(20P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 31(20P12.1) MUTATED      21
  DEL PEAK 31(20P12.1) WILD-TYPE   148
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                                                               21
                                           clus
vv                                          DEL PEAK 31(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             20
  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"
D59V11, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED     2  18
  DEL PEAK 31(20P12.1) WILD-TYPE  14 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      2   18
  DEL PEAK 31(20P12.1) WILD-TYPE   14  131
                        clus
vv                       DEL PEAK 31(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           18
                        clus
vv                       DEL PEAK 31(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            131
[1] 2 2
[1] FALSE
D59V12, continuous
D59V13, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED    6  5
  DEL PEAK 31(20P12.1) WILD-TYPE 65 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      6    5
  DEL PEAK 31(20P12.1) WILD-TYPE   65   20
            clus
vv           DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  TUMOR FREE                            6                             65
  WITH TUMOR                            5                             20
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 31(20P12.1) MUTATED        2      1       0      2       0
  DEL PEAK 31(20P12.1) WILD-TYPE     21      4       1      8       7
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 31(20P12.1) MUTATED              23       3
  DEL PEAK 31(20P12.1) WILD-TYPE           155      11
D59V14, multiclass
               clus
vv              DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  BRAZIL                                   2                             21
  CANADA                                   1                              4
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  0                              7
  UNITED STATES                           23                            155
  VIETNAM                                  3                             11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 31(20P12.1) MUTATED    2 14 12  0  2
  DEL PEAK 31(20P12.1) WILD-TYPE 15 92 85  1 12
D59V15, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  G1                            2                             15
  G2                           14                             92
  G3                           12                             85
  G4                            0                              1
  GX                            2                             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V16, continuous
D59V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 31(20P12.1) MUTATED                                             5
  DEL PEAK 31(20P12.1) WILD-TYPE                                          26
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 31(20P12.1) MUTATED                                        3
  DEL PEAK 31(20P12.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 31(20P12.1) MUTATED                                                 1
  DEL PEAK 31(20P12.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 31(20P12.1) MUTATED                7                  12
  DEL PEAK 31(20P12.1) WILD-TYPE             45                 100
D59V18, multiclass
                                                 clus
vv                                                DEL PEAK 31(20P12.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             7
  LIFELONG NON-SMOKER                                                       12
                                                 clus
vv                                                DEL PEAK 31(20P12.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  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"
D59V19, continuous
D59V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 31(20P12.1) MUTATED             2        8             1        3
  DEL PEAK 31(20P12.1) WILD-TYPE          17       67            11        9
D59V21, multiclass
               clus
vv              DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  COMBINATION                              2                             17
  EXTERNAL                                 8                             67
  EXTERNAL BEAM                            1                             11
  INTERNAL                                 3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     4             0
  DEL PEAK 31(20P12.1) WILD-TYPE                  24            16
D59V23, multiclass
                     clus
vv                    DEL PEAK 31(20P12.1) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               0
  PRIMARY TUMOR FIELD                            4
  REGIONAL SITE                                  0
                     clus
vv                    DEL PEAK 31(20P12.1) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 2
  PRIMARY TUMOR FIELD                             24
  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"
D59V24, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED    2  1
  DEL PEAK 31(20P12.1) WILD-TYPE 32  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      2    1
  DEL PEAK 31(20P12.1) WILD-TYPE   32    2
     clus
vv    DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  CGY                            2                             32
  GY                             1                              2
[1] 2 2
[1] FALSE
D59V25, continuous
D59V26, continuous
D59V27, continuous
D59V28, continuous
D59V29, continuous
D59V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 31(20P12.1) MUTATED                         4
  DEL PEAK 31(20P12.1) WILD-TYPE                      25
                                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                       6
D59V31, multiclass
                                     clus
vv                                    DEL PEAK 31(20P12.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        4
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 31(20P12.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         25
  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 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                                                1
  DEL PEAK 31(20P12.1) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 31(20P12.1) MUTATED                                                                                  11
  DEL PEAK 31(20P12.1) WILD-TYPE                                                                                57
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 31(20P12.1) MUTATED                                                                                             14
  DEL PEAK 31(20P12.1) WILD-TYPE                                                                                           91
D59V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 31(20P12.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           14
                                                                                              clus
vv                                                                                             DEL PEAK 31(20P12.1) 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)                                        57
  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"
D59V33, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED    9  9
  DEL PEAK 31(20P12.1) WILD-TYPE 59 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      9    9
  DEL PEAK 31(20P12.1) WILD-TYPE   59   61
         clus
vv        DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  ABSENT                             9                             59
  PRESENT                            9                             61
[1] 2 2
[1] FALSE
D59V34, continuous
D59V35, continuous
D59V36, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED    6 11
  DEL PEAK 31(20P12.1) WILD-TYPE 37 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      6   11
  DEL PEAK 31(20P12.1) WILD-TYPE   37   83
                                          clus
vv                                         DEL PEAK 31(20P12.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           11
                                          clus
vv                                         DEL PEAK 31(20P12.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             83
[1] 2 2
[1] FALSE
D59V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 31(20P12.1) MUTATED              2           9          5
  DEL PEAK 31(20P12.1) WILD-TYPE            8          40         52
D59V38, multiclass
              clus
vv             DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  CURRENT USER                            2                              8
  FORMER USER                             9                             40
  NEVER USED                              5                             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V39, continuous
D59V40, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED   13  3
  DEL PEAK 31(20P12.1) WILD-TYPE 76 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     13    3
  DEL PEAK 31(20P12.1) WILD-TYPE   76   13
         clus
vv        DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  ABSENT                            13                             76
  PRESENT                            3                             13
[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                             11 
                    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-MU-A51Y 
"DEL PEAK 31(20P12.1) WILD-TYPE" "DEL PEAK 31(20P12.1) WILD-TYPE" 
                    TCGA-MU-A8JM 
"DEL PEAK 31(20P12.1) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 31(20P12.1) MUTATED     0    1   7    8    2  0   0    0    1   4  0
  DEL PEAK 31(20P12.1) WILD-TYPE   1    0  23   57   22  4   8    7    8  18  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 31(20P12.1) MUTATED     0  1   1  1
  DEL PEAK 31(20P12.1) WILD-TYPE   8  1   0 13
D59V42, multiclass
      clus
vv     DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  T1A                             0                              1
  T1A1                            1                              0
  T1B                             7                             23
  T1B1                            8                             57
  T1B2                            2                             22
  T2                              0                              4
  T2A                             0                              8
  T2A1                            0                              7
  T2A2                            1                              8
  T2B                             4                             18
  T3                              0                              1
  T3B                             0                              8
  T4                              1                              1
  TIS                             1                              0
  TX                              1                             13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 31(20P12.1) MUTATED         0        0         1         0        5
  DEL PEAK 31(20P12.1) WILD-TYPE       4        2         0         1       26
                                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        60        29        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 31(20P12.1) MUTATED            0          0         6         0
  DEL PEAK 31(20P12.1) WILD-TYPE          5          7        21         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 31(20P12.1) MUTATED            4         1         1
  DEL PEAK 31(20P12.1) WILD-TYPE         30         2         6
D59V44, multiclass
            clus
vv           DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              0                              2
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                              5                             26
  STAGE IB1                             9                             60
  STAGE IB2                             3                             29
  STAGE II                              0                              3
  STAGE IIA                             1                              5
  STAGE IIA1                            0                              5
  STAGE IIA2                            0                              7
  STAGE IIB                             6                             21
  STAGE III                             0                              1
  STAGE IIIB                            4                             30
  STAGE IVA                             1                              2
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 32(21Q11.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(21Q11.2) MUTATED    33  16
  DEL PEAK 32(21Q11.2) WILD-TYPE 150  34
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                            49                            184 
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                            16                             34 
$`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         1.32         1.35        14.50 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R8 
        0.26        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        23.70         0.03         6.94        23.84         0.66 
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 
        0.20         2.96        12.16        10.03        20.22        14.07 
TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       19.96        46.03         4.73        42.08        39.35        38.96 
TCGA-WL-A834 
       18.05 

$`DEL PEAK 32(21Q11.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      173.29        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       46.32        30.21        57.73        53.16        38.99        35.61 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY 
        2.43        20.91         3.58        44.22        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93       154.32       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
      147.35        17.19        85.55        60.69        94.95        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
        6.12        20.91         4.47         1.12        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       40.04        58.88        36.76       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.74         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35         1.81        12.66        12.82         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       15.02        14.99        14.96        13.58        13.48        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
       26.27         6.64         0.43         0.59         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RM 
       16.08         0.07         4.04         0.03         0.36         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.07         0.10         0.10        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
       14.70        19.79         6.12         4.73         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        2.17         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        1.35         1.32         1.97         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC 
        7.13        20.78        14.93       147.39       137.16       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        26.56        36.36         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        6.71        21.11       195.85        30.31         7.99        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.07         0.30         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         5.49        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 
       93.99        61.28        34.52        29.03        53.52        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       23.28        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       23.24        44.88        42.58        43.82 

  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                         195.85 
  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE 
                        14.500                         16.015 
[1] "0.0 - 101.8 (14.5)" "0.0 - 195.8 (16.0)"
[1] "hr=" "2.2"
D60V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 32(21Q11.2) MUTATED   23 13     6
  DEL PEAK 32(21Q11.2) WILD-TYPE 98 37     5
D60V3, multiclass
       clus
vv      DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  T1                              23                             98
  T2                              13                             37
  T3+T4                            6                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   20 13
  DEL PEAK 32(21Q11.2) WILD-TYPE 91 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     20   13
  DEL PEAK 32(21Q11.2) WILD-TYPE   91   34
   clus
vv  DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  0                           20                             91
  1                           13                             34
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 32(21Q11.2) MUTATED   21  3 18
  DEL PEAK 32(21Q11.2) WILD-TYPE 70  5 75
D60V5, multiclass
    clus
vv   DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  M0                           21                             70
  M1                            3                              5
  MX                           18                             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(21Q11.2) MUTATED               1                               43
  DEL PEAK 32(21Q11.2) WILD-TYPE             4                              154
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 32(21Q11.2) MUTATED                                               0
  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                                              0
  DEL PEAK 32(21Q11.2) WILD-TYPE                                            6
D60V6, multiclass
                                               clus
vv                                              DEL PEAK 32(21Q11.2) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        43
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              DEL PEAK 32(21Q11.2) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(21Q11.2) MUTATED     5  45
  DEL PEAK 32(21Q11.2) WILD-TYPE  25 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED      5   45
  DEL PEAK 32(21Q11.2) WILD-TYPE   25  163
     clus
vv    DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  NO                             5                             25
  YES                           45                            163
[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                           8
  DEL PEAK 32(21Q11.2) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 32(21Q11.2) MUTATED                                           0
  DEL PEAK 32(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 32(21Q11.2) MUTATED      33
  DEL PEAK 32(21Q11.2) WILD-TYPE   136
D60V10, multiclass
                                           clus
vv                                          DEL PEAK 32(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               33
                                           clus
vv                                          DEL PEAK 32(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                136
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                                cls
clus                               0   1
  DEL PEAK 32(21Q11.2) MUTATED     1  34
  DEL PEAK 32(21Q11.2) WILD-TYPE  15 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED      1   34
  DEL PEAK 32(21Q11.2) WILD-TYPE   15  115
                        clus
vv                       DEL PEAK 32(21Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           34
                        clus
vv                       DEL PEAK 32(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            115
[1] 2 2
[1] FALSE
D60V12, continuous
D60V13, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   13  6
  DEL PEAK 32(21Q11.2) WILD-TYPE 58 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     13    6
  DEL PEAK 32(21Q11.2) WILD-TYPE   58   19
            clus
vv           DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  TUMOR FREE                           13                             58
  WITH TUMOR                            6                             19
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 32(21Q11.2) MUTATED        9      1       1      3       1
  DEL PEAK 32(21Q11.2) WILD-TYPE     14      4       0      7       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 32(21Q11.2) MUTATED              31       4
  DEL PEAK 32(21Q11.2) WILD-TYPE           147      10
D60V14, multiclass
               clus
vv              DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  BRAZIL                                   9                             14
  CANADA                                   1                              4
  NIGERIA                                  1                              0
  RUSSIA                                   3                              7
  UKRAINE                                  1                              6
  UNITED STATES                           31                            147
  VIETNAM                                  4                             10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 32(21Q11.2) MUTATED    2 16 29  0  3
  DEL PEAK 32(21Q11.2) WILD-TYPE 15 90 68  1 11
D60V15, multiclass
    clus
vv   DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  G1                            2                             15
  G2                           16                             90
  G3                           29                             68
  G4                            0                              1
  GX                            3                             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                             32 
                    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-MU-A5YI 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-Q1-A6DW 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-Q1-A73S                     TCGA-RA-A741 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-VS-A8QF                     TCGA-VS-A94Z 
"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                                          30
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 32(21Q11.2) MUTATED                                        1
  DEL PEAK 32(21Q11.2) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 32(21Q11.2) MUTATED                                                 0
  DEL PEAK 32(21Q11.2) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 32(21Q11.2) MUTATED               14                  23
  DEL PEAK 32(21Q11.2) WILD-TYPE             38                  89
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                                                            14
  LIFELONG NON-SMOKER                                                       23
                                                 clus
vv                                                DEL PEAK 32(21Q11.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              38
  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"
D60V19, continuous
D60V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 32(21Q11.2) MUTATED             1       20             4        0
  DEL PEAK 32(21Q11.2) WILD-TYPE          18       55             8       12
D60V21, multiclass
               clus
vv              DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  COMBINATION                              1                             18
  EXTERNAL                                20                             55
  EXTERNAL BEAM                            4                              8
  INTERNAL                                 0                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     9             3
  DEL PEAK 32(21Q11.2) WILD-TYPE                  19            13
D60V23, multiclass
                     clus
vv                    DEL PEAK 32(21Q11.2) MUTATED
  DISTANT RECURRENCE                             0
  LOCAL RECURRENCE                               2
  PRIMARY TUMOR FIELD                            9
  REGIONAL SITE                                  3
                     clus
vv                    DEL PEAK 32(21Q11.2) WILD-TYPE
  DISTANT RECURRENCE                               2
  LOCAL RECURRENCE                                 0
  PRIMARY TUMOR FIELD                             19
  REGIONAL SITE                                   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"
D60V24, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   13  0
  DEL PEAK 32(21Q11.2) WILD-TYPE 21  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     13    0
  DEL PEAK 32(21Q11.2) WILD-TYPE   21    3
     clus
vv    DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  CGY                           13                             21
  GY                             0                              3
[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                                     2
  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                      23
                                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                       7
D60V31, multiclass
                                     clus
vv                                    DEL PEAK 32(21Q11.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  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                                         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 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                                                3
  DEL PEAK 32(21Q11.2) WILD-TYPE                                             13
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 32(21Q11.2) MUTATED                                                                                  14
  DEL PEAK 32(21Q11.2) WILD-TYPE                                                                                54
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 32(21Q11.2) MUTATED                                                                                             24
  DEL PEAK 32(21Q11.2) WILD-TYPE                                                                                           81
D60V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 32(21Q11.2) 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)                                      14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           24
                                                                                              clus
vv                                                                                             DEL PEAK 32(21Q11.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D60V33, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   13 15
  DEL PEAK 32(21Q11.2) WILD-TYPE 55 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     13   15
  DEL PEAK 32(21Q11.2) WILD-TYPE   55   55
         clus
vv        DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  ABSENT                            13                             55
  PRESENT                           15                             55
[1] 2 2
[1] FALSE
D60V34, continuous
D60V35, continuous
D60V36, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED    7 23
  DEL PEAK 32(21Q11.2) WILD-TYPE 36 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED      7   23
  DEL PEAK 32(21Q11.2) WILD-TYPE   36   71
                                          clus
vv                                         DEL PEAK 32(21Q11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           23
                                          clus
vv                                         DEL PEAK 32(21Q11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             71
[1] 2 2
[1] FALSE
D60V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 32(21Q11.2) MUTATED              3           9         16
  DEL PEAK 32(21Q11.2) WILD-TYPE            7          40         41
D60V38, multiclass
              clus
vv             DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  CURRENT USER                            3                              7
  FORMER USER                             9                             40
  NEVER USED                             16                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V39, continuous
D60V40, binary
                                cls
clus                              0  1
  DEL PEAK 32(21Q11.2) MUTATED   17  5
  DEL PEAK 32(21Q11.2) WILD-TYPE 72 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(21Q11.2) MUTATED     17    5
  DEL PEAK 32(21Q11.2) WILD-TYPE   72   11
         clus
vv        DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  ABSENT                            17                             72
  PRESENT                            5                             11
[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                             12 
                    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-MU-A51Y 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-MY-A913 
"DEL PEAK 32(21Q11.2) WILD-TYPE" "DEL PEAK 32(21Q11.2) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 32(21Q11.2) MUTATED     0    0   6   13    4  1   4    3    0   5  0
  DEL PEAK 32(21Q11.2) WILD-TYPE   1    1  24   52   20  3   4    4    9  17  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 32(21Q11.2) MUTATED     5  1   0  2
  DEL PEAK 32(21Q11.2) WILD-TYPE   3  1   1 12
D60V42, multiclass
      clus
vv     DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  T1A                             0                              1
  T1A1                            0                              1
  T1B                             6                             24
  T1B1                           13                             52
  T1B2                            4                             20
  T2                              1                              3
  T2A                             4                              4
  T2A1                            3                              4
  T2A2                            0                              9
  T2B                             5                             17
  T3                              0                              1
  T3B                             5                              3
  T4                              1                              1
  TIS                             0                              1
  TX                              2                             12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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       4        1         1         1       24
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 32(21Q11.2) MUTATED          12         5        2         2
  DEL PEAK 32(21Q11.2) WILD-TYPE        57        27        1         4
                                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        21         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 32(21Q11.2) MUTATED            8         1         1
  DEL PEAK 32(21Q11.2) WILD-TYPE         26         2         6
D60V44, multiclass
            clus
vv           DEL PEAK 32(21Q11.2) MUTATED DEL PEAK 32(21Q11.2) WILD-TYPE
  STAGE I                               0                              4
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              7                             24
  STAGE IB1                            12                             57
  STAGE IB2                             5                             27
  STAGE II                              2                              1
  STAGE IIA                             2                              4
  STAGE IIA1                            3                              2
  STAGE IIA2                            0                              7
  STAGE IIB                             6                             21
  STAGE III                             0                              1
  STAGE IIIB                            8                             26
  STAGE IVA                             1                              2
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 33(22Q13.32) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(22Q13.32) MUTATED    51  16
  DEL PEAK 33(22Q13.32) WILD-TYPE 132  34
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             67                             166 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             16                              34 
$`DEL PEAK 33(22Q13.32) MUTATED`
TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 
       23.67        18.74       173.29         5.46        31.40        30.21 
TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD 
       57.73         0.46        40.93        73.18        83.05        52.01 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL 
        9.34         2.73        27.52         1.12        58.88        44.94 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S 
      118.65        12.36         1.32         1.35        14.50        12.66 
TCGA-EA-A556 TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 
       14.89        13.58         0.36        12.59         1.51         0.59 
TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A8YF 
        1.45         1.18         0.10         0.10        20.35         4.73 
TCGA-FU-A23K TCGA-FU-A3HY TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LA 
        1.22         0.66         9.01        21.67        14.93       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A852 TCGA-JX-A5QV 
       66.81       117.40        27.42        24.56         5.13         7.99 
TCGA-LP-A4AW TCGA-LP-A7HU TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        0.89         0.20         5.49        15.58        13.35         3.39 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ 
       19.59        11.67        12.16        34.52        14.07        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 
       53.52        46.03        39.78        16.64         4.73        44.88 
TCGA-VS-A957 
       42.08 

$`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         0.82 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       182.93       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       60.69        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 
       75.78        99.91        23.51         6.12        20.91         4.47 
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 
        0.76         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       14.50         1.35         1.81        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 
       13.91        15.02        14.99        14.96        13.48        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA 
       26.27         6.64         0.43         0.59         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         4.04         0.03         0.36        23.70         2.24 
TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.07         0.10         0.03         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
       19.79         6.12        23.84         0.92         2.17         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41         7.13        20.78 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
        9.44       147.39        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       36.36         3.29        21.44        20.48        15.58        10.06 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX 
        6.71        21.11       195.85        30.31        11.28         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.30         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        0.07         4.34         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         5.88         6.25        10.39         3.88 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 
       93.99        61.28        10.03        29.03        20.22        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A954 
       23.28        11.51        49.55        31.27        23.24        42.58 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

  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                          195.85 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                          14.50                           16.16 
[1] "0.1 - 173.3 (14.5)" "0.0 - 195.8 (16.2)"
[1] "hr=" "1.3"
D61V2, continuous
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 33(22Q13.32) MUTATED   34 17     3
  DEL PEAK 33(22Q13.32) WILD-TYPE 87 33     8
D61V3, multiclass
       clus
vv      DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  T1                               34                              87
  T2                               17                              33
  T3+T4                             3                               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   31 16
  DEL PEAK 33(22Q13.32) WILD-TYPE 80 31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     31   16
  DEL PEAK 33(22Q13.32) WILD-TYPE   80   31
   clus
vv  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  0                            31                              80
  1                            16                              31
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 33(22Q13.32) MUTATED   31  2 26
  DEL PEAK 33(22Q13.32) WILD-TYPE 60  6 67
D61V5, multiclass
    clus
vv   DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  M0                            31                              60
  M1                             2                               6
  MX                            26                              67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  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                                 57
  DEL PEAK 33(22Q13.32) WILD-TYPE                              140
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 33(22Q13.32) MUTATED                                               0
  DEL PEAK 33(22Q13.32) WILD-TYPE                                             5
                                 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                                              4
  DEL PEAK 33(22Q13.32) WILD-TYPE                                            2
D61V6, multiclass
                                               clus
vv                                              DEL PEAK 33(22Q13.32) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         57
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
                                               clus
vv                                              DEL PEAK 33(22Q13.32) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          140
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED    12  57
  DEL PEAK 33(22Q13.32) WILD-TYPE  18 151
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     12   57
  DEL PEAK 33(22Q13.32) WILD-TYPE   18  151
     clus
vv    DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  NO                             12                              18
  YES                            57                             151
[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                           7
  DEL PEAK 33(22Q13.32) WILD-TYPE                        17
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 33(22Q13.32) MUTATED                                           1
  DEL PEAK 33(22Q13.32) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 33(22Q13.32) MUTATED      51
  DEL PEAK 33(22Q13.32) WILD-TYPE   118
D61V10, multiclass
                                           clus
vv                                          DEL PEAK 33(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 4
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                51
                                           clus
vv                                          DEL PEAK 33(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        5
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 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"
D61V11, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED     5  39
  DEL PEAK 33(22Q13.32) WILD-TYPE  11 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED      5   39
  DEL PEAK 33(22Q13.32) WILD-TYPE   11  110
                        clus
vv                       DEL PEAK 33(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            39
                        clus
vv                       DEL PEAK 33(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             110
[1] 2 2
[1] FALSE
D61V12, continuous
D61V13, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   24  7
  DEL PEAK 33(22Q13.32) WILD-TYPE 47 18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     24    7
  DEL PEAK 33(22Q13.32) WILD-TYPE   47   18
            clus
vv           DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  TUMOR FREE                            24                              47
  WITH TUMOR                             7                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 33(22Q13.32) MUTATED       10      3       0      4       2
  DEL PEAK 33(22Q13.32) WILD-TYPE     13      2       1      6       5
                                 vv
clus                              UNITED STATES VIETNAM
  DEL PEAK 33(22Q13.32) MUTATED              46       4
  DEL PEAK 33(22Q13.32) WILD-TYPE           132      10
D61V14, multiclass
               clus
vv              DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  BRAZIL                                   10                              13
  CANADA                                    3                               2
  NIGERIA                                   0                               1
  RUSSIA                                    4                               6
  UKRAINE                                   2                               5
  UNITED STATES                            46                             132
  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 26 34  0  4
  DEL PEAK 33(22Q13.32) WILD-TYPE 12 80 63  1 10
D61V15, multiclass
    clus
vv   DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  G1                             5                              12
  G2                            26                              80
  G3                            34                              63
  G4                             0                               1
  GX                             4                              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V16, continuous
D61V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 33(22Q13.32) MUTATED                                             4
  DEL PEAK 33(22Q13.32) WILD-TYPE                                          27
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 33(22Q13.32) MUTATED                                        2
  DEL PEAK 33(22Q13.32) WILD-TYPE                                      6
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 33(22Q13.32) MUTATED                                                 1
  DEL PEAK 33(22Q13.32) WILD-TYPE                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 33(22Q13.32) MUTATED               15                  35
  DEL PEAK 33(22Q13.32) WILD-TYPE             37                  77
D61V18, multiclass
                                                 clus
vv                                                DEL PEAK 33(22Q13.32) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             15
  LIFELONG NON-SMOKER                                                        35
                                                 clus
vv                                                DEL PEAK 33(22Q13.32) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               37
  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"
D61V19, continuous
D61V20, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 33(22Q13.32) MUTATED             7       23             4        4
  DEL PEAK 33(22Q13.32) WILD-TYPE          12       52             8        8
D61V21, multiclass
               clus
vv              DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  COMBINATION                               7                              12
  EXTERNAL                                 23                              52
  EXTERNAL BEAM                             4                               8
  INTERNAL                                  4                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                    12             3
  DEL PEAK 33(22Q13.32) WILD-TYPE                  16            13
D61V23, multiclass
                     clus
vv                    DEL PEAK 33(22Q13.32) MUTATED
  DISTANT RECURRENCE                              1
  LOCAL RECURRENCE                                1
  PRIMARY TUMOR FIELD                            12
  REGIONAL SITE                                   3
                     clus
vv                    DEL PEAK 33(22Q13.32) WILD-TYPE
  DISTANT RECURRENCE                                1
  LOCAL RECURRENCE                                  1
  PRIMARY TUMOR FIELD                              16
  REGIONAL SITE                                    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"
D61V24, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   13  2
  DEL PEAK 33(22Q13.32) WILD-TYPE 21  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     13    2
  DEL PEAK 33(22Q13.32) WILD-TYPE   21    1
     clus
vv    DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  CGY                            13                              21
  GY                              2                               1
[1] 2 2
[1] FALSE
D61V25, continuous
D61V26, continuous
D61V27, continuous
D61V28, continuous
D61V29, continuous
D61V30, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   4
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 33(22Q13.32) MUTATED                         9
  DEL PEAK 33(22Q13.32) WILD-TYPE                      20
                                 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                         2
  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                                         9
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         2
                                     clus
vv                                    DEL PEAK 33(22Q13.32) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               4
  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 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                                                4
  DEL PEAK 33(22Q13.32) WILD-TYPE                                             12
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 33(22Q13.32) MUTATED                                                                                  22
  DEL PEAK 33(22Q13.32) WILD-TYPE                                                                                46
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 33(22Q13.32) MUTATED                                                                                             30
  DEL PEAK 33(22Q13.32) WILD-TYPE                                                                                           75
D61V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 33(22Q13.32) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            30
                                                                                              clus
vv                                                                                             DEL PEAK 33(22Q13.32) 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)                                         46
  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"
D61V33, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   18 24
  DEL PEAK 33(22Q13.32) WILD-TYPE 50 46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     18   24
  DEL PEAK 33(22Q13.32) WILD-TYPE   50   46
         clus
vv        DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  ABSENT                             18                              50
  PRESENT                            24                              46
[1] 2 2
[1] FALSE
D61V34, continuous
D61V35, continuous
D61V36, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   12 29
  DEL PEAK 33(22Q13.32) WILD-TYPE 31 65
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     12   29
  DEL PEAK 33(22Q13.32) WILD-TYPE   31   65
                                          clus
vv                                         DEL PEAK 33(22Q13.32) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            29
                                          clus
vv                                         DEL PEAK 33(22Q13.32) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              65
[1] 2 2
[1] FALSE
D61V37, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 33(22Q13.32) MUTATED              5          15         18
  DEL PEAK 33(22Q13.32) WILD-TYPE            5          34         39
D61V38, multiclass
              clus
vv             DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  CURRENT USER                             5                               5
  FORMER USER                             15                              34
  NEVER USED                              18                              39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V39, continuous
D61V40, binary
                                 cls
clus                               0  1
  DEL PEAK 33(22Q13.32) MUTATED   30  2
  DEL PEAK 33(22Q13.32) WILD-TYPE 59 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     30    2
  DEL PEAK 33(22Q13.32) WILD-TYPE   59   14
         clus
vv        DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  ABSENT                             30                              59
  PRESENT                             2                              14
[1] 2 2
[1] FALSE
D61V41, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 33(22Q13.32) MUTATED     0    0  11   17    6  2   4    2    1   8
  DEL PEAK 33(22Q13.32) WILD-TYPE   1    1  19   48   18  2   4    5    8  14
                                 vv
clus                              T3 T3B T4 TIS TX
  DEL PEAK 33(22Q13.32) MUTATED    0   3  0   1  5
  DEL PEAK 33(22Q13.32) WILD-TYPE  1   5  2   0  9
D61V42, multiclass
      clus
vv     DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  T1A                              0                               1
  T1A1                             0                               1
  T1B                             11                              19
  T1B1                            17                              48
  T1B2                             6                              18
  T2                               2                               2
  T2A                              4                               4
  T2A1                             2                               5
  T2A2                             1                               8
  T2B                              8                              14
  T3                               0                               1
  T3B                              3                               5
  T4                               0                               2
  TIS                              1                               0
  TX                               5                               9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V43, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 33(22Q13.32) MUTATED         1        1         0         0        9
  DEL PEAK 33(22Q13.32) WILD-TYPE       3        1         1         1       22
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 33(22Q13.32) MUTATED          24         5        2         4
  DEL PEAK 33(22Q13.32) WILD-TYPE        45        27        1         2
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 33(22Q13.32) MUTATED            1          0        10         0
  DEL PEAK 33(22Q13.32) WILD-TYPE          4          7        17         1
                                 vv
clus                              STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 33(22Q13.32) MUTATED           10         0         0
  DEL PEAK 33(22Q13.32) WILD-TYPE         24         3         7
D61V44, multiclass
            clus
vv           DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  STAGE I                                1                               3
  STAGE IA                               1                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               9                              22
  STAGE IB1                             24                              45
  STAGE IB2                              5                              27
  STAGE II                               2                               1
  STAGE IIA                              4                               2
  STAGE IIA1                             1                               4
  STAGE IIA2                             0                               7
  STAGE IIB                             10                              17
  STAGE III                              0                               1
  STAGE IIIB                            10                              24
  STAGE IVA                              0                               3
  STAGE IVB                              0                               7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = DEL PEAK 34(XP11.3) MUTATION ANALYSIS
D62V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 34(XP11.3) MUTATED    42  14
  DEL PEAK 34(XP11.3) WILD-TYPE 141  36
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           56                           177 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           14                            36 
$`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 
       60.69        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         1.32         1.18         1.81        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         0.66 
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        26.56        21.11 
TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MY-A5BF TCGA-Q1-A6DT TCGA-UC-A7PI 
       30.31         0.89         0.82         4.34         3.39        61.28 
TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X 
       10.03        20.22        14.07        11.51        49.55        16.64 
TCGA-VS-A94Y TCGA-VS-A9U5 
        4.73        38.96 

$`DEL PEAK 34(XP11.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL 
       49.48        68.84        18.74        36.56       144.16       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME 
       82.85        19.86        67.46        31.40        35.01        57.73 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         0.46         2.43         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.18        83.05        78.35       100.14        38.43         0.82 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       182.93       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19        85.55 
TCGA-C5-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-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
        8.35        75.78        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A5RQ TCGA-DS-A7WH 
       58.88        36.76         2.66       117.99        16.83        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        8.28         0.76         1.74         0.82         0.62        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         1.35         1.35        14.50        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        1.48        13.91        15.02        14.99        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2R8 
        0.36        12.59        26.27         6.64         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.13        16.08         4.04         0.03         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        2.24         0.10         0.07         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         6.12         4.73         1.22        23.84 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        2.17         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.35         1.32         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC 
       21.67        20.78        14.93         9.44       147.39       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        78.71        81.96        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 
        6.71       195.85         7.99        11.28         0.07         0.30 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.20        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        5.49         2.96        15.58        13.35        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EC 
       19.59         3.88        11.67        93.99        12.16        34.52 
TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       29.03        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       39.78        31.27        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  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                        195.85 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                        15.57                         15.88 
[1] "0.1 - 177.0 (15.6)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.3"
D62V2, continuous
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 34(XP11.3) MUTATED   30  8     4
  DEL PEAK 34(XP11.3) WILD-TYPE 91 42     7
D62V3, multiclass
       clus
vv      DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  T1                             30                            91
  T2                              8                            42
  T3+T4                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   27  8
  DEL PEAK 34(XP11.3) WILD-TYPE 84 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     27    8
  DEL PEAK 34(XP11.3) WILD-TYPE   84   39
   clus
vv  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  0                          27                            84
  1                           8                            39
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 34(XP11.3) MUTATED   19  1 23
  DEL PEAK 34(XP11.3) WILD-TYPE 72  7 70
D62V5, multiclass
    clus
vv   DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  M0                          19                            72
  M1                           1                             7
  MX                          23                            70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(XP11.3) MUTATED               1                               50
  DEL PEAK 34(XP11.3) WILD-TYPE             4                              147
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 34(XP11.3) MUTATED                                               0
  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                                              0
  DEL PEAK 34(XP11.3) WILD-TYPE                                            6
D62V6, multiclass
                                               clus
vv                                              DEL PEAK 34(XP11.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            0
                                               clus
vv                                              DEL PEAK 34(XP11.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        147
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  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"
D62V7, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP11.3) MUTATED    11  46
  DEL PEAK 34(XP11.3) WILD-TYPE  19 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     11   46
  DEL PEAK 34(XP11.3) WILD-TYPE   19  162
     clus
vv    DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  NO                           11                            19
  YES                          46                           162
[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                           7
  DEL PEAK 34(XP11.3) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 34(XP11.3) MUTATED                                           1    42
  DEL PEAK 34(XP11.3) WILD-TYPE                                         0   127
D62V10, multiclass
                                           clus
vv                                          DEL PEAK 34(XP11.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              42
                                           clus
vv                                          DEL PEAK 34(XP11.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               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"
D62V11, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP11.3) MUTATED     1  37
  DEL PEAK 34(XP11.3) WILD-TYPE  15 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED      1   37
  DEL PEAK 34(XP11.3) WILD-TYPE   15  112
                        clus
vv                       DEL PEAK 34(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       DEL PEAK 34(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           112
[1] 2 2
[1] FALSE
D62V12, continuous
D62V13, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   16  7
  DEL PEAK 34(XP11.3) WILD-TYPE 55 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     16    7
  DEL PEAK 34(XP11.3) WILD-TYPE   55   18
            clus
vv           DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  TUMOR FREE                          16                            55
  WITH TUMOR                           7                            18
[1] 2 2
[1] FALSE
                               vv
clus                            BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 34(XP11.3) MUTATED        8      0       0      4       2
  DEL PEAK 34(XP11.3) WILD-TYPE     15      5       1      6       5
                               vv
clus                            UNITED STATES VIETNAM
  DEL PEAK 34(XP11.3) MUTATED              40       3
  DEL PEAK 34(XP11.3) WILD-TYPE           138      11
D62V14, multiclass
               clus
vv              DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  BRAZIL                                  8                            15
  CANADA                                  0                             5
  NIGERIA                                 0                             1
  RUSSIA                                  4                             6
  UKRAINE                                 2                             5
  UNITED STATES                          40                           138
  VIETNAM                                 3                            11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 34(XP11.3) MUTATED    3 23 26  0  4
  DEL PEAK 34(XP11.3) WILD-TYPE 14 83 71  1 10
D62V15, multiclass
    clus
vv   DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  G1                           3                            14
  G2                          23                            83
  G3                          26                            71
  G4                           0                             1
  GX                           4                            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V16, continuous
D62V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 34(XP11.3) MUTATED                                             4
  DEL PEAK 34(XP11.3) WILD-TYPE                                          27
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 34(XP11.3) MUTATED                                        2
  DEL PEAK 34(XP11.3) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 34(XP11.3) MUTATED                                                 0
  DEL PEAK 34(XP11.3) WILD-TYPE                                               2
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 34(XP11.3) MUTATED               18                  23
  DEL PEAK 34(XP11.3) WILD-TYPE             34                  89
D62V18, multiclass
                                                 clus
vv                                                DEL PEAK 34(XP11.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           18
  LIFELONG NON-SMOKER                                                      23
                                                 clus
vv                                                DEL PEAK 34(XP11.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             2
  CURRENT SMOKER                                                             34
  LIFELONG NON-SMOKER                                                        89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V19, continuous
D62V20, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 34(XP11.3) MUTATED             5       14             5        2
  DEL PEAK 34(XP11.3) WILD-TYPE          14       61             7       10
D62V21, multiclass
               clus
vv              DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  COMBINATION                             5                            14
  EXTERNAL                               14                            61
  EXTERNAL BEAM                           5                             7
  INTERNAL                                2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     4             5
  DEL PEAK 34(XP11.3) WILD-TYPE                  24            11
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                           4                            24
  REGIONAL SITE                                 5                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V24, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED    9  0
  DEL PEAK 34(XP11.3) WILD-TYPE 25  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED      9    0
  DEL PEAK 34(XP11.3) WILD-TYPE   25    3
     clus
vv    DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  CGY                           9                            25
  GY                            0                             3
[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                                   2
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 34(XP11.3) MUTATED                         6                       0
  DEL PEAK 34(XP11.3) WILD-TYPE                      23                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 34(XP11.3) MUTATED                         0
  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                                       6
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    DEL PEAK 34(XP11.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        23
  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                                                6
  DEL PEAK 34(XP11.3) WILD-TYPE                                             10
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 34(XP11.3) MUTATED                                                                                  13
  DEL PEAK 34(XP11.3) WILD-TYPE                                                                                55
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 34(XP11.3) MUTATED                                                                                             28
  DEL PEAK 34(XP11.3) WILD-TYPE                                                                                           77
D62V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 34(XP11.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          28
                                                                                              clus
vv                                                                                             DEL PEAK 34(XP11.3) 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)                                       55
  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"
D62V33, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   17 16
  DEL PEAK 34(XP11.3) WILD-TYPE 51 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     17   16
  DEL PEAK 34(XP11.3) WILD-TYPE   51   54
         clus
vv        DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  ABSENT                           17                            51
  PRESENT                          16                            54
[1] 2 2
[1] FALSE
D62V34, continuous
D62V35, continuous
D62V36, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   13 19
  DEL PEAK 34(XP11.3) WILD-TYPE 30 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     13   19
  DEL PEAK 34(XP11.3) WILD-TYPE   30   75
                                          clus
vv                                         DEL PEAK 34(XP11.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          19
                                          clus
vv                                         DEL PEAK 34(XP11.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            75
[1] 2 2
[1] FALSE
D62V37, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 34(XP11.3) MUTATED              2          11         21
  DEL PEAK 34(XP11.3) WILD-TYPE            8          38         36
D62V38, multiclass
              clus
vv             DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  CURRENT USER                           2                             8
  FORMER USER                           11                            38
  NEVER USED                            21                            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V39, continuous
D62V40, binary
                               cls
clus                             0  1
  DEL PEAK 34(XP11.3) MUTATED   24  1
  DEL PEAK 34(XP11.3) WILD-TYPE 65 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     24    1
  DEL PEAK 34(XP11.3) WILD-TYPE   65   15
         clus
vv        DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  ABSENT                           24                            65
  PRESENT                           1                            15
[1] 2 2
[1] FALSE
D62V41, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 34(XP11.3) MUTATED     1    0   9   14    6  0   1    0    3   4  0
  DEL PEAK 34(XP11.3) WILD-TYPE   0    1  21   51   18  4   7    7    6  18  1
                               vv
clus                            T3B T4 TIS TX
  DEL PEAK 34(XP11.3) MUTATED     4  0   0  3
  DEL PEAK 34(XP11.3) WILD-TYPE   4  2   1 11
D62V42, multiclass
      clus
vv     DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  T1A                            1                             0
  T1A1                           0                             1
  T1B                            9                            21
  T1B1                          14                            51
  T1B2                           6                            18
  T2                             0                             4
  T2A                            1                             7
  T2A1                           0                             7
  T2A2                           3                             6
  T2B                            4                            18
  T3                             0                             1
  T3B                            4                             4
  T4                             0                             2
  TIS                            0                             1
  TX                             3                            11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V43, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 34(XP11.3) MUTATED         1        2         0         1        8
  DEL PEAK 34(XP11.3) WILD-TYPE       3        0         1         0       23
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 34(XP11.3) MUTATED          14         7        1         1
  DEL PEAK 34(XP11.3) WILD-TYPE        55        25        2         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 34(XP11.3) MUTATED            0          1         9         0
  DEL PEAK 34(XP11.3) WILD-TYPE          5          6        18         1
                               vv
clus                            STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 34(XP11.3) MUTATED            8         1         1
  DEL PEAK 34(XP11.3) WILD-TYPE         26         2         6
D62V44, multiclass
            clus
vv           DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  STAGE I                              1                             3
  STAGE IA                             2                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             8                            23
  STAGE IB1                           14                            55
  STAGE IB2                            7                            25
  STAGE II                             1                             2
  STAGE IIA                            1                             5
  STAGE IIA1                           0                             5
  STAGE IIA2                           1                             6
  STAGE IIB                            9                            18
  STAGE III                            0                             1
  STAGE IIIB                           8                            26
  STAGE IVA                            1                             2
  STAGE IVB                            1                             6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 35(XQ21.33) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(XQ21.33) MUTATED    29  15
  DEL PEAK 35(XQ21.33) WILD-TYPE 154  35
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            44                            189 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            15                             35 
$`DEL PEAK 35(XQ21.33) MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1MK 
       23.67        11.44        19.86        67.46        30.21         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CJ TCGA-C5-A7CO 
       20.91        40.93        83.05        52.01       101.82       147.35 
TCGA-C5-A7X5 TCGA-C5-A8XK TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WF TCGA-EA-A1QT 
       13.61        99.91        36.76       118.65        16.18        12.36 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
       12.66        14.89        14.99         6.64         0.43         0.59 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A69M TCGA-FU-A2QG 
        0.10         0.10        20.35         7.92         6.12         0.92 
TCGA-FU-A3HY TCGA-FU-A5XV TCGA-IR-A3LK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3PZ 
        0.66         1.97        26.56        15.58         5.13        21.11 
TCGA-JX-A3Q8 TCGA-LP-A5U3 TCGA-MY-A5BF TCGA-Q1-A73Q TCGA-UC-A7PI TCGA-VS-A8EB 
       30.31         0.82         4.34         5.88        61.28        10.03 
TCGA-VS-A8QA TCGA-VS-A94Y 
       23.28         4.73 

$`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         0.82        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      154.32       134.33        15.48        20.35        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       60.69        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        75.78        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        4.47         1.12        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-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         0.76         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50         1.81        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       15.02        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       45.96        26.27         1.51         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-A3GN TCGA-EX-A3L1 
       23.70         2.24         0.10         0.07         0.03         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       14.70        19.79         4.73         1.22        23.84         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.35         1.32         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-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-A5VK TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        20.48        10.06 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
        6.71       195.85         7.99        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.30         0.20        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         5.49         2.96        15.58        13.35        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R 
        3.39        16.14        17.56        14.07        15.88         6.25 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       10.39        19.59         3.88        11.67        93.99        12.16 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       34.52        29.03        20.22        14.07        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        46.03        11.51        49.55        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       16.64        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

  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                         195.85 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                         14.94                          16.08 
[1] "0.1 - 147.3 (14.9)" "0.0 - 195.8 (16.1)"
[1] "hr=" "2"  
D63V2, continuous
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 35(XQ21.33) MUTATED   26  7     1
  DEL PEAK 35(XQ21.33) WILD-TYPE 95 43    10
D63V3, multiclass
       clus
vv      DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  T1                              26                             95
  T2                               7                             43
  T3+T4                            1                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   22  9
  DEL PEAK 35(XQ21.33) WILD-TYPE 89 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     22    9
  DEL PEAK 35(XQ21.33) WILD-TYPE   89   38
   clus
vv  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  0                           22                             89
  1                            9                             38
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 35(XQ21.33) MUTATED   12  1 20
  DEL PEAK 35(XQ21.33) WILD-TYPE 79  7 73
D63V5, multiclass
    clus
vv   DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  M0                           12                             79
  M1                            1                              7
  MX                           20                             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(XQ21.33) MUTATED               1                               39
  DEL PEAK 35(XQ21.33) WILD-TYPE             4                              158
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 35(XQ21.33) MUTATED                                               0
  DEL PEAK 35(XQ21.33) WILD-TYPE                                             5
                                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                                              0
  DEL PEAK 35(XQ21.33) WILD-TYPE                                            6
D63V6, multiclass
                                               clus
vv                                              DEL PEAK 35(XQ21.33) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        39
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              DEL PEAK 35(XQ21.33) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         158
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(XQ21.33) MUTATED     9  36
  DEL PEAK 35(XQ21.33) WILD-TYPE  21 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED      9   36
  DEL PEAK 35(XQ21.33) WILD-TYPE   21  172
     clus
vv    DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  NO                             9                             21
  YES                           36                            172
[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                           4
  DEL PEAK 35(XQ21.33) WILD-TYPE                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 35(XQ21.33) MUTATED                                           1
  DEL PEAK 35(XQ21.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 35(XQ21.33) MUTATED      34
  DEL PEAK 35(XQ21.33) WILD-TYPE   135
D63V10, multiclass
                                           clus
vv                                          DEL PEAK 35(XQ21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               34
                                           clus
vv                                          DEL PEAK 35(XQ21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D63V11, binary
                                cls
clus                               0   1
  DEL PEAK 35(XQ21.33) MUTATED     3  29
  DEL PEAK 35(XQ21.33) WILD-TYPE  13 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED      3   29
  DEL PEAK 35(XQ21.33) WILD-TYPE   13  120
                        clus
vv                       DEL PEAK 35(XQ21.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK 35(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            120
[1] 2 2
[1] FALSE
D63V12, continuous
D63V13, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   15  6
  DEL PEAK 35(XQ21.33) WILD-TYPE 56 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     15    6
  DEL PEAK 35(XQ21.33) WILD-TYPE   56   19
            clus
vv           DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  TUMOR FREE                           15                             56
  WITH TUMOR                            6                             19
[1] 2 2
[1] FALSE
                                vv
clus                             BRAZIL CANADA NIGERIA RUSSIA UKRAINE
  DEL PEAK 35(XQ21.33) MUTATED        3      0       0      2       1
  DEL PEAK 35(XQ21.33) WILD-TYPE     20      5       1      8       6
                                vv
clus                             UNITED STATES VIETNAM
  DEL PEAK 35(XQ21.33) MUTATED              37       2
  DEL PEAK 35(XQ21.33) WILD-TYPE           141      12
D63V14, multiclass
               clus
vv              DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  BRAZIL                                   3                             20
  CANADA                                   0                              5
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  1                              6
  UNITED STATES                           37                            141
  VIETNAM                                  2                             12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 35(XQ21.33) MUTATED    4 15 21  0  4
  DEL PEAK 35(XQ21.33) WILD-TYPE 13 91 76  1 10
D63V15, multiclass
    clus
vv   DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  G1                            4                             13
  G2                           15                             91
  G3                           21                             76
  G4                            0                              1
  GX                            4                             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V16, continuous
D63V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 35(XQ21.33) MUTATED                                             5
  DEL PEAK 35(XQ21.33) WILD-TYPE                                          26
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 35(XQ21.33) MUTATED                                        1
  DEL PEAK 35(XQ21.33) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 35(XQ21.33) MUTATED                                                 0
  DEL PEAK 35(XQ21.33) WILD-TYPE                                               2
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 35(XQ21.33) MUTATED               12                  18
  DEL PEAK 35(XQ21.33) WILD-TYPE             40                  94
D63V18, multiclass
                                                 clus
vv                                                DEL PEAK 35(XQ21.33) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            12
  LIFELONG NON-SMOKER                                                       18
                                                 clus
vv                                                DEL PEAK 35(XQ21.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              2
  CURRENT SMOKER                                                              40
  LIFELONG NON-SMOKER                                                         94
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V19, continuous
D63V20, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 35(XQ21.33) MUTATED             6       10             4        1
  DEL PEAK 35(XQ21.33) WILD-TYPE          13       65             8       11
D63V21, multiclass
               clus
vv              DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  COMBINATION                              6                             13
  EXTERNAL                                10                             65
  EXTERNAL BEAM                            4                              8
  INTERNAL                                 1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                     3             1
  DEL PEAK 35(XQ21.33) WILD-TYPE                  25            15
D63V23, multiclass
                     clus
vv                    DEL PEAK 35(XQ21.33) MUTATED
  DISTANT RECURRENCE                             1
  LOCAL RECURRENCE                               1
  PRIMARY TUMOR FIELD                            3
  REGIONAL SITE                                  1
                     clus
vv                    DEL PEAK 35(XQ21.33) WILD-TYPE
  DISTANT RECURRENCE                               1
  LOCAL RECURRENCE                                 1
  PRIMARY TUMOR FIELD                             25
  REGIONAL SITE                                   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"
D63V24, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED    3  0
  DEL PEAK 35(XQ21.33) WILD-TYPE 31  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED      3    0
  DEL PEAK 35(XQ21.33) WILD-TYPE   31    3
     clus
vv    DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  CGY                            3                             31
  GY                             0                              3
[1] 2 2
[1] FALSE
D63V25, continuous
D63V26, continuous
D63V27, continuous
D63V28, continuous
D63V29, continuous
D63V30, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  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                                   2
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 35(XQ21.33) MUTATED                         4
  DEL PEAK 35(XQ21.33) WILD-TYPE                      25
                                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                       4
D63V31, multiclass
                                     clus
vv                                    DEL PEAK 35(XQ21.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                        4
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        3
                                     clus
vv                                    DEL PEAK 35(XQ21.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  OTHER LOCATION, SPECIFY                                         25
  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 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                                                3
  DEL PEAK 35(XQ21.33) WILD-TYPE                                             13
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 35(XQ21.33) MUTATED                                                                                  12
  DEL PEAK 35(XQ21.33) WILD-TYPE                                                                                56
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 35(XQ21.33) MUTATED                                                                                             19
  DEL PEAK 35(XQ21.33) WILD-TYPE                                                                                           86
D63V32, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 35(XQ21.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           19
                                                                                              clus
vv                                                                                             DEL PEAK 35(XQ21.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V33, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   12 12
  DEL PEAK 35(XQ21.33) WILD-TYPE 56 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     12   12
  DEL PEAK 35(XQ21.33) WILD-TYPE   56   58
         clus
vv        DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  ABSENT                            12                             56
  PRESENT                           12                             58
[1] 2 2
[1] FALSE
D63V34, continuous
D63V35, continuous
D63V36, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   15 15
  DEL PEAK 35(XQ21.33) WILD-TYPE 28 79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     15   15
  DEL PEAK 35(XQ21.33) WILD-TYPE   28   79
                                          clus
vv                                         DEL PEAK 35(XQ21.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           15
                                          clus
vv                                         DEL PEAK 35(XQ21.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             79
[1] 2 2
[1] FALSE
D63V37, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 35(XQ21.33) MUTATED              3           9         12
  DEL PEAK 35(XQ21.33) WILD-TYPE            7          40         45
D63V38, multiclass
              clus
vv             DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  CURRENT USER                            3                              7
  FORMER USER                             9                             40
  NEVER USED                             12                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V39, continuous
D63V40, binary
                                cls
clus                              0  1
  DEL PEAK 35(XQ21.33) MUTATED   19  1
  DEL PEAK 35(XQ21.33) WILD-TYPE 70 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     19    1
  DEL PEAK 35(XQ21.33) WILD-TYPE   70   15
         clus
vv        DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  ABSENT                            19                             70
  PRESENT                            1                             15
[1] 2 2
[1] FALSE
D63V41, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3
  DEL PEAK 35(XQ21.33) MUTATED     1    0   5   13    7  1   1    0    2   3  0
  DEL PEAK 35(XQ21.33) WILD-TYPE   0    1  25   52   17  3   7    7    7  19  1
                                vv
clus                             T3B T4 TIS TX
  DEL PEAK 35(XQ21.33) MUTATED     1  0   0  1
  DEL PEAK 35(XQ21.33) WILD-TYPE   7  2   1 13
D63V42, multiclass
      clus
vv     DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  T1A                             1                              0
  T1A1                            0                              1
  T1B                             5                             25
  T1B1                           13                             52
  T1B2                            7                             17
  T2                              1                              3
  T2A                             1                              7
  T2A1                            0                              7
  T2A2                            2                              7
  T2B                             3                             19
  T3                              0                              1
  T3B                             1                              7
  T4                              0                              2
  TIS                             0                              1
  TX                              1                             13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V43, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 35(XQ21.33) MUTATED         1        1         0         1        5
  DEL PEAK 35(XQ21.33) WILD-TYPE       3        1         1         0       26
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 35(XQ21.33) MUTATED          13         8        0         1
  DEL PEAK 35(XQ21.33) WILD-TYPE        56        24        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 35(XQ21.33) MUTATED            0          1         5         0
  DEL PEAK 35(XQ21.33) WILD-TYPE          5          6        22         1
                                vv
clus                             STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 35(XQ21.33) MUTATED            7         0         1
  DEL PEAK 35(XQ21.33) WILD-TYPE         27         3         6
D63V44, multiclass
            clus
vv           DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  STAGE I                               1                              3
  STAGE IA                              1                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              5                             26
  STAGE IB1                            13                             56
  STAGE IB2                             8                             24
  STAGE II                              0                              3
  STAGE IIA                             1                              5
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             5                             22
  STAGE III                             0                              1
  STAGE IIIB                            7                             27
  STAGE IVA                             0                              3
  STAGE IVB                             1                              6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
