[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/22489370/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/22507940/transformed.cor.cli.txt"

nPatients in clinical file=307, in cluster file=295, common to both=295
[1]  63 295
[1] "AMP PEAK  1(1P31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           96                           199 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           96                           199 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          158                           137 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          158                           137 
[1] "AMP PEAK  3(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           79                           216 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           79                           216 
[1] "AMP PEAK  4(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                           41                           254 
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                           41                           254 
[1] "AMP PEAK  5(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                           227                             68 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                           227                             68 
[1] "AMP PEAK  6(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         21                         274 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         21                         274 
[1] "AMP PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           138                            157 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           138                            157 
[1] "AMP PEAK  8(6P21.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE 
                            82                            213 
  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE 
                            82                            213 
[1] "AMP PEAK  9(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           52                           243 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           52                           243 
[1] "AMP PEAK 10(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           127                            168 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           127                            168 
[1] "AMP PEAK 11(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE 
                           63                           232 
  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE 
                           63                           232 
[1] "AMP PEAK 12(11P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                          23                          272 
  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                          23                          272 
[1] "AMP PEAK 13(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            41                            254 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            41                            254 
[1] "AMP PEAK 14(11Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE 
                            47                            248 
  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE 
                            47                            248 
[1] "AMP PEAK 15(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                            65                            230 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                            65                            230 
[1] "AMP PEAK 16(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE 
                          69                          226 
  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE 
                          69                          226 
[1] "AMP PEAK 17(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            76                            219 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            76                            219 
[1] "AMP PEAK 18(16P13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                             65                             230 
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                             65                             230 
[1] "AMP PEAK 19(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          55                          240 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          55                          240 
[1] "AMP PEAK 20(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            74                            221 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            74                            221 
[1] "AMP PEAK 21(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE 
                            39                            256 
  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE 
                            39                            256 
[1] "AMP PEAK 22(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                            43                            252 
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                            43                            252 
[1] "AMP PEAK 23(19Q13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE 
                             93                             202 
  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE 
                             93                             202 
[1] "AMP PEAK 24(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                            135                             160 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                            135                             160 
[1] "AMP PEAK 25(21Q22.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE 
                             48                             247 
  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE 
                             48                             247 
[1] "AMP PEAK 26(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE 
                         75                         220 
  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE 
                         75                         220 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            40                            255 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            40                            255 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           34                           261 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           34                           261 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           65                           230 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           65                           230 
[1] "DEL PEAK  4(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          129                           166 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          129                           166 
[1] "DEL PEAK  5(3P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                          113                           182 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                          113                           182 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          134                           161 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          134                           161 
[1] "DEL PEAK  7(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE 
                          127                           168 
  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE 
                          127                           168 
[1] "DEL PEAK  8(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE 
                          103                           192 
  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE 
                          103                           192 
[1] "DEL PEAK  9(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                          100                           195 
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                          100                           195 
[1] "DEL PEAK 10(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE 
                          114                           181 
  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE 
                          114                           181 
[1] "DEL PEAK 11(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                           76                           219 
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                           76                           219 
[1] "DEL PEAK 12(5Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE 
                           71                           224 
  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE 
                           71                           224 
[1] "DEL PEAK 13(6P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE 
                           46                           249 
  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE 
                           46                           249 
[1] "DEL PEAK 14(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        100                         195 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        100                         195 
[1] "DEL PEAK 15(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE 
                         60                         235 
  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE 
                         60                         235 
[1] "DEL PEAK 16(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                          104                           191 
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                          104                           191 
[1] "DEL PEAK 17(8P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE 
                           97                           198 
  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE 
                           97                           198 
[1] "DEL PEAK 18(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                             86                             209 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                             86                             209 
[1] "DEL PEAK 19(11P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE 
                           102                            193 
  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE 
                           102                            193 
[1] "DEL PEAK 20(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE 
                           162                            133 
  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE 
                           162                            133 
[1] "DEL PEAK 21(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                         160                          135 
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                         160                          135 
[1] "DEL PEAK 22(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE 
                             98                             197 
  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE 
                             98                             197 
[1] "DEL PEAK 23(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           118                            177 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           118                            177 
[1] "DEL PEAK 24(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE 
                             50                             245 
  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE 
                             50                             245 
[1] "DEL PEAK 25(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE 
                            70                            225 
  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE 
                            70                            225 
[1] "DEL PEAK 26(16Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE 
                            53                            242 
  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE 
                            53                            242 
[1] "DEL PEAK 27(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            55                            240 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            55                            240 
[1] "DEL PEAK 28(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE 
                         109                          186 
  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE 
                         109                          186 
[1] "DEL PEAK 29(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                            51                            244 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                            51                            244 
[1] "DEL PEAK 30(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                            82                            213 
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                            82                            213 
[1] "DEL PEAK 31(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                           105                            190 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                           105                            190 
[1] "DEL PEAK 32(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                             38                             257 
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                             38                             257 
[1] "DEL PEAK 33(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            36                            259 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            36                            259 
[1] "DEL PEAK 34(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                            58                            237 
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                            58                            237 
[1] "DEL PEAK 35(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE 
                             87                             208 
  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE 
                             87                             208 
[1] "DEL PEAK 36(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                           72                           223 
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                           72                           223 
[1] "DEL PEAK 37(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                            59                            236 
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                            59                            236 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                          
 [2] "VITAL_STATUS"                            
 [3] "DAYS_TO_DEATH"                           
 [4] "DAYS_TO_LAST_FOLLOWUP"                   
 [5] "TUMOR_TISSUE_SITE"                       
 [6] "PATHOLOGIC_STAGE"                        
 [7] "PATHOLOGY_T_STAGE"                       
 [8] "PATHOLOGY_N_STAGE"                       
 [9] "PATHOLOGY_M_STAGE"                       
[10] "GENDER"                                  
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"    
[12] "RADIATION_THERAPY"                       
[13] "HISTOLOGICAL_TYPE"                       
[14] "NUMBER_PACK_YEARS_SMOKED"                
[15] "NUMBER_OF_LYMPH_NODES"                   
[16] "RACE"                                    
[17] "ETHNICITY"                               
[18] "WEIGHT_KG_AT_DIAGNOSIS"                  
[19] "TUMOR_STATUS"                            
[20] "NEOPLASM_HISTOLOGIC_GRADE"               
[21] "TOBACCO_SMOKING_YEAR_STOPPED"            
[22] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"       
[23] "TOBACCO_SMOKING_HISTORY"                 
[24] "AGEBEGANSMOKINGINYEARS"                  
[25] "RADIATION_THERAPY_STATUS"                
[26] "PREGNANCIES_COUNT_TOTAL"                 
[27] "PREGNANCIES_COUNT_STILLBIRTH"            
[28] "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"    
[29] "PREGNANCIES_COUNT_LIVE_BIRTH"            
[30] "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"    
[31] "PREGNANCIES_COUNT_ECTOPIC"               
[32] "CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT"
[33] "LYMPH_NODE_LOCATION"                     
[34] "POS_LYMPH_NODE_LOCATION"                 
[35] "MENOPAUSE_STATUS"                        
[36] "LYMPHOVASCULAR_INVOLVEMENT"              
[37] "LYMPH_NODES_EXAMINED_HE_COUNT"           
[38] "LYMPH_NODES_EXAMINED"                    
[39] "KERATINIZATION_SQUAMOUS_CELL"            
[40] "INITIAL_PATHOLOGIC_DX_YEAR"              
[41] "HYSTERECTOMY_TYPE"                       
[42] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"     
[43] "HEIGHT_CM_AT_DIAGNOSIS"                  
[44] "CORPUS_INVOLVEMENT"                      
[45] "CHEMO_CONCURRENT_TYPE"                   
[46] "CERVIX_SUV_RESULTS"                      
[47] "CAUSE_OF_DEATH"                          
[48] "AGE_AT_DIAGNOSIS"                        
[49] "CLINICAL_STAGE"                          

Input Data has 49 rows and 295 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=198,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'NEOPLASM_HISTOLOGIC_GRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'AGEBEGANSMOKINGINYEARS':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'PREGNANCY_SPONTANEOUS_ABORTION_COUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 29:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'PREGNANCY_THERAPEUTIC_ABORTION_COUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 31:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 32:'CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT excluded in the analysis because there is no case of (both >= 3) in the table below"
              BILATERAL PELVIC WALL INVOLVEMENT ON IMAGING
freq.values   "1"                                         
freq.contrast "10"                                        
both >= 3     "FALSE"                                     
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "10"                                                                                                                               
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NEGATIVE NO EXTENSION NO PELVIC SPREAD
freq.values   "1"                       "2"      "1"          "1"             
freq.contrast "10"                      "9"      "10"         "10"            
both >= 3     "FALSE"                   "FALSE"  "FALSE"      "FALSE"         
              PELVIC SPREAD
freq.values   "1"          
freq.contrast "10"         
both >= 3     "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "10"                                                                        
both >= 3     "FALSE"                                                                     
              THE PELVIC NODULES SHOW CIRCUMSCRIBED AREA OF ADIPOSE TISSUE WITH LOCAL FAT NECROSIS. NO EVIDENCE OF MALIGNANCY WITHIN THIS PELVIC NODULE.
freq.values   "1"                                                                                                                                       
freq.contrast "10"                                                                                                                                      
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "10"                                                                     
both >= 3     "FALSE"                                                                  
Variable 33:'LYMPH_NODE_LOCATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "LYMPH_NODE_LOCATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 34:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 35:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 36:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 37:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'LYMPH_NODES_EXAMINED':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 40:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 41:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HYSTERECTOMY_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 42:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 44:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 45:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 46:'CERVIX_SUV_RESULTS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'CAUSE_OF_DEATH':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CAUSE_OF_DEATH excluded in the analysis because there is no case of (both >= 3) in the table below"
              CARDIOPULMONARY ARREST LUNG CANCER RENAL FAILURE
freq.values   "1"                    "1"         "1"          
freq.contrast "2"                    "2"         "2"          
both >= 3     "FALSE"                "FALSE"     "FALSE"      
Variable 48:'AGE_AT_DIAGNOSIS':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'CLINICAL_STAGE':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 295 columns, 1 survival variables, and 38 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                      
 [2] "PATHOLOGY_T_STAGE"                   
 [3] "PATHOLOGY_N_STAGE"                   
 [4] "PATHOLOGY_M_STAGE"                   
 [5] "RADIATION_THERAPY"                   
 [6] "HISTOLOGICAL_TYPE"                   
 [7] "NUMBER_PACK_YEARS_SMOKED"            
 [8] "NUMBER_OF_LYMPH_NODES"               
 [9] "RACE"                                
[10] "ETHNICITY"                           
[11] "WEIGHT_KG_AT_DIAGNOSIS"              
[12] "TUMOR_STATUS"                        
[13] "NEOPLASM_HISTOLOGIC_GRADE"           
[14] "TOBACCO_SMOKING_YEAR_STOPPED"        
[15] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"   
[16] "TOBACCO_SMOKING_HISTORY"             
[17] "AGEBEGANSMOKINGINYEARS"              
[18] "RADIATION_THERAPY_STATUS"            
[19] "PREGNANCIES_COUNT_TOTAL"             
[20] "PREGNANCIES_COUNT_STILLBIRTH"        
[21] "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"
[22] "PREGNANCIES_COUNT_LIVE_BIRTH"        
[23] "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"
[24] "PREGNANCIES_COUNT_ECTOPIC"           
[25] "POS_LYMPH_NODE_LOCATION"             
[26] "MENOPAUSE_STATUS"                    
[27] "LYMPHOVASCULAR_INVOLVEMENT"          
[28] "LYMPH_NODES_EXAMINED_HE_COUNT"       
[29] "LYMPH_NODES_EXAMINED"                
[30] "KERATINIZATION_SQUAMOUS_CELL"        
[31] "INITIAL_PATHOLOGIC_DX_YEAR"          
[32] "HISTORY_HORMONAL_CONTRACEPTIVES_USE" 
[33] "HEIGHT_CM_AT_DIAGNOSIS"              
[34] "CORPUS_INVOLVEMENT"                  
[35] "CHEMO_CONCURRENT_TYPE"               
[36] "CERVIX_SUV_RESULTS"                  
[37] "AGE_AT_DIAGNOSIS"                    
[38] "CLINICAL_STAGE"                      
YEARS_TO_BIRTH, nv=61, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
135  70  21   8 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
135  70  21   8 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
135  70  21   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
135  70  21   8 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=73, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM_HISTOLOGIC_GRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=22, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=TRUE
AGEBEGANSMOKINGINYEARS, nv=28, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=15, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PREGNANCY_SPONTANEOUS_ABORTION_COUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=12, binary=FALSE, numeric=TRUE
PREGNANCY_THERAPEUTIC_ABORTION_COUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=49, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=36, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=3, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=17, binary=FALSE, numeric=TRUE
AGE_AT_DIAGNOSIS, nv=61, binary=FALSE, numeric=TRUE
CLINICAL_STAGE, nv=17, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P31.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P31.3) MUTATED    66  26
  AMP PEAK  1(1P31.3) WILD-TYPE 148  42
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           92                           190 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           26                            42 
$`AMP PEAK  1(1P31.3) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        57.04        36.56        82.85        31.40        46.32 
TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A2LZ TCGA-C5-A3HF 
       38.99         0.46         2.43        20.91       100.14        17.85 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      154.32       101.82        13.61         2.73        50.99        45.83 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DS-A0VL TCGA-DS-A0VN 
       23.51        27.52         1.12        44.94        55.63       118.65 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A411 
        8.28        39.55        37.35        31.36        25.02        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A97N 
       31.73        26.01        25.91        27.29        27.22         0.36 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ 
        1.51         0.39         0.59         0.89        40.96         1.74 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A69L TCGA-FU-A3NI 
        1.64         2.33         0.07         0.89        19.79        20.98 
TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-IR-A3LL 
       26.14        14.01        20.78        14.93       129.37        36.36 
TCGA-JW-A5VK TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A5U2 
       20.48        18.15       209.59        44.61        20.91         0.30 
TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE 
       13.35        20.28        11.38        28.08        34.62        35.05 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-R2-A69V TCGA-UC-A7PF 
        2.96        16.41         9.04        17.56        19.59        93.99 
TCGA-UC-A7PG TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       12.16        45.57        19.96        11.51        59.18        31.27 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA 
       15.68        56.35        55.50        51.32        50.47        28.50 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9V0 
       24.30        46.92        45.11        14.53        27.25        18.84 
TCGA-ZJ-AAXA TCGA-ZX-AA5X 
        1.41         3.91 

$`AMP PEAK  1(1P31.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
        0.69        17.52        17.82        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ 
       18.74       144.16       177.04       173.29         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       67.46        30.21        35.01        57.73        53.16        35.61 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL 
       78.35        38.43        33.24        52.01        18.02        20.42 
TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      210.67       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XK 
      155.77       131.11        94.95         9.34         8.35        99.91 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM 
       20.81        20.91        14.73        95.11        82.06        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       87.75        58.88        36.76       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD 
       16.18        17.52        40.87        30.90        31.53        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       36.89        26.40        12.13        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 
       26.79        27.25        24.00        13.48        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB 
        6.64        19.27         0.43         1.45         0.13         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ 
        4.24         0.07         1.87         0.43        47.77         0.10 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-FU-A23K 
        0.49        20.35         7.92        15.22        15.55        12.23 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB 
       23.84        19.04        16.11        31.36        36.26        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       16.57        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        29.85        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        28.37         8.28        21.11 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3Y 
       11.28         0.89        12.49         0.82        22.52        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
       19.56         9.17         8.52        19.96        54.81        20.84 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P 
       17.23        15.58        15.95        16.14        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI 
        9.34        18.64        22.62        14.60        11.67        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 
       10.03        46.52        32.42        23.97        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       53.59        36.13        39.78        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 
       33.37        40.14        58.45        50.14        43.40        48.39 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
       29.95        27.12         1.71        47.87        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       26.07        15.85        14.53         3.42        18.25        67.20 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        18.25        17.75        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.16 

  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                       209.59                        210.67 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                       24.790                        21.275 
[1] "0.1 - 209.6 (24.8)" "0.1 - 210.7 (21.3)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  1(1P31.3) MUTATED   38 23 10  2
  AMP PEAK  1(1P31.3) WILD-TYPE 97 47 11  6
D1V3, multiclass
    clus
vv   AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  T1                          38                            97
  T2                          23                            47
  T3                          10                            11
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   38 15
  AMP PEAK  1(1P31.3) WILD-TYPE 91 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     38   15
  AMP PEAK  1(1P31.3) WILD-TYPE   91   41
   clus
vv  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  0                          38                            91
  1                          15                            41
[1] 2 2
[1] FALSE
D1V5, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   36  2
  AMP PEAK  1(1P31.3) WILD-TYPE 72  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     36    2
  AMP PEAK  1(1P31.3) WILD-TYPE   72    8
   clus
vv  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  0                          36                            72
  1                           2                             8
[1] 2 2
[1] FALSE
D1V6, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   18 40
  AMP PEAK  1(1P31.3) WILD-TYPE 35 85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     18   40
  AMP PEAK  1(1P31.3) WILD-TYPE   35   85
     clus
vv    AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  NO                           18                            35
  YES                          40                            85
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1P31.3) MUTATED               1                               87
  AMP PEAK  1(1P31.3) WILD-TYPE             5                              155
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  1(1P31.3) MUTATED                                               1
  AMP PEAK  1(1P31.3) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  1(1P31.3) MUTATED                                     4
  AMP PEAK  1(1P31.3) WILD-TYPE                                  17
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  1(1P31.3) MUTATED                                           0
  AMP PEAK  1(1P31.3) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  1(1P31.3) MUTATED                                              3
  AMP PEAK  1(1P31.3) WILD-TYPE                                           14
D1V7, multiclass
                                               clus
vv                                              AMP PEAK  1(1P31.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              AMP PEAK  1(1P31.3) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P31.3) MUTATED                          11
  AMP PEAK  1(1P31.3) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  1(1P31.3) MUTATED                                           0    63
  AMP PEAK  1(1P31.3) WILD-TYPE                                         2   139
D1V10, multiclass
                                           clus
vv                                          AMP PEAK  1(1P31.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              63
                                           clus
vv                                          AMP PEAK  1(1P31.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  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"
D1V11, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P31.3) MUTATED     4  58
  AMP PEAK  1(1P31.3) WILD-TYPE  19 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      4   58
  AMP PEAK  1(1P31.3) WILD-TYPE   19  105
                        clus
vv                       AMP PEAK  1(1P31.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       AMP PEAK  1(1P31.3) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           105
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P31.3) MUTATED    60  27
  AMP PEAK  1(1P31.3) WILD-TYPE 133  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     60   27
  AMP PEAK  1(1P31.3) WILD-TYPE  133   49
            clus
vv           AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  TUMOR FREE                          60                           133
  WITH TUMOR                          27                            49
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  1(1P31.3) MUTATED    4 43 40  0  8
  AMP PEAK  1(1P31.3) WILD-TYPE 14 86 75  1 16
D1V14, multiclass
    clus
vv   AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  G1                           4                            14
  G2                          43                            86
  G3                          40                            75
  G4                           0                             1
  GX                           8                            16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, continuous
D1V16, continuous
D1V17, continuous
D1V18, continuous
D1V19, 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
D1V20, continuous
D1V21, continuous
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  1(1P31.3) MUTATED                                     0
  AMP PEAK  1(1P31.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  1(1P31.3) MUTATED                                     0
  AMP PEAK  1(1P31.3) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  1(1P31.3) MUTATED                        11                       0
  AMP PEAK  1(1P31.3) WILD-TYPE                      25                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  1(1P31.3) MUTATED                         2
  AMP PEAK  1(1P31.3) WILD-TYPE                       8
D1V26, multiclass
                                     clus
vv                                    AMP PEAK  1(1P31.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                      11
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    AMP PEAK  1(1P31.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        25
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  1(1P31.3) MUTATED                                               1
  AMP PEAK  1(1P31.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  1(1P31.3) MUTATED                                                7
  AMP PEAK  1(1P31.3) WILD-TYPE                                             18
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  1(1P31.3) MUTATED                                                                                  38
  AMP PEAK  1(1P31.3) WILD-TYPE                                                                                44
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  1(1P31.3) MUTATED                                                                                             32
  AMP PEAK  1(1P31.3) WILD-TYPE                                                                                           89
D1V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  1(1P31.3) 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)                                     38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          32
                                                                                              clus
vv                                                                                             AMP PEAK  1(1P31.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       44
  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"
D1V28, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   22 24
  AMP PEAK  1(1P31.3) WILD-TYPE 49 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     22   24
  AMP PEAK  1(1P31.3) WILD-TYPE   49   50
         clus
vv        AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  ABSENT                           22                            49
  PRESENT                          24                            50
[1] 2 2
[1] FALSE
D1V29, continuous
D1V30, continuous
D1V31, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   19 37
  AMP PEAK  1(1P31.3) WILD-TYPE 30 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     19   37
  AMP PEAK  1(1P31.3) WILD-TYPE   30   80
                                          clus
vv                                         AMP PEAK  1(1P31.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          37
                                          clus
vv                                         AMP PEAK  1(1P31.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            80
[1] 2 2
[1] FALSE
D1V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  1(1P31.3) MUTATED              3           9         30
  AMP PEAK  1(1P31.3) WILD-TYPE           12          45         55
D1V33, multiclass
              clus
vv             AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                            9                            45
  NEVER USED                            30                            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"
D1V34, continuous
D1V35, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   26  6
  AMP PEAK  1(1P31.3) WILD-TYPE 66 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     26    6
  AMP PEAK  1(1P31.3) WILD-TYPE   66   12
         clus
vv        AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  ABSENT                           26                            66
  PRESENT                           6                            12
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  1(1P31.3) MUTATED             2        26     0
  AMP PEAK  1(1P31.3) WILD-TYPE           3        74     2
D1V36, multiclass
             clus
vv            AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  CARBOPLATIN                           2                             3
  CISPLATIN                            26                            74
  OTHER                                 0                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V37, continuous
D1V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  1(1P31.3) MUTATED         2        0         1         0       13
  AMP PEAK  1(1P31.3) WILD-TYPE       3        1         0         1       21
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  1(1P31.3) MUTATED          25         6        2         2
  AMP PEAK  1(1P31.3) WILD-TYPE        52        31        2         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  1(1P31.3) MUTATED            2          3        12         1
  AMP PEAK  1(1P31.3) WILD-TYPE          3          4        32         0
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  1(1P31.3) MUTATED            2         17         3         3
  AMP PEAK  1(1P31.3) WILD-TYPE          1         25         4         9
D1V39, multiclass
            clus
vv           AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IA1                            1                             0
  STAGE IA2                            0                             1
  STAGE IB                            13                            21
  STAGE IB1                           25                            52
  STAGE IB2                            6                            31
  STAGE II                             2                             2
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           3                             4
  STAGE IIB                           12                            32
  STAGE III                            1                             0
  STAGE IIIA                           2                             1
  STAGE IIIB                          17                            25
  STAGE IVA                            3                             4
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED   109  39
  AMP PEAK  2(1Q21.3) WILD-TYPE 105  29
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          148                           134 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           39                            29 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32        17.82        49.48        57.04 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
        5.46        31.40        46.32        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY 
        0.46         2.43        20.91         3.58        44.22        78.35 
TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
      100.14        17.85       154.32       101.82       134.33        15.48 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ 
       94.95        13.61         2.73        45.83         8.35        23.51 
TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       27.52         1.12        44.94        87.75        58.88        55.63 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
      117.99        22.98        17.52         8.28        39.55        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       30.90        31.53        31.36        24.56        31.73        26.01 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N 
       25.91        27.29        27.25        27.22        24.00         0.36 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA 
        1.51        19.27         0.39         0.59         0.89        40.96 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN 
        1.74        47.77         1.64         2.33         0.49         0.89 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI 
       15.22        19.79        15.55        23.84        16.11        20.98 
TCGA-FU-A40J TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       14.01        25.41        16.57        20.78        14.93         9.44 
TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK 
      129.37        78.71        81.96        36.36        21.44        20.48 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        8.28        18.15       209.59        44.61        20.91        11.28 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MA-AA42 
        0.30         0.82        22.52        20.28         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       11.38        28.08        35.05         2.96        16.41        15.95 
TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG 
       17.56         9.34        18.64        19.59        93.99        12.16 
TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       10.03        32.42        19.96        65.49        32.15        53.59 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 
       11.51        59.18        31.27        16.64         4.73        40.14 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       58.45        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       43.40        28.50        27.12        24.30        46.92        45.11 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UV TCGA-VS-A9V0 TCGA-VS-A9V3 
       14.53        27.25        47.47         3.42        18.84        17.75 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       26.01        29.26         1.41         3.91 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-BI-A20A 
      146.86         1.48         4.34         0.69        17.52        23.67 
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 
       11.44        68.84        19.86        67.46        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 
       57.73        40.93        73.18        73.45        83.05        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CM 
       33.24        52.01        18.02        20.42       210.67        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7XC 
      147.35        17.19       155.77       131.11         9.34        50.99 
TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK 
       99.91        20.81        20.91        14.73        95.11        82.06 
TCGA-DG-A2KM TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QT 
       63.98        36.76       118.65        16.83        16.18        40.87 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA 
       13.05        25.02        36.89        26.40        12.13        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 
        7.46        14.89        26.79        13.48        60.72        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         0.30         4.24 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 
        0.07         1.87         0.43         0.07         0.10        20.35 
TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
        7.92        12.23        19.04        31.36        36.26        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       16.14        28.31        35.44        10.55         1.12        17.75 
TCGA-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK 
       21.67       147.39       137.16        66.81        96.95        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ 
       27.42         3.29        24.56        15.58        28.37        21.11 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MU-A5YI 
        0.89        12.49        13.35        17.82        19.56        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A6DT 
       19.96        54.81        20.84        17.23        15.58         9.04 
TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       16.14        14.07        15.88        22.62        14.60        11.67 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8QA TCGA-VS-A8QH 
       69.50        46.52        45.57        23.97        36.13        39.78 
TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A953 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UJ 
       40.87        33.37        15.68        48.39        29.95         1.71 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UY 
       47.87        41.52        26.07        15.85        14.53        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       67.20         5.16        18.25        16.24        15.42        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       19.13         0.16 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.30                          0.07 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       209.59                        210.67 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       23.920                        20.875 
[1] "0.3 - 209.6 (23.9)" "0.1 - 210.7 (20.9)"
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  2(1Q21.3) MUTATED   61 44 15  4
  AMP PEAK  2(1Q21.3) WILD-TYPE 74 26  6  4
D2V3, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                          61                            74
  T2                          44                            26
  T3                          15                             6
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   64 30
  AMP PEAK  2(1Q21.3) WILD-TYPE 65 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     64   30
  AMP PEAK  2(1Q21.3) WILD-TYPE   65   26
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                          64                            65
  1                          30                            26
[1] 2 2
[1] FALSE
D2V5, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   58  8
  AMP PEAK  2(1Q21.3) WILD-TYPE 50  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     58    8
  AMP PEAK  2(1Q21.3) WILD-TYPE   50    2
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                          58                            50
  1                           8                             2
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   26 69
  AMP PEAK  2(1Q21.3) WILD-TYPE 27 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     26   69
  AMP PEAK  2(1Q21.3) WILD-TYPE   27   56
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           26                            27
  YES                          69                            56
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED               3                              136
  AMP PEAK  2(1Q21.3) WILD-TYPE             3                              106
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                               3
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                                    10
  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                                              6
  AMP PEAK  2(1Q21.3) WILD-TYPE                                           11
D2V7, multiclass
                                               clus
vv                                              AMP PEAK  2(1Q21.3) MUTATED
  ADENOSQUAMOUS                                                           3
  CERVICAL SQUAMOUS CELL CARCINOMA                                      136
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
                                               clus
vv                                              AMP PEAK  2(1Q21.3) WILD-TYPE
  ADENOSQUAMOUS                                                             3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        106
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1Q21.3) MUTATED                          21
  AMP PEAK  2(1Q21.3) WILD-TYPE                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           0   105
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         2    97
D2V10, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                              12
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             105
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  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"
D2V11, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   10 86
  AMP PEAK  2(1Q21.3) WILD-TYPE 13 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     10   86
  AMP PEAK  2(1Q21.3) WILD-TYPE   13   77
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                          86
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                            77
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   97 46
  AMP PEAK  2(1Q21.3) WILD-TYPE 96 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     97   46
  AMP PEAK  2(1Q21.3) WILD-TYPE   96   30
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  TUMOR FREE                          97                            96
  WITH TUMOR                          46                            30
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  2(1Q21.3) MUTATED    7 67 67  1 11
  AMP PEAK  2(1Q21.3) WILD-TYPE 11 62 48  0 13
D2V14, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  G1                           7                            11
  G2                          67                            62
  G3                          67                            48
  G4                           1                             0
  GX                          11                            13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, continuous
D2V16, continuous
D2V17, continuous
D2V18, continuous
D2V19, 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
D2V20, continuous
D2V21, continuous
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  2(1Q21.3) MUTATED                                     1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  2(1Q21.3) MUTATED                                     2
  AMP PEAK  2(1Q21.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  2(1Q21.3) MUTATED                        19                       0
  AMP PEAK  2(1Q21.3) WILD-TYPE                      17                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  2(1Q21.3) MUTATED                         4
  AMP PEAK  2(1Q21.3) WILD-TYPE                       6
D2V26, multiclass
                                     clus
vv                                    AMP PEAK  2(1Q21.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  OTHER LOCATION, SPECIFY                                      19
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       4
                                     clus
vv                                    AMP PEAK  2(1Q21.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                        17
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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  2(1Q21.3) MUTATED                                               1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  2(1Q21.3) MUTATED                                               13
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             12
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  2(1Q21.3) MUTATED                                                                                  49
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                                33
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  2(1Q21.3) MUTATED                                                                                             63
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                                           58
D2V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  2(1Q21.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          63
                                                                                              clus
vv                                                                                             AMP PEAK  2(1Q21.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       33
  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"
D2V28, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   35 40
  AMP PEAK  2(1Q21.3) WILD-TYPE 36 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     35   40
  AMP PEAK  2(1Q21.3) WILD-TYPE   36   34
         clus
vv        AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ABSENT                           35                            36
  PRESENT                          40                            34
[1] 2 2
[1] FALSE
D2V29, continuous
D2V30, continuous
D2V31, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   26 63
  AMP PEAK  2(1Q21.3) WILD-TYPE 23 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     26   63
  AMP PEAK  2(1Q21.3) WILD-TYPE   23   54
                                          clus
vv                                         AMP PEAK  2(1Q21.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          63
                                          clus
vv                                         AMP PEAK  2(1Q21.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            54
[1] 2 2
[1] FALSE
D2V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  2(1Q21.3) MUTATED              5          26         47
  AMP PEAK  2(1Q21.3) WILD-TYPE           10          28         38
D2V33, multiclass
              clus
vv             AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  CURRENT USER                           5                            10
  FORMER USER                           26                            28
  NEVER USED                            47                            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"
D2V34, continuous
D2V35, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   44 10
  AMP PEAK  2(1Q21.3) WILD-TYPE 48  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     44   10
  AMP PEAK  2(1Q21.3) WILD-TYPE   48    8
         clus
vv        AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ABSENT                           44                            48
  PRESENT                          10                             8
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  2(1Q21.3) MUTATED             2        54     0
  AMP PEAK  2(1Q21.3) WILD-TYPE           3        46     2
D2V36, multiclass
             clus
vv            AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  CARBOPLATIN                           2                             3
  CISPLATIN                            54                            46
  OTHER                                 0                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V37, continuous
D2V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  2(1Q21.3) MUTATED         3        0         0         0       19
  AMP PEAK  2(1Q21.3) WILD-TYPE       2        1         1         1       15
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED          35        16        2         4
  AMP PEAK  2(1Q21.3) WILD-TYPE        42        21        2         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  2(1Q21.3) MUTATED            5          3        25         1
  AMP PEAK  2(1Q21.3) WILD-TYPE          0          4        19         0
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  2(1Q21.3) MUTATED            3         26         4         8
  AMP PEAK  2(1Q21.3) WILD-TYPE          0         16         3         4
D2V39, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            19                            15
  STAGE IB1                           35                            42
  STAGE IB2                           16                            21
  STAGE II                             2                             2
  STAGE IIA                            4                             4
  STAGE IIA1                           5                             0
  STAGE IIA2                           3                             4
  STAGE IIB                           25                            19
  STAGE III                            1                             0
  STAGE IIIA                           3                             0
  STAGE IIIB                          26                            16
  STAGE IVA                            4                             3
  STAGE IVB                            8                             4
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(2P24.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(2P24.3) MUTATED    58  18
  AMP PEAK  3(2P24.3) WILD-TYPE 156  50
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           76                           206 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           18                            50 
$`AMP PEAK  3(2P24.3) MUTATED`
TCGA-EK-A2GZ TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1ME 
       12.59        57.04        23.67         5.46        31.40        57.73 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LT TCGA-C5-A2M2 TCGA-C5-A7UH TCGA-C5-A7X3 
       35.61         0.46        73.18        33.24       131.11         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR 
       13.61         2.73        50.99        45.83        23.51        27.52 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A3HR 
        1.12        95.11        44.94        22.98        17.52        30.90 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5O9 
       24.56        31.73        26.01        12.13        14.89        25.91 
TCGA-EA-A5ZF TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2RA TCGA-EK-A2RJ 
       27.22        26.27         1.51        19.27        40.96         1.74 
TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG 
        1.64         0.10         7.92        15.22        23.84        19.04 
TCGA-FU-A3HY TCGA-FU-A40J TCGA-IR-A3LA TCGA-IR-A3LC TCGA-JW-A5VJ TCGA-JX-A5QV 
       31.36        14.01       137.16       129.37        21.44        20.91 
TCGA-LP-A7HU TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       13.35        19.56         9.17        17.23        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8EJ 
       15.95        22.62        11.67        93.99        23.97        19.96 
TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 TCGA-VS-A959 TCGA-VS-A9U5 
       59.18        16.64         4.73        58.45        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL 
       43.40        29.95        27.12        24.30        45.11        14.53 
TCGA-VS-A9UP TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 
       47.47        17.75        16.24        26.01 

$`AMP PEAK  3(2P24.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 
      146.86        14.70         8.32         1.48         4.34         0.69 
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       17.52        17.82        49.48        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-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH 
       67.46        46.32        30.21        35.01        53.16        38.99 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        2.43        20.91        40.93         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35       100.14        38.43        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK 
        8.35        99.91        20.81        20.91        14.73        82.06 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
      118.65        16.83        16.18         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       37.35        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       26.40        24.82         7.46        26.79        27.29        27.25 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PK 
       24.00        13.48         0.36        60.72         6.64         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB 
        0.43         0.59         0.89         1.45         0.13         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
        4.24         0.07         1.87         0.43        47.77         2.33 
TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A69L TCGA-EX-A8YF 
        0.07         0.49         0.89        20.35        19.79        15.55 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       12.23        16.11        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        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        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
        8.28        18.15        21.11       209.59        44.61        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89        12.49         0.30         0.82        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       17.82         8.52        11.38        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A6DV 
       54.81        35.05        20.84         2.96         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
       17.56        14.07        15.88         9.34        18.64        19.59 
TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       14.60        12.16        69.50        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       32.42        65.49        32.15        53.59        36.13        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 
       39.78        31.27        40.87        33.37        40.14        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UH 
       56.35        55.50        50.14        48.39        28.50        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
        1.71        27.25        47.87        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       18.25        15.42        29.26        67.59        19.13         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                       137.16                        210.67 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                       23.590                        21.045 
[1] "0.1 - 137.2 (23.6)" "0.1 - 210.7 (21.0)"
[1] "hr=" "1.1"
D3V2, continuous
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  3(2P24.3) MUTATED    33  23   5   2
  AMP PEAK  3(2P24.3) WILD-TYPE 102  47  16   6
D3V3, multiclass
    clus
vv   AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  T1                          33                           102
  T2                          23                            47
  T3                           5                            16
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   35 13
  AMP PEAK  3(2P24.3) WILD-TYPE 94 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     35   13
  AMP PEAK  3(2P24.3) WILD-TYPE   94   43
   clus
vv  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  0                          35                            94
  1                          13                            43
[1] 2 2
[1] FALSE
D3V5, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   31  4
  AMP PEAK  3(2P24.3) WILD-TYPE 77  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     31    4
  AMP PEAK  3(2P24.3) WILD-TYPE   77    6
   clus
vv  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  0                          31                            77
  1                           4                             6
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   11 37
  AMP PEAK  3(2P24.3) WILD-TYPE 42 88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     11   37
  AMP PEAK  3(2P24.3) WILD-TYPE   42   88
     clus
vv    AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  NO                           11                            42
  YES                          37                            88
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(2P24.3) MUTATED               2                               62
  AMP PEAK  3(2P24.3) WILD-TYPE             4                              180
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  3(2P24.3) MUTATED                                               1
  AMP PEAK  3(2P24.3) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  3(2P24.3) MUTATED                                     6
  AMP PEAK  3(2P24.3) WILD-TYPE                                  15
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  3(2P24.3) MUTATED                                           2
  AMP PEAK  3(2P24.3) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  3(2P24.3) MUTATED                                              6
  AMP PEAK  3(2P24.3) WILD-TYPE                                           11
D3V7, multiclass
                                               clus
vv                                              AMP PEAK  3(2P24.3) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       62
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
                                               clus
vv                                              AMP PEAK  3(2P24.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        180
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(2P24.3) MUTATED                                  2     3
  AMP PEAK  3(2P24.3) WILD-TYPE                                6    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(2P24.3) MUTATED                           5
  AMP PEAK  3(2P24.3) WILD-TYPE                        23
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(2P24.3) MUTATED                                           1    57
  AMP PEAK  3(2P24.3) WILD-TYPE                                         1   145
D3V10, multiclass
                                           clus
vv                                          AMP PEAK  3(2P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              57
                                           clus
vv                                          AMP PEAK  3(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            23
  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"
D3V11, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED     5  40
  AMP PEAK  3(2P24.3) WILD-TYPE  18 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      5   40
  AMP PEAK  3(2P24.3) WILD-TYPE   18  123
                        clus
vv                       AMP PEAK  3(2P24.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       AMP PEAK  3(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           123
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED    49  22
  AMP PEAK  3(2P24.3) WILD-TYPE 144  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     49   22
  AMP PEAK  3(2P24.3) WILD-TYPE  144   54
            clus
vv           AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  TUMOR FREE                          49                           144
  WITH TUMOR                          22                            54
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  3(2P24.3) MUTATED    3 30 37  0  6
  AMP PEAK  3(2P24.3) WILD-TYPE 15 99 78  1 18
D3V14, multiclass
    clus
vv   AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  G1                           3                            15
  G2                          30                            99
  G3                          37                            78
  G4                           0                             1
  GX                           6                            18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, continuous
D3V16, continuous
D3V17, continuous
D3V18, continuous
D3V19, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED    5  0
  AMP PEAK  3(2P24.3) WILD-TYPE 20  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      5    0
  AMP PEAK  3(2P24.3) WILD-TYPE   20    3
                         clus
vv                        AMP PEAK  3(2P24.3) MUTATED
  COMPLETED AS PLANNED                              5
  TREATMENT NOT COMPLETED                           0
                         clus
vv                        AMP PEAK  3(2P24.3) WILD-TYPE
  COMPLETED AS PLANNED                               20
  TREATMENT NOT COMPLETED                             3
[1] 2 2
[1] FALSE
D3V20, continuous
D3V21, continuous
D3V22, continuous
D3V23, continuous
D3V24, continuous
D3V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  3(2P24.3) MUTATED                                     0
  AMP PEAK  3(2P24.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  3(2P24.3) MUTATED                                     2
  AMP PEAK  3(2P24.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  3(2P24.3) MUTATED                         8                       0
  AMP PEAK  3(2P24.3) WILD-TYPE                      28                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  3(2P24.3) MUTATED                         1
  AMP PEAK  3(2P24.3) WILD-TYPE                       9
D3V26, multiclass
                                     clus
vv                                    AMP PEAK  3(2P24.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  OTHER LOCATION, SPECIFY                                       8
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    AMP PEAK  3(2P24.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                        28
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  3(2P24.3) MUTATED                                               0
  AMP PEAK  3(2P24.3) WILD-TYPE                                             3
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  3(2P24.3) MUTATED                                                6
  AMP PEAK  3(2P24.3) WILD-TYPE                                             19
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  3(2P24.3) MUTATED                                                                                  22
  AMP PEAK  3(2P24.3) WILD-TYPE                                                                                60
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  3(2P24.3) MUTATED                                                                                             32
  AMP PEAK  3(2P24.3) WILD-TYPE                                                                                           89
D3V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  3(2P24.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          32
                                                                                              clus
vv                                                                                             AMP PEAK  3(2P24.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V28, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   20 18
  AMP PEAK  3(2P24.3) WILD-TYPE 51 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     20   18
  AMP PEAK  3(2P24.3) WILD-TYPE   51   56
         clus
vv        AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  ABSENT                           20                            51
  PRESENT                          18                            56
[1] 2 2
[1] FALSE
D3V29, continuous
D3V30, continuous
D3V31, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   11 29
  AMP PEAK  3(2P24.3) WILD-TYPE 38 88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     11   29
  AMP PEAK  3(2P24.3) WILD-TYPE   38   88
                                          clus
vv                                         AMP PEAK  3(2P24.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          29
                                          clus
vv                                         AMP PEAK  3(2P24.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            88
[1] 2 2
[1] FALSE
D3V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  3(2P24.3) MUTATED              6          18         24
  AMP PEAK  3(2P24.3) WILD-TYPE            9          36         61
D3V33, multiclass
              clus
vv             AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  CURRENT USER                           6                             9
  FORMER USER                           18                            36
  NEVER USED                            24                            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"
D3V34, continuous
D3V35, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   22  6
  AMP PEAK  3(2P24.3) WILD-TYPE 70 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     22    6
  AMP PEAK  3(2P24.3) WILD-TYPE   70   12
         clus
vv        AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  ABSENT                           22                            70
  PRESENT                           6                            12
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  3(2P24.3) MUTATED             2        28     1
  AMP PEAK  3(2P24.3) WILD-TYPE           3        72     1
D3V36, multiclass
             clus
vv            AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  CARBOPLATIN                           2                             3
  CISPLATIN                            28                            72
  OTHER                                 1                             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"
D3V37, continuous
D3V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  3(2P24.3) MUTATED         0        0         0         0        5
  AMP PEAK  3(2P24.3) WILD-TYPE       5        1         1         1       29
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  3(2P24.3) MUTATED          24         8        2         3
  AMP PEAK  3(2P24.3) WILD-TYPE        53        29        2         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  3(2P24.3) MUTATED            3          1        15         0
  AMP PEAK  3(2P24.3) WILD-TYPE          2          6        29         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  3(2P24.3) MUTATED            1         10         0         3
  AMP PEAK  3(2P24.3) WILD-TYPE          2         32         7         9
D3V39, multiclass
            clus
vv           AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             5                            29
  STAGE IB1                           24                            53
  STAGE IB2                            8                            29
  STAGE II                             2                             2
  STAGE IIA                            3                             5
  STAGE IIA1                           3                             2
  STAGE IIA2                           1                             6
  STAGE IIB                           15                            29
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          10                            32
  STAGE IVA                            0                             7
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(2Q33.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2Q33.1) MUTATED    29  11
  AMP PEAK  4(2Q33.1) WILD-TYPE 185  57
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                           40                           242 
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                           11                            57 
$`AMP PEAK  4(2Q33.1) MUTATED`
TCGA-EK-A2GZ TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LY 
       12.59        57.04        31.40        35.61         0.46        78.35 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CK TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A8XH 
       33.24        52.01       134.33       131.11         2.73        45.83 
TCGA-C5-A8XK TCGA-DG-A2KJ TCGA-DS-A7WI TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5ZF 
       99.91        95.11         8.28        31.73        26.01        27.22 
TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RM 
       24.00        60.72        26.27        19.27         0.59         1.64 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-HG-A9SC TCGA-JW-A5VL TCGA-LP-A4AX TCGA-LP-A5U2 
       20.98        14.01        16.57        15.58        12.49         0.30 
TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8QF 
       22.62        11.67        93.99        10.03        23.97        59.18 
TCGA-VS-A959 TCGA-VS-A9UD TCGA-VS-A9UO TCGA-ZJ-A8QQ 
       51.32        24.30        47.87        67.59 

$`AMP PEAK  4(2Q33.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 
      146.86        14.70         8.32         1.48         4.34         0.69 
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
        5.46        19.86        67.46        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       57.73        53.16        38.99         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ 
        3.58        44.22        73.18        73.45        83.05       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       38.43        18.02        17.85        20.42       210.67       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       155.77 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ 
       94.95         9.34        13.61        50.99         8.35        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52        20.81        20.91        14.73         1.12        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18        17.52 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S 
       13.05        25.02        36.89        26.40        24.56        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK 
       27.25        13.48         0.36         6.64         1.51         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL 
        4.24         0.07         1.87         1.74         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.33         0.07         0.10         0.49         0.89        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        7.92        15.22        19.79        15.55        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
       19.04        16.11        31.36        36.26        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        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       129.37        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       20.91        11.28         0.89         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       20.28        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       28.08        34.62        19.96        54.81        35.05        20.84 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       17.23         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
       19.59        14.60        12.16        69.50        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       32.42        19.96        65.49        32.15        53.59        36.13 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       27.12        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       16.24        15.42        26.01        29.26        19.13         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                         0.30                          0.07 
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                       134.33                        210.67 
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                        26.14                         20.91 
[1] "0.3 - 134.3 (26.1)" "0.1 - 210.7 (20.9)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(2Q33.1) MUTATED    16   8   3   0
  AMP PEAK  4(2Q33.1) WILD-TYPE 119  62  18   8
D4V3, multiclass
    clus
vv   AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  T1                          16                           119
  T2                           8                            62
  T3                           3                            18
  T4                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED    11  10
  AMP PEAK  4(2Q33.1) WILD-TYPE 118  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED     11   10
  AMP PEAK  4(2Q33.1) WILD-TYPE  118   46
   clus
vv  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  0                          11                           118
  1                          10                            46
[1] 2 2
[1] FALSE
D4V5, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q33.1) MUTATED   14  1
  AMP PEAK  4(2Q33.1) WILD-TYPE 94  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED     14    1
  AMP PEAK  4(2Q33.1) WILD-TYPE   94    9
   clus
vv  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  0                          14                            94
  1                           1                             9
[1] 2 2
[1] FALSE
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED     6  18
  AMP PEAK  4(2Q33.1) WILD-TYPE  47 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED      6   18
  AMP PEAK  4(2Q33.1) WILD-TYPE   47  107
     clus
vv    AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  NO                            6                            47
  YES                          18                           107
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(2Q33.1) MUTATED               2                               32
  AMP PEAK  4(2Q33.1) WILD-TYPE             4                              210
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  4(2Q33.1) MUTATED                                               1
  AMP PEAK  4(2Q33.1) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  4(2Q33.1) MUTATED                                     4
  AMP PEAK  4(2Q33.1) WILD-TYPE                                  17
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  4(2Q33.1) MUTATED                                           0
  AMP PEAK  4(2Q33.1) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  4(2Q33.1) MUTATED                                              2
  AMP PEAK  4(2Q33.1) WILD-TYPE                                           15
D4V7, multiclass
                                               clus
vv                                              AMP PEAK  4(2Q33.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       32
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              AMP PEAK  4(2Q33.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        210
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(2Q33.1) MUTATED                                  2     5
  AMP PEAK  4(2Q33.1) WILD-TYPE                                6    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(2Q33.1) MUTATED                           2
  AMP PEAK  4(2Q33.1) WILD-TYPE                        26
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(2Q33.1) MUTATED                                           0    29
  AMP PEAK  4(2Q33.1) WILD-TYPE                                         2   173
D4V10, multiclass
                                           clus
vv                                          AMP PEAK  4(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              29
                                           clus
vv                                          AMP PEAK  4(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               173
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED     2  22
  AMP PEAK  4(2Q33.1) WILD-TYPE  21 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED      2   22
  AMP PEAK  4(2Q33.1) WILD-TYPE   21  141
                        clus
vv                       AMP PEAK  4(2Q33.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       AMP PEAK  4(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           141
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED    28  10
  AMP PEAK  4(2Q33.1) WILD-TYPE 165  66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED     28   10
  AMP PEAK  4(2Q33.1) WILD-TYPE  165   66
            clus
vv           AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  TUMOR FREE                          28                           165
  WITH TUMOR                          10                            66
[1] 2 2
[1] FALSE
                               vv
clus                             G1  G2  G3  G4  GX
  AMP PEAK  4(2Q33.1) MUTATED     1  20  16   0   3
  AMP PEAK  4(2Q33.1) WILD-TYPE  17 109  99   1  21
D4V14, multiclass
    clus
vv   AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  G1                           1                            17
  G2                          20                           109
  G3                          16                            99
  G4                           0                             1
  GX                           3                            21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, continuous
D4V16, continuous
D4V17, continuous
D4V18, continuous
D4V19, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q33.1) MUTATED    4  1
  AMP PEAK  4(2Q33.1) WILD-TYPE 21  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED      4    1
  AMP PEAK  4(2Q33.1) WILD-TYPE   21    2
                         clus
vv                        AMP PEAK  4(2Q33.1) MUTATED
  COMPLETED AS PLANNED                              4
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        AMP PEAK  4(2Q33.1) WILD-TYPE
  COMPLETED AS PLANNED                               21
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
D4V20, continuous
D4V21, continuous
D4V22, continuous
D4V23, continuous
D4V24, continuous
D4V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  4(2Q33.1) MUTATED                                     0
  AMP PEAK  4(2Q33.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  4(2Q33.1) MUTATED                                     0
  AMP PEAK  4(2Q33.1) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  4(2Q33.1) MUTATED                         4                       0
  AMP PEAK  4(2Q33.1) WILD-TYPE                      32                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  4(2Q33.1) MUTATED                         0
  AMP PEAK  4(2Q33.1) WILD-TYPE                      10
D4V26, multiclass
                                     clus
vv                                    AMP PEAK  4(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  4(2Q33.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        32
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                        10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  4(2Q33.1) MUTATED                                               0
  AMP PEAK  4(2Q33.1) WILD-TYPE                                             3
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  4(2Q33.1) MUTATED                                                5
  AMP PEAK  4(2Q33.1) WILD-TYPE                                             20
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  4(2Q33.1) MUTATED                                                                                   9
  AMP PEAK  4(2Q33.1) WILD-TYPE                                                                                73
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  4(2Q33.1) MUTATED                                                                                             18
  AMP PEAK  4(2Q33.1) WILD-TYPE                                                                                          103
D4V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  4(2Q33.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          18
                                                                                              clus
vv                                                                                             AMP PEAK  4(2Q33.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       73
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V28, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q33.1) MUTATED    5 14
  AMP PEAK  4(2Q33.1) WILD-TYPE 66 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED      5   14
  AMP PEAK  4(2Q33.1) WILD-TYPE   66   60
         clus
vv        AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  ABSENT                            5                            66
  PRESENT                          14                            60
[1] 2 2
[1] FALSE
D4V29, continuous
D4V30, continuous
D4V31, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED     7  13
  AMP PEAK  4(2Q33.1) WILD-TYPE  42 104
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED      7   13
  AMP PEAK  4(2Q33.1) WILD-TYPE   42  104
                                          clus
vv                                         AMP PEAK  4(2Q33.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          13
                                          clus
vv                                         AMP PEAK  4(2Q33.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           104
[1] 2 2
[1] FALSE
D4V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  4(2Q33.1) MUTATED              0           9          9
  AMP PEAK  4(2Q33.1) WILD-TYPE           15          45         76
D4V33, multiclass
              clus
vv             AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  CURRENT USER                           0                            15
  FORMER USER                            9                            45
  NEVER USED                             9                            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"
D4V34, continuous
D4V35, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q33.1) MUTATED    9  3
  AMP PEAK  4(2Q33.1) WILD-TYPE 83 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED      9    3
  AMP PEAK  4(2Q33.1) WILD-TYPE   83   15
         clus
vv        AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  ABSENT                            9                            83
  PRESENT                           3                            15
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  4(2Q33.1) MUTATED             0        18     1
  AMP PEAK  4(2Q33.1) WILD-TYPE           5        82     1
D4V36, multiclass
             clus
vv            AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  CARBOPLATIN                           0                             5
  CISPLATIN                            18                            82
  OTHER                                 1                             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"
D4V37, continuous
D4V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  4(2Q33.1) MUTATED         0        0         0         0        3
  AMP PEAK  4(2Q33.1) WILD-TYPE       5        1         1         1       31
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  4(2Q33.1) MUTATED          11         3        0         1
  AMP PEAK  4(2Q33.1) WILD-TYPE        66        34        4         7
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  4(2Q33.1) MUTATED            1          1        10         0
  AMP PEAK  4(2Q33.1) WILD-TYPE          4          6        34         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  4(2Q33.1) MUTATED            1          8         1         0
  AMP PEAK  4(2Q33.1) WILD-TYPE          2         34         6        12
D4V39, multiclass
            clus
vv           AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             3                            31
  STAGE IB1                           11                            66
  STAGE IB2                            3                            34
  STAGE II                             0                             4
  STAGE IIA                            1                             7
  STAGE IIA1                           1                             4
  STAGE IIA2                           1                             6
  STAGE IIB                           10                            34
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                           8                            34
  STAGE IVA                            1                             6
  STAGE IVB                            0                            12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(3Q26.31) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(3Q26.31) MUTATED   163  54
  AMP PEAK  5(3Q26.31) WILD-TYPE  51  14
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                           217                             65 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                            54                             14 
$`AMP PEAK  5(3Q26.31) MUTATED`
TCGA-EK-A2GZ TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-BI-A0VR 
       12.59         8.32         1.48         0.69        17.82        49.48 
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        23.67        11.44        68.84        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29        82.85         5.46        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-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-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       33.24        18.02        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48        20.35       147.35       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       94.95         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        8.35        23.51        20.91         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        63.98        87.75        36.76        55.63       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
      118.65        22.98        16.83        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       40.87        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       24.56        31.73        12.13         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N 
       25.91        27.29        27.25        27.22        13.48         0.36 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         1.51        19.27         0.43         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A1H5 
       47.77         1.64         2.33         0.07         0.89        20.35 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ 
       15.22        19.79        23.84        20.98        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       14.01        10.55        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LH 
       20.78        14.93         9.44       137.16       129.37        78.71 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
       81.96        36.36        21.44        20.48        15.58         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       18.15       209.59        44.61        20.91        11.28         0.89 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z 
        0.30         0.82        13.35        22.52        20.28        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        9.17         8.52        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       35.05        20.84        17.23         2.96        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R 
       15.95         9.04        17.56        14.07         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       22.62        19.59        14.60        11.67        93.99        12.16 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        46.52        45.57        32.42        23.97        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       65.49        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       15.68        56.35        55.50        51.32        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       48.39        28.50        29.95        27.12        24.30        46.92 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
       45.11        14.53        27.25        47.87        47.47        41.52 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       18.25        15.42        26.01        29.26        19.13         1.41 
TCGA-ZJ-AAXU 
        0.16 

$`AMP PEAK  5(3Q26.31) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-C5-A1BF TCGA-C5-A1BQ 
      146.86        14.70         4.34        17.52        18.74        19.86 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7UC TCGA-C5-A8XK TCGA-C5-A8YR 
       38.43        52.01       210.67        17.19        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A907 TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 
       20.81        14.73        58.88        16.18        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP 
       26.40        26.01        24.82        24.00        60.72         6.64 
TCGA-EK-A2PK TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.39         1.87         1.74         0.43         0.10         0.49 
TCGA-EX-A1H6 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        7.92        15.55        12.23        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-FU-A770 TCGA-IR-A3L7 TCGA-IR-A3LB 
       36.26        26.14        35.44         1.12       147.39        66.81 
TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A69B 
       96.95        29.85        27.42         3.29        24.56        28.37 
TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-Q1-A6DV TCGA-Q1-A73P 
       21.11        12.49        17.82        11.38        16.14        15.88 
TCGA-UC-A7PI TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A958 TCGA-VS-A9UJ TCGA-VS-A9UR 
       69.50        39.78        58.45        50.14         1.71        26.07 
TCGA-VS-A9UT TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-ZJ-A8QQ TCGA-ZX-AA5X 
       15.85        17.75        16.24        67.59         3.91 

  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                        209.59                         210.67 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                         22.98                          20.81 
[1] "0.1 - 209.6 (23.0)" "0.1 - 210.7 (20.8)"
[1] "hr=" "1"  
D5V2, continuous
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  5(3Q26.31) MUTATED   99 54 19  5
  AMP PEAK  5(3Q26.31) WILD-TYPE 36 16  2  3
D5V3, multiclass
    clus
vv   AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  T1                           99                             36
  T2                           54                             16
  T3                           19                              2
  T4                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   91 48
  AMP PEAK  5(3Q26.31) WILD-TYPE 38  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     91   48
  AMP PEAK  5(3Q26.31) WILD-TYPE   38    8
   clus
vv  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  0                           91                             38
  1                           48                              8
[1] 2 2
[1] FALSE
D5V5, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   84  8
  AMP PEAK  5(3Q26.31) WILD-TYPE 24  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     84    8
  AMP PEAK  5(3Q26.31) WILD-TYPE   24    2
   clus
vv  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  0                           84                             24
  1                            8                              2
[1] 2 2
[1] FALSE
D5V6, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED    37 104
  AMP PEAK  5(3Q26.31) WILD-TYPE  16  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     37  104
  AMP PEAK  5(3Q26.31) WILD-TYPE   16   21
     clus
vv    AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  NO                            37                             16
  YES                          104                             21
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(3Q26.31) MUTATED               4                              196
  AMP PEAK  5(3Q26.31) WILD-TYPE             2                               46
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  5(3Q26.31) MUTATED                                               4
  AMP PEAK  5(3Q26.31) WILD-TYPE                                             2
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  5(3Q26.31) MUTATED                                    11
  AMP PEAK  5(3Q26.31) WILD-TYPE                                  10
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  5(3Q26.31) MUTATED                                           2
  AMP PEAK  5(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  5(3Q26.31) MUTATED                                             10
  AMP PEAK  5(3Q26.31) WILD-TYPE                                            7
D5V7, multiclass
                                               clus
vv                                              AMP PEAK  5(3Q26.31) MUTATED
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       196
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            10
                                               clus
vv                                              AMP PEAK  5(3Q26.31) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          46
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(3Q26.31) MUTATED                                  5    15
  AMP PEAK  5(3Q26.31) WILD-TYPE                                3     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(3Q26.31) MUTATED                          27
  AMP PEAK  5(3Q26.31) WILD-TYPE                         1
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  5(3Q26.31) MUTATED                                           1
  AMP PEAK  5(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK  5(3Q26.31) MUTATED     146
  AMP PEAK  5(3Q26.31) WILD-TYPE    56
D5V10, multiclass
                                           clus
vv                                          AMP PEAK  5(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                           27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              146
                                           clus
vv                                          AMP PEAK  5(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                  4
  BLACK OR AFRICAN AMERICAN                                              1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED    16 125
  AMP PEAK  5(3Q26.31) WILD-TYPE   7  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     16  125
  AMP PEAK  5(3Q26.31) WILD-TYPE    7   38
                        clus
vv                       AMP PEAK  5(3Q26.31) MUTATED
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          125
                        clus
vv                       AMP PEAK  5(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             38
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED   147  60
  AMP PEAK  5(3Q26.31) WILD-TYPE  46  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED    147   60
  AMP PEAK  5(3Q26.31) WILD-TYPE   46   16
            clus
vv           AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  TUMOR FREE                          147                             46
  WITH TUMOR                           60                             16
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK  5(3Q26.31) MUTATED    13 101  86   1  20
  AMP PEAK  5(3Q26.31) WILD-TYPE   5  28  29   0   4
D5V14, multiclass
    clus
vv   AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  G1                           13                              5
  G2                          101                             28
  G3                           86                             29
  G4                            1                              0
  GX                           20                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, continuous
D5V16, continuous
D5V17, continuous
D5V18, continuous
D5V19, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   22  2
  AMP PEAK  5(3Q26.31) WILD-TYPE  3  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     22    2
  AMP PEAK  5(3Q26.31) WILD-TYPE    3    1
                         clus
vv                        AMP PEAK  5(3Q26.31) MUTATED
  COMPLETED AS PLANNED                              22
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        AMP PEAK  5(3Q26.31) WILD-TYPE
  COMPLETED AS PLANNED                                 3
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
D5V20, continuous
D5V21, continuous
D5V22, continuous
D5V23, continuous
D5V24, continuous
D5V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  5(3Q26.31) MUTATED                                     0
  AMP PEAK  5(3Q26.31) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  5(3Q26.31) MUTATED                                     6
  AMP PEAK  5(3Q26.31) WILD-TYPE                                   1
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  5(3Q26.31) MUTATED                        31
  AMP PEAK  5(3Q26.31) WILD-TYPE                       5
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK  5(3Q26.31) MUTATED                         1
  AMP PEAK  5(3Q26.31) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK  5(3Q26.31) MUTATED                         8
  AMP PEAK  5(3Q26.31) WILD-TYPE                       2
D5V26, multiclass
                                     clus
vv                                    AMP PEAK  5(3Q26.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            6
  OTHER LOCATION, SPECIFY                                       31
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        8
                                     clus
vv                                    AMP PEAK  5(3Q26.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  OTHER LOCATION, SPECIFY                                          5
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  5(3Q26.31) MUTATED                                               2
  AMP PEAK  5(3Q26.31) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  5(3Q26.31) MUTATED                                               21
  AMP PEAK  5(3Q26.31) WILD-TYPE                                              4
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  5(3Q26.31) MUTATED                                                                                  67
  AMP PEAK  5(3Q26.31) WILD-TYPE                                                                                15
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  5(3Q26.31) MUTATED                                                                                             91
  AMP PEAK  5(3Q26.31) WILD-TYPE                                                                                           30
D5V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  5(3Q26.31) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           91
                                                                                              clus
vv                                                                                             AMP PEAK  5(3Q26.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V28, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   50 59
  AMP PEAK  5(3Q26.31) WILD-TYPE 21 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     50   59
  AMP PEAK  5(3Q26.31) WILD-TYPE   21   15
         clus
vv        AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  ABSENT                            50                             21
  PRESENT                           59                             15
[1] 2 2
[1] FALSE
D5V29, continuous
D5V30, continuous
D5V31, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   39 89
  AMP PEAK  5(3Q26.31) WILD-TYPE 10 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     39   89
  AMP PEAK  5(3Q26.31) WILD-TYPE   10   28
                                          clus
vv                                         AMP PEAK  5(3Q26.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           89
                                          clus
vv                                         AMP PEAK  5(3Q26.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             28
[1] 2 2
[1] FALSE
D5V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  5(3Q26.31) MUTATED             11          40         64
  AMP PEAK  5(3Q26.31) WILD-TYPE            4          14         21
D5V33, multiclass
              clus
vv             AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  CURRENT USER                           11                              4
  FORMER USER                            40                             14
  NEVER USED                             64                             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"
D5V34, continuous
D5V35, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   69 14
  AMP PEAK  5(3Q26.31) WILD-TYPE 23  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     69   14
  AMP PEAK  5(3Q26.31) WILD-TYPE   23    4
         clus
vv        AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  ABSENT                            69                             23
  PRESENT                           14                              4
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  5(3Q26.31) MUTATED             2        83     1
  AMP PEAK  5(3Q26.31) WILD-TYPE           3        17     1
D5V36, multiclass
             clus
vv            AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  CARBOPLATIN                            2                              3
  CISPLATIN                             83                             17
  OTHER                                  1                              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"
D5V37, continuous
[1] "Remove cluster labels:"         "AMP PEAK  5(3Q26.31) WILD-TYPE"
clus
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                            16                              1 
                  TCGA-C5-A1BN                   TCGA-C5-A1MH 
"AMP PEAK  5(3Q26.31) MUTATED" "AMP PEAK  5(3Q26.31) MUTATED" 
                  TCGA-C5-A1ML                   TCGA-C5-A1MN 
"AMP PEAK  5(3Q26.31) MUTATED" "AMP PEAK  5(3Q26.31) MUTATED" 
                  TCGA-C5-A1MP                   TCGA-EK-A2RO 
"AMP PEAK  5(3Q26.31) MUTATED" "AMP PEAK  5(3Q26.31) MUTATED" 
                  TCGA-GH-A9DA                   TCGA-HM-A3JK 
"AMP PEAK  5(3Q26.31) MUTATED" "AMP PEAK  5(3Q26.31) MUTATED" 
                  TCGA-JW-A852                   TCGA-JX-A3Q8 
"AMP PEAK  5(3Q26.31) MUTATED" "AMP PEAK  5(3Q26.31) MUTATED" 
                  TCGA-MA-AA3W                   TCGA-MA-AA3Z 
"AMP PEAK  5(3Q26.31) MUTATED" "AMP PEAK  5(3Q26.31) MUTATED" 
                  TCGA-MA-AA42                   TCGA-MU-A51Y 
"AMP PEAK  5(3Q26.31) MUTATED" "AMP PEAK  5(3Q26.31) MUTATED" 
                  TCGA-MU-A8JM                   TCGA-MY-A913 
"AMP PEAK  5(3Q26.31) MUTATED" "AMP PEAK  5(3Q26.31) MUTATED" 
D5V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  5(3Q26.31) MUTATED         5        1         1         0       25
  AMP PEAK  5(3Q26.31) WILD-TYPE       0        0         0         1        9
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  5(3Q26.31) MUTATED          57        27        4         5
  AMP PEAK  5(3Q26.31) WILD-TYPE        20        10        0         3
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  5(3Q26.31) MUTATED            5          5        35         1
  AMP PEAK  5(3Q26.31) WILD-TYPE          0          2         9         0
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  5(3Q26.31) MUTATED            3         33         6         9
  AMP PEAK  5(3Q26.31) WILD-TYPE          0          9         1         3
D5V39, multiclass
            clus
vv           AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  STAGE I                               5                              0
  STAGE IA                              1                              0
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                             25                              9
  STAGE IB1                            57                             20
  STAGE IB2                            27                             10
  STAGE II                              4                              0
  STAGE IIA                             5                              3
  STAGE IIA1                            5                              0
  STAGE IIA2                            5                              2
  STAGE IIB                            35                              9
  STAGE III                             1                              0
  STAGE IIIA                            3                              0
  STAGE IIIB                           33                              9
  STAGE IVA                             6                              1
  STAGE IVB                             9                              3
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(4Q12) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  6(4Q12) MUTATED    17   2
  AMP PEAK  6(4Q12) WILD-TYPE 197  66
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         19                         263 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                          2                          66 
$`AMP PEAK  6(4Q12) MUTATED`
TCGA-EK-A2GZ TCGA-ZJ-AAX4 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MN TCGA-C5-A1MP 
       12.59         0.69        35.01        53.16        40.93         3.58 
TCGA-C5-A8XI TCGA-C5-A907 TCGA-DS-A3LQ TCGA-EK-A2PI TCGA-EK-A3GK TCGA-FU-A23K 
        8.35        14.73        22.98        19.27         0.49        12.23 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JX-A3Q8 TCGA-MA-AA41 TCGA-MY-A5BF TCGA-VS-A8EC 
       96.95        78.71        44.61         9.17        20.84        46.52 
TCGA-VS-A950 
       40.14 

$`AMP PEAK  6(4Q12) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY 
      146.86        14.70         8.32         1.48         4.34        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.82        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       57.73        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ 
       13.61         2.73        50.99        45.83        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       27.52        20.81        20.91         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
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 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.13        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK 
        0.36        60.72        26.27         6.64         1.51         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.89         1.45         0.13        40.96 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK 
        0.30         4.24         0.07         1.87         1.74         0.43 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
       47.77         1.64         2.33         0.07         0.10         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L 
       20.35         7.92        15.22        19.79        15.55        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI 
        9.44       147.39       137.16        66.81       129.37        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
      209.59        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        20.28        17.82        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       35.05        17.23         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       12.16        69.50        10.03        45.57        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       19.96        65.49        32.15        53.59        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       59.18        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       33.37        58.45        15.68        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       27.12        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       18.25        17.75        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                       0.49                        0.07 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                      96.95                      210.67 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                      20.84                       22.62 
[1] "0.5 - 97.0 (20.8)"  "0.1 - 210.7 (22.6)"
[1] "hr=" "2.2"
D6V2, continuous
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  6(4Q12) MUTATED     7   4   5   0
  AMP PEAK  6(4Q12) WILD-TYPE 128  66  16   8
D6V3, multiclass
    clus
vv   AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  T1                         7                         128
  T2                         4                          66
  T3                         5                          16
  T4                         0                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                             cls
clus                            0   1
  AMP PEAK  6(4Q12) MUTATED     8   6
  AMP PEAK  6(4Q12) WILD-TYPE 121  50
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      8    6
  AMP PEAK  6(4Q12) WILD-TYPE  121   50
   clus
vv  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  0                         8                         121
  1                         6                          50
[1] 2 2
[1] FALSE
D6V5, binary
                             cls
clus                            0   1
  AMP PEAK  6(4Q12) MUTATED     7   1
  AMP PEAK  6(4Q12) WILD-TYPE 101   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      7    1
  AMP PEAK  6(4Q12) WILD-TYPE  101    9
   clus
vv  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  0                         7                         101
  1                         1                           9
[1] 2 2
[1] FALSE
D6V6, binary
                             cls
clus                            0   1
  AMP PEAK  6(4Q12) MUTATED     3   8
  AMP PEAK  6(4Q12) WILD-TYPE  50 117
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      3    8
  AMP PEAK  6(4Q12) WILD-TYPE   50  117
     clus
vv    AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  NO                          3                          50
  YES                         8                         117
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(4Q12) MUTATED               0                               17
  AMP PEAK  6(4Q12) WILD-TYPE             6                              225
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  6(4Q12) MUTATED                                               1
  AMP PEAK  6(4Q12) WILD-TYPE                                             5
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  6(4Q12) MUTATED                                     3
  AMP PEAK  6(4Q12) WILD-TYPE                                  18
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  6(4Q12) MUTATED                                           0
  AMP PEAK  6(4Q12) WILD-TYPE                                         3
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  6(4Q12) MUTATED                                              0
  AMP PEAK  6(4Q12) WILD-TYPE                                           17
D6V7, multiclass
                                               clus
vv                                              AMP PEAK  6(4Q12) MUTATED
  ADENOSQUAMOUS                                                         0
  CERVICAL SQUAMOUS CELL CARCINOMA                                     17
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          0
                                               clus
vv                                              AMP PEAK  6(4Q12) WILD-TYPE
  ADENOSQUAMOUS                                                           6
  CERVICAL SQUAMOUS CELL CARCINOMA                                      225
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(4Q12) MUTATED                                  0     1
  AMP PEAK  6(4Q12) WILD-TYPE                                8    18
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(4Q12) MUTATED                           4
  AMP PEAK  6(4Q12) WILD-TYPE                        24
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(4Q12) MUTATED                                           0    12
  AMP PEAK  6(4Q12) WILD-TYPE                                         2   190
D6V10, multiclass
                                           clus
vv                                          AMP PEAK  6(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  0
  ASIAN                                                             1
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            12
                                           clus
vv                                          AMP PEAK  6(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    8
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                          24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                             190
[1] 5 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(4Q12) MUTATED     1  10
  AMP PEAK  6(4Q12) WILD-TYPE  22 153
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      1   10
  AMP PEAK  6(4Q12) WILD-TYPE   22  153
                        clus
vv                       AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                          22
  NOT HISPANIC OR LATINO                        10                         153
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                             cls
clus                            0   1
  AMP PEAK  6(4Q12) MUTATED    13   5
  AMP PEAK  6(4Q12) WILD-TYPE 180  71
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED     13    5
  AMP PEAK  6(4Q12) WILD-TYPE  180   71
            clus
vv           AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  TUMOR FREE                        13                         180
  WITH TUMOR                         5                          71
[1] 2 2
[1] FALSE
                             vv
clus                           G1  G2  G3  G4  GX
  AMP PEAK  6(4Q12) MUTATED     1   8   9   1   0
  AMP PEAK  6(4Q12) WILD-TYPE  17 121 106   0  24
D6V14, multiclass
    clus
vv   AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  G1                         1                          17
  G2                         8                         121
  G3                         9                         106
  G4                         1                           0
  GX                         0                          24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, continuous
D6V16, continuous
D6V17, continuous
D6V18, continuous
D6V19, binary
                             cls
clus                           0  1
  AMP PEAK  6(4Q12) MUTATED    4  0
  AMP PEAK  6(4Q12) WILD-TYPE 21  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      4    0
  AMP PEAK  6(4Q12) WILD-TYPE   21    3
                         clus
vv                        AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  COMPLETED AS PLANNED                            4                          21
  TREATMENT NOT COMPLETED                         0                           3
[1] 2 2
[1] FALSE
D6V20, continuous
D6V21, continuous
D6V22, continuous
D6V23, continuous
D6V24, continuous
D6V25, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  6(4Q12) MUTATED                                     0
  AMP PEAK  6(4Q12) WILD-TYPE                                   2
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  6(4Q12) MUTATED                                     0
  AMP PEAK  6(4Q12) WILD-TYPE                                   7
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  6(4Q12) MUTATED                         5                       0
  AMP PEAK  6(4Q12) WILD-TYPE                      31                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  6(4Q12) MUTATED                         2
  AMP PEAK  6(4Q12) WILD-TYPE                       8
D6V26, multiclass
                                     clus
vv                                    AMP PEAK  6(4Q12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  OTHER LOCATION, SPECIFY                                     5
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     2
                                     clus
vv                                    AMP PEAK  6(4Q12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           7
  OTHER LOCATION, SPECIFY                                      31
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  6(4Q12) MUTATED                                               0
  AMP PEAK  6(4Q12) WILD-TYPE                                             3
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  6(4Q12) MUTATED                                                1
  AMP PEAK  6(4Q12) WILD-TYPE                                             24
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  6(4Q12) MUTATED                                                                                   4
  AMP PEAK  6(4Q12) WILD-TYPE                                                                                78
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  6(4Q12) MUTATED                                                                                             10
  AMP PEAK  6(4Q12) WILD-TYPE                                                                                          111
D6V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  6(4Q12) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        10
                                                                                              clus
vv                                                                                             AMP PEAK  6(4Q12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     78
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V28, binary
                             cls
clus                           0  1
  AMP PEAK  6(4Q12) MUTATED    3  8
  AMP PEAK  6(4Q12) WILD-TYPE 68 66
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      3    8
  AMP PEAK  6(4Q12) WILD-TYPE   68   66
         clus
vv        AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  ABSENT                          3                          68
  PRESENT                         8                          66
[1] 2 2
[1] FALSE
D6V29, continuous
D6V30, continuous
D6V31, binary
                             cls
clus                            0   1
  AMP PEAK  6(4Q12) MUTATED     2   8
  AMP PEAK  6(4Q12) WILD-TYPE  47 109
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      2    8
  AMP PEAK  6(4Q12) WILD-TYPE   47  109
                                          clus
vv                                         AMP PEAK  6(4Q12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         8
                                          clus
vv                                         AMP PEAK  6(4Q12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              47
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         109
[1] 2 2
[1] FALSE
D6V32, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  6(4Q12) MUTATED              1           8          3
  AMP PEAK  6(4Q12) WILD-TYPE           14          46         82
D6V33, multiclass
              clus
vv             AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  CURRENT USER                         1                          14
  FORMER USER                          8                          46
  NEVER USED                           3                          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"
D6V34, continuous
D6V35, binary
                             cls
clus                           0  1
  AMP PEAK  6(4Q12) MUTATED    6  0
  AMP PEAK  6(4Q12) WILD-TYPE 86 18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      6    0
  AMP PEAK  6(4Q12) WILD-TYPE   86   18
         clus
vv        AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  ABSENT                          6                          86
  PRESENT                         0                          18
[1] 2 2
[1] FALSE
                             vv
clus                          CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  6(4Q12) MUTATED             0         5     0
  AMP PEAK  6(4Q12) WILD-TYPE           5        95     2
D6V36, multiclass
             clus
vv            AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  CARBOPLATIN                         0                           5
  CISPLATIN                           5                          95
  OTHER                               0                           2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V37, continuous
D6V38, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  6(4Q12) MUTATED         0        0         0         0        0
  AMP PEAK  6(4Q12) WILD-TYPE       5        1         1         1       34
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK  6(4Q12) MUTATED           4         4        1         0          1
  AMP PEAK  6(4Q12) WILD-TYPE        73        33        3         8          4
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  AMP PEAK  6(4Q12) MUTATED            1         1         0          1
  AMP PEAK  6(4Q12) WILD-TYPE          6        43         1          2
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  6(4Q12) MUTATED            7         0         0
  AMP PEAK  6(4Q12) WILD-TYPE         35         7        12
D6V39, multiclass
            clus
vv           AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  STAGE I                            0                           5
  STAGE IA                           0                           1
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           0                          34
  STAGE IB1                          4                          73
  STAGE IB2                          4                          33
  STAGE II                           1                           3
  STAGE IIA                          0                           8
  STAGE IIA1                         1                           4
  STAGE IIA2                         1                           6
  STAGE IIB                          1                          43
  STAGE III                          0                           1
  STAGE IIIA                         1                           2
  STAGE IIIB                         7                          35
  STAGE IVA                          0                           7
  STAGE IVB                          0                          12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(5P15.33) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(5P15.33) MUTATED    98  30
  AMP PEAK  7(5P15.33) WILD-TYPE 116  38
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           128                            154 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                            30                             38 
$`AMP PEAK  7(5P15.33) MUTATED`
TCGA-C5-A8XJ TCGA-VS-A9V4 TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN 
      146.86         4.34        17.82        49.48        57.04        11.44 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME 
      144.16       173.29        19.86        31.40        46.32        57.73 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A2M1 
       20.91        40.93         3.58        73.18       100.14        38.43 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
       52.01        18.02        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      155.77       131.11         9.34         2.73        50.99        45.83 
TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL 
       99.91        27.52        14.73         1.12        95.11        44.94 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3Y4 
       55.63       117.99        22.98        39.55        30.90        36.89 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A78R 
       31.73        26.01        14.89        25.91        27.22        13.48 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       60.72         1.51        19.27         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RN 
        0.89        40.96         1.74         0.43         1.64         2.33 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF 
        0.49         0.89        20.35        15.22        19.79        15.55 
TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA 
       23.84        31.36        20.98        10.55        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       16.57        21.67        78.71        29.85        36.36        27.42 
TCGA-JW-A5VI TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U3 
       24.56         8.28        18.15        20.91         0.89         0.82 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 
       22.52        20.28        17.82        19.56         8.52        11.38 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       35.05         2.96        16.41        15.95         9.04        17.56 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI 
       11.67        12.16        69.50        10.03        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y 
       19.96        65.49        11.51        59.18        16.64         4.73 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA 
       40.14        15.68        50.14        51.32        50.47        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL 
       29.95        27.12        24.30        46.92        45.11        14.53 
TCGA-VS-A9UP TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       47.47        18.25        18.84        26.01        29.26        67.59 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        1.41         0.16 

$`AMP PEAK  7(5P15.33) WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
       12.59        14.70         8.32         1.48         0.69        17.52 
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM 
       23.67        68.84        18.74        36.56       177.04        82.85 
TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH 
        5.46        67.46        30.21        35.01        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       35.61         0.46         2.43        44.22        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       78.35        33.24        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A8XI TCGA-C5-A8YQ 
      101.82       134.33        94.95        13.61         8.35        23.51 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       20.81        20.91        82.06        63.98        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 
       40.87        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       26.40        24.56        12.13        24.82         7.46        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2IP 
       27.29        27.25        24.00         0.36        26.27         6.64 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45         0.13         0.30         4.24         0.07         1.87 
TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A2QG 
       47.77         0.07         0.10         7.92        12.23        19.04 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       16.11        36.26        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       35.44         1.12        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH 
      137.16        66.81       129.37        96.95        81.96         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q0 
       21.44        20.48        15.58        28.37        21.11       209.59 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA41 
       44.61        11.28        12.49         0.30        13.35         9.17 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       28.08        34.62        19.96        54.81        20.84        17.23 
TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       15.58        16.14        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG 
       22.62        19.59        14.60        93.99        46.52        45.57 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       32.15        53.59        36.13        39.78        31.27        40.87 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A9U6 TCGA-VS-A9U7 
       33.37        58.45        56.35        55.50        43.40        48.39 
TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
        1.71        27.25        47.87        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       14.53         3.42        67.20         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       16.24        15.42        19.13         3.91 

  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                          0.16                           0.07 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                        173.29                         210.67 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                        21.325                         23.590 
[1] "0.2 - 173.3 (21.3)" "0.1 - 210.7 (23.6)"
[1] "hr=" "1"  
D7V2, continuous
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  7(5P15.33) MUTATED   56 33 14  3
  AMP PEAK  7(5P15.33) WILD-TYPE 79 37  7  5
D7V3, multiclass
    clus
vv   AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  T1                           56                             79
  T2                           33                             37
  T3                           14                              7
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   54 23
  AMP PEAK  7(5P15.33) WILD-TYPE 75 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     54   23
  AMP PEAK  7(5P15.33) WILD-TYPE   75   33
   clus
vv  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  0                           54                             75
  1                           23                             33
[1] 2 2
[1] FALSE
D7V5, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   56  2
  AMP PEAK  7(5P15.33) WILD-TYPE 52  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     56    2
  AMP PEAK  7(5P15.33) WILD-TYPE   52    8
   clus
vv  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  0                           56                             52
  1                            2                              8
[1] 2 2
[1] FALSE
D7V6, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   21 65
  AMP PEAK  7(5P15.33) WILD-TYPE 32 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     21   65
  AMP PEAK  7(5P15.33) WILD-TYPE   32   60
     clus
vv    AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  NO                            21                             32
  YES                           65                             60
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(5P15.33) MUTATED               2                              124
  AMP PEAK  7(5P15.33) WILD-TYPE             4                              118
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  7(5P15.33) MUTATED                                               2
  AMP PEAK  7(5P15.33) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  7(5P15.33) MUTATED                                     4
  AMP PEAK  7(5P15.33) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  7(5P15.33) MUTATED                                           2
  AMP PEAK  7(5P15.33) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  7(5P15.33) MUTATED                                              4
  AMP PEAK  7(5P15.33) WILD-TYPE                                           13
D7V7, multiclass
                                               clus
vv                                              AMP PEAK  7(5P15.33) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       124
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              AMP PEAK  7(5P15.33) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         118
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(5P15.33) MUTATED                                  3     7
  AMP PEAK  7(5P15.33) WILD-TYPE                                5    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(5P15.33) MUTATED                          14
  AMP PEAK  7(5P15.33) WILD-TYPE                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  7(5P15.33) MUTATED                                           0
  AMP PEAK  7(5P15.33) WILD-TYPE                                         2
                                vv
clus                             WHITE
  AMP PEAK  7(5P15.33) MUTATED      95
  AMP PEAK  7(5P15.33) WILD-TYPE   107
D7V10, multiclass
                                           clus
vv                                          AMP PEAK  7(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               95
                                           clus
vv                                          AMP PEAK  7(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  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"
D7V11, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   13 71
  AMP PEAK  7(5P15.33) WILD-TYPE 10 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     13   71
  AMP PEAK  7(5P15.33) WILD-TYPE   10   92
                        clus
vv                       AMP PEAK  7(5P15.33) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       AMP PEAK  7(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             92
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED    85  36
  AMP PEAK  7(5P15.33) WILD-TYPE 108  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     85   36
  AMP PEAK  7(5P15.33) WILD-TYPE  108   40
            clus
vv           AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  TUMOR FREE                           85                            108
  WITH TUMOR                           36                             40
[1] 2 2
[1] FALSE
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK  7(5P15.33) MUTATED    5 51 63  1 11
  AMP PEAK  7(5P15.33) WILD-TYPE 13 78 52  0 13
D7V14, multiclass
    clus
vv   AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  G1                            5                             13
  G2                           51                             78
  G3                           63                             52
  G4                            1                              0
  GX                           11                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, continuous
D7V16, continuous
D7V17, continuous
D7V18, continuous
D7V19, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   10  2
  AMP PEAK  7(5P15.33) WILD-TYPE 15  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     10    2
  AMP PEAK  7(5P15.33) WILD-TYPE   15    1
                         clus
vv                        AMP PEAK  7(5P15.33) MUTATED
  COMPLETED AS PLANNED                              10
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        AMP PEAK  7(5P15.33) WILD-TYPE
  COMPLETED AS PLANNED                                15
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
D7V20, continuous
D7V21, continuous
D7V22, continuous
D7V23, continuous
D7V24, continuous
D7V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  7(5P15.33) MUTATED                                     0
  AMP PEAK  7(5P15.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  7(5P15.33) MUTATED                                     4
  AMP PEAK  7(5P15.33) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  7(5P15.33) MUTATED                        16
  AMP PEAK  7(5P15.33) WILD-TYPE                      20
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK  7(5P15.33) MUTATED                         0
  AMP PEAK  7(5P15.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK  7(5P15.33) MUTATED                         3
  AMP PEAK  7(5P15.33) WILD-TYPE                       7
D7V26, multiclass
                                     clus
vv                                    AMP PEAK  7(5P15.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                       16
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        3
                                     clus
vv                                    AMP PEAK  7(5P15.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              3
  OTHER LOCATION, SPECIFY                                         20
  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  7(5P15.33) MUTATED                                               1
  AMP PEAK  7(5P15.33) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  7(5P15.33) MUTATED                                                9
  AMP PEAK  7(5P15.33) WILD-TYPE                                             16
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  7(5P15.33) MUTATED                                                                                  36
  AMP PEAK  7(5P15.33) WILD-TYPE                                                                                46
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  7(5P15.33) MUTATED                                                                                             54
  AMP PEAK  7(5P15.33) WILD-TYPE                                                                                           67
D7V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  7(5P15.33) 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)                                      36
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           54
                                                                                              clus
vv                                                                                             AMP PEAK  7(5P15.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        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"
D7V28, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   25 31
  AMP PEAK  7(5P15.33) WILD-TYPE 46 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     25   31
  AMP PEAK  7(5P15.33) WILD-TYPE   46   43
         clus
vv        AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  ABSENT                            25                             46
  PRESENT                           31                             43
[1] 2 2
[1] FALSE
D7V29, continuous
D7V30, continuous
D7V31, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   19 62
  AMP PEAK  7(5P15.33) WILD-TYPE 30 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     19   62
  AMP PEAK  7(5P15.33) WILD-TYPE   30   55
                                          clus
vv                                         AMP PEAK  7(5P15.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           62
                                          clus
vv                                         AMP PEAK  7(5P15.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             55
[1] 2 2
[1] FALSE
D7V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  7(5P15.33) MUTATED              5          23         37
  AMP PEAK  7(5P15.33) WILD-TYPE           10          31         48
D7V33, multiclass
              clus
vv             AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  CURRENT USER                            5                             10
  FORMER USER                            23                             31
  NEVER USED                             37                             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"
D7V34, continuous
D7V35, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   34  6
  AMP PEAK  7(5P15.33) WILD-TYPE 58 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     34    6
  AMP PEAK  7(5P15.33) WILD-TYPE   58   12
         clus
vv        AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  ABSENT                            34                             58
  PRESENT                            6                             12
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  7(5P15.33) MUTATED             0        52     0
  AMP PEAK  7(5P15.33) WILD-TYPE           5        48     2
D7V36, multiclass
             clus
vv            AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  CARBOPLATIN                            0                              5
  CISPLATIN                             52                             48
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V37, continuous
D7V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  7(5P15.33) MUTATED         2        1         0         1       15
  AMP PEAK  7(5P15.33) WILD-TYPE       3        0         1         0       19
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  7(5P15.33) MUTATED          30        16        1         4
  AMP PEAK  7(5P15.33) WILD-TYPE        47        21        3         4
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  7(5P15.33) MUTATED            4          1        28         0
  AMP PEAK  7(5P15.33) WILD-TYPE          1          6        16         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  7(5P15.33) MUTATED            3         22         4         1
  AMP PEAK  7(5P15.33) WILD-TYPE          0         20         3        11
D7V39, multiclass
            clus
vv           AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             15                             19
  STAGE IB1                            30                             47
  STAGE IB2                            16                             21
  STAGE II                              1                              3
  STAGE IIA                             4                              4
  STAGE IIA1                            4                              1
  STAGE IIA2                            1                              6
  STAGE IIB                            28                             16
  STAGE III                             0                              1
  STAGE IIIA                            3                              0
  STAGE IIIB                           22                             20
  STAGE IVA                             4                              3
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(6P21.33) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(6P21.33) MUTATED    57  24
  AMP PEAK  8(6P21.33) WILD-TYPE 157  44
  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE 
                            81                            201 
  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE 
                            24                             44 
$`AMP PEAK  8(6P21.33) MUTATED`
TCGA-EX-A69M TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BN 
        8.32        17.82        49.48        57.04        11.44         5.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1ML 
       31.40        46.32        35.01        38.99        35.61        20.91 
TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7UE 
       78.35        52.01        18.02        17.85       154.32       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-DG-A2KJ TCGA-DG-A2KL 
      131.11        94.95         2.73        45.83        95.11        44.94 
TCGA-DS-A0VM TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A43B 
      117.99        17.52         8.28        39.55        31.73        26.01 
TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2PK 
       14.89        25.91        27.22         0.36        19.27         0.39 
TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-FU-A23K 
        0.59        40.96         1.74         1.64         0.10        12.23 
TCGA-FU-A23L TCGA-FU-A57G TCGA-HG-A2PA TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JX-A3PZ 
       23.84        35.44        25.41        96.95        78.71        21.11 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-MU-A5YI 
       44.61        11.28        12.49        17.82        11.38        34.62 
TCGA-MY-A5BD TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD TCGA-UC-A7PF 
       54.81        17.23         2.96        16.41        11.67        93.99 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A953 
       23.97        19.96        11.51        39.78        58.45        15.68 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC 
       51.32        50.47        43.40        48.39        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UY 
       24.30        46.92        45.11        14.53        47.87        18.25 
TCGA-VS-A9V2 TCGA-VS-AA62 TCGA-ZJ-AAXA 
       18.25        15.42         1.41 

$`AMP PEAK  8(6P21.33) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 
      146.86        12.59        14.70         1.48         4.34         0.69 
TCGA-2W-A8YY TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       17.52        23.67        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 
      177.04       173.29        82.85        19.86        67.46        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       57.73        53.16         0.46         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       33.24        20.42       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
       20.35       147.35        17.19         9.34        13.61        50.99 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       14.73         1.12        82.06        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76        55.63       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 
       40.87        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA 
       25.02        36.89        26.40        24.56        12.13        24.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        7.46        26.79        27.29        27.25        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 
       60.72        26.27         6.64         1.51         0.43         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45         0.13         0.30         4.24         0.07         1.87 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
        0.43        47.77         2.33         0.07         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG 
       20.35         7.92        15.22        19.79        15.55        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC 
       28.31        14.01        10.55         1.12        17.75        16.57 
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-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       66.81       129.37        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U2 
        8.28        18.15       209.59        20.91         0.89         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        13.35        22.52        20.28        19.56         9.17 
TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
        8.52        28.08        19.96        35.05        20.84        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG 
        9.34        18.64        22.62        19.59        14.60        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL 
       69.50        10.03        46.52        45.57        32.42        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       32.15        53.59        36.13        59.18        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        33.37        40.14        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A9UA TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ 
       50.14        28.50         1.71        27.25        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 
       26.07        15.85        14.53         3.42        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        5.16        17.75        16.24        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.16         3.91 

  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE 
                        155.77                         210.67 
  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE 
                         25.91                          20.91 
[1] "0.1 - 155.8 (25.9)" "0.1 - 210.7 (20.9)"
[1] "hr=" "1.2"
D8V2, continuous
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  8(6P21.33) MUTATED   37 20  5  3
  AMP PEAK  8(6P21.33) WILD-TYPE 98 50 16  5
D8V3, multiclass
    clus
vv   AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  T1                           37                             98
  T2                           20                             50
  T3                            5                             16
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                                cls
clus                              0  1
  AMP PEAK  8(6P21.33) MUTATED   37 13
  AMP PEAK  8(6P21.33) WILD-TYPE 92 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED     37   13
  AMP PEAK  8(6P21.33) WILD-TYPE   92   43
   clus
vv  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  0                           37                             92
  1                           13                             43
[1] 2 2
[1] FALSE
D8V5, binary
                                cls
clus                              0  1
  AMP PEAK  8(6P21.33) MUTATED   32  3
  AMP PEAK  8(6P21.33) WILD-TYPE 76  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED     32    3
  AMP PEAK  8(6P21.33) WILD-TYPE   76    7
   clus
vv  AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  0                           32                             76
  1                            3                              7
[1] 2 2
[1] FALSE
D8V6, binary
                                cls
clus                              0  1
  AMP PEAK  8(6P21.33) MUTATED   15 38
  AMP PEAK  8(6P21.33) WILD-TYPE 38 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED     15   38
  AMP PEAK  8(6P21.33) WILD-TYPE   38   87
     clus
vv    AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  NO                            15                             38
  YES                           38                             87
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(6P21.33) MUTATED               0                               71
  AMP PEAK  8(6P21.33) WILD-TYPE             6                              171
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  8(6P21.33) MUTATED                                               1
  AMP PEAK  8(6P21.33) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  8(6P21.33) MUTATED                                     3
  AMP PEAK  8(6P21.33) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  8(6P21.33) MUTATED                                           1
  AMP PEAK  8(6P21.33) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  8(6P21.33) MUTATED                                              6
  AMP PEAK  8(6P21.33) WILD-TYPE                                           11
D8V7, multiclass
                                               clus
vv                                              AMP PEAK  8(6P21.33) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        71
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             6
                                               clus
vv                                              AMP PEAK  8(6P21.33) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         171
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(6P21.33) MUTATED                                  1     5
  AMP PEAK  8(6P21.33) WILD-TYPE                                7    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(6P21.33) MUTATED                           7
  AMP PEAK  8(6P21.33) WILD-TYPE                        21
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  8(6P21.33) MUTATED                                           1
  AMP PEAK  8(6P21.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK  8(6P21.33) MUTATED      59
  AMP PEAK  8(6P21.33) WILD-TYPE   143
D8V10, multiclass
                                           clus
vv                                          AMP PEAK  8(6P21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               59
                                           clus
vv                                          AMP PEAK  8(6P21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             21
  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"
D8V11, binary
                                cls
clus                               0   1
  AMP PEAK  8(6P21.33) MUTATED     5  41
  AMP PEAK  8(6P21.33) WILD-TYPE  18 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED      5   41
  AMP PEAK  8(6P21.33) WILD-TYPE   18  122
                        clus
vv                       AMP PEAK  8(6P21.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       AMP PEAK  8(6P21.33) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            122
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                                cls
clus                               0   1
  AMP PEAK  8(6P21.33) MUTATED    50  28
  AMP PEAK  8(6P21.33) WILD-TYPE 143  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED     50   28
  AMP PEAK  8(6P21.33) WILD-TYPE  143   48
            clus
vv           AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  TUMOR FREE                           50                            143
  WITH TUMOR                           28                             48
[1] 2 2
[1] FALSE
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK  8(6P21.33) MUTATED    2 33 39  1  5
  AMP PEAK  8(6P21.33) WILD-TYPE 16 96 76  0 19
D8V14, multiclass
    clus
vv   AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  G1                            2                             16
  G2                           33                             96
  G3                           39                             76
  G4                            1                              0
  GX                            5                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, continuous
D8V16, continuous
D8V17, continuous
D8V18, continuous
D8V19, binary
                                cls
clus                              0  1
  AMP PEAK  8(6P21.33) MUTATED    9  1
  AMP PEAK  8(6P21.33) WILD-TYPE 16  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED      9    1
  AMP PEAK  8(6P21.33) WILD-TYPE   16    2
                         clus
vv                        AMP PEAK  8(6P21.33) MUTATED
  COMPLETED AS PLANNED                               9
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK  8(6P21.33) WILD-TYPE
  COMPLETED AS PLANNED                                16
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D8V20, continuous
D8V21, continuous
D8V22, continuous
D8V23, continuous
D8V24, continuous
D8V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  8(6P21.33) MUTATED                                     0
  AMP PEAK  8(6P21.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  8(6P21.33) MUTATED                                     1
  AMP PEAK  8(6P21.33) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  8(6P21.33) MUTATED                         8
  AMP PEAK  8(6P21.33) WILD-TYPE                      28
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK  8(6P21.33) MUTATED                         0
  AMP PEAK  8(6P21.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK  8(6P21.33) MUTATED                         2
  AMP PEAK  8(6P21.33) WILD-TYPE                       8
D8V26, multiclass
                                     clus
vv                                    AMP PEAK  8(6P21.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        8
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK  8(6P21.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         28
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  8(6P21.33) MUTATED                                               1
  AMP PEAK  8(6P21.33) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  8(6P21.33) MUTATED                                               10
  AMP PEAK  8(6P21.33) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  8(6P21.33) MUTATED                                                                                  23
  AMP PEAK  8(6P21.33) WILD-TYPE                                                                                59
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  8(6P21.33) MUTATED                                                                                             30
  AMP PEAK  8(6P21.33) WILD-TYPE                                                                                           91
D8V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  8(6P21.33) 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)                                      23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           30
                                                                                              clus
vv                                                                                             AMP PEAK  8(6P21.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        59
  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"
D8V28, binary
                                cls
clus                              0  1
  AMP PEAK  8(6P21.33) MUTATED   16 20
  AMP PEAK  8(6P21.33) WILD-TYPE 55 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED     16   20
  AMP PEAK  8(6P21.33) WILD-TYPE   55   54
         clus
vv        AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  ABSENT                            16                             55
  PRESENT                           20                             54
[1] 2 2
[1] FALSE
D8V29, continuous
D8V30, continuous
D8V31, binary
                                cls
clus                              0  1
  AMP PEAK  8(6P21.33) MUTATED   13 29
  AMP PEAK  8(6P21.33) WILD-TYPE 36 88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED     13   29
  AMP PEAK  8(6P21.33) WILD-TYPE   36   88
                                          clus
vv                                         AMP PEAK  8(6P21.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           29
                                          clus
vv                                         AMP PEAK  8(6P21.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             88
[1] 2 2
[1] FALSE
D8V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  8(6P21.33) MUTATED              2          14         29
  AMP PEAK  8(6P21.33) WILD-TYPE           13          40         56
D8V33, multiclass
              clus
vv             AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                            14                             40
  NEVER USED                             29                             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"
D8V34, continuous
D8V35, binary
                                cls
clus                              0  1
  AMP PEAK  8(6P21.33) MUTATED   21  7
  AMP PEAK  8(6P21.33) WILD-TYPE 71 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(6P21.33) MUTATED     21    7
  AMP PEAK  8(6P21.33) WILD-TYPE   71   11
         clus
vv        AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  ABSENT                            21                             71
  PRESENT                            7                             11
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  8(6P21.33) MUTATED             0        31     1
  AMP PEAK  8(6P21.33) WILD-TYPE           5        69     1
D8V36, multiclass
             clus
vv            AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  CARBOPLATIN                            0                              5
  CISPLATIN                             31                             69
  OTHER                                  1                              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"
D8V37, continuous
D8V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  8(6P21.33) MUTATED         0        0         1         0        6
  AMP PEAK  8(6P21.33) WILD-TYPE       5        1         0         1       28
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  8(6P21.33) MUTATED          24        12        0         2
  AMP PEAK  8(6P21.33) WILD-TYPE        53        25        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  8(6P21.33) MUTATED            3          2        16         0
  AMP PEAK  8(6P21.33) WILD-TYPE          2          5        28         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  8(6P21.33) MUTATED            1          9         3         2
  AMP PEAK  8(6P21.33) WILD-TYPE          2         33         4        10
D8V39, multiclass
            clus
vv           AMP PEAK  8(6P21.33) MUTATED AMP PEAK  8(6P21.33) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                              6                             28
  STAGE IB1                            24                             53
  STAGE IB2                            12                             25
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            3                              2
  STAGE IIA2                            2                              5
  STAGE IIB                            16                             28
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                            9                             33
  STAGE IVA                             3                              4
  STAGE IVB                             2                             10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(7P11.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(7P11.2) MUTATED    33  18
  AMP PEAK  9(7P11.2) WILD-TYPE 181  50
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           51                           231 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           18                            50 
$`AMP PEAK  9(7P11.2) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-C5-A0TN TCGA-C5-A1BL TCGA-C5-A1MK TCGA-C5-A1MN 
       12.59         4.34        11.44       173.29         2.43        40.93 
TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UH 
       73.18        78.35       100.14       154.32       147.35       131.11 
TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A3LQ 
       45.83        23.51        95.11        87.75        36.76        22.98 
TCGA-DS-A7WI TCGA-EA-A50E TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ 
        8.28         7.46         1.51         0.30         1.87         1.74 
TCGA-EK-A2RM TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A40J TCGA-HM-A3JJ 
        1.64        15.22        15.55        23.84        14.01        21.67 
TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ 
       78.71        36.36        21.44        20.48        28.37        21.11 
TCGA-MA-AA41 TCGA-MY-A913 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EI 
        9.17        17.23         9.04        19.59        12.16        23.97 
TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A953 TCGA-VS-A9U5 TCGA-VS-A9UB 
       19.96        11.51        59.18        15.68        50.47        29.95 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UY 
       24.30        46.92        18.25 

$`AMP PEAK  9(7P11.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        14.70         8.32         1.48         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF 
       17.82        49.48        57.04        23.67        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MP 
       53.16        38.99        35.61         0.46        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       44.22        73.45        83.05        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       15.48        20.35        17.19       155.77        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR 
       13.61         2.73        50.99         8.35        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       20.81        20.91        14.73         1.12        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       63.98        58.88        55.63       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        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 
       24.56        31.73        26.01        12.13        24.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       13.48         0.36        60.72        26.27         6.64        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.24         0.07         0.43        47.77         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.49         0.89        20.35         7.92 
TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       19.79        12.23        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
       20.98        26.14        16.14        28.31        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12        17.75        25.41        16.57        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       129.37        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VL 
       81.96        29.85        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 
        8.28        18.15       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
        0.89        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       20.28        17.82        19.56         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       15.88         9.34        18.64        22.62        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM 
       65.49        32.15        53.59        36.13        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       40.87        16.64         4.73        33.37        40.14        58.45 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 
       56.35        55.50        50.14        51.32        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       28.50        27.12        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
        3.42        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                         0.30                          0.07 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                       173.29                        210.67 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                        21.44                         23.67 
[1] "0.3 - 173.3 (21.4)" "0.1 - 210.7 (23.7)"
[1] "hr=" "1.5"
D9V2, continuous
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  9(7P11.2) MUTATED    15  12   5   4
  AMP PEAK  9(7P11.2) WILD-TYPE 120  58  16   4
D9V3, multiclass
    clus
vv   AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  T1                          15                           120
  T2                          12                            58
  T3                           5                            16
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                               cls
clus                              0   1
  AMP PEAK  9(7P11.2) MUTATED    15  11
  AMP PEAK  9(7P11.2) WILD-TYPE 114  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED     15   11
  AMP PEAK  9(7P11.2) WILD-TYPE  114   45
   clus
vv  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  0                          15                           114
  1                          11                            45
[1] 2 2
[1] FALSE
D9V5, binary
                               cls
clus                             0  1
  AMP PEAK  9(7P11.2) MUTATED   15  3
  AMP PEAK  9(7P11.2) WILD-TYPE 93  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED     15    3
  AMP PEAK  9(7P11.2) WILD-TYPE   93    7
   clus
vv  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  0                          15                            93
  1                           3                             7
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                             0  1
  AMP PEAK  9(7P11.2) MUTATED    6 26
  AMP PEAK  9(7P11.2) WILD-TYPE 47 99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED      6   26
  AMP PEAK  9(7P11.2) WILD-TYPE   47   99
     clus
vv    AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  NO                            6                            47
  YES                          26                            99
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(7P11.2) MUTATED               0                               49
  AMP PEAK  9(7P11.2) WILD-TYPE             6                              193
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  9(7P11.2) MUTATED                                               0
  AMP PEAK  9(7P11.2) WILD-TYPE                                             6
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  9(7P11.2) MUTATED                                     2
  AMP PEAK  9(7P11.2) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  9(7P11.2) MUTATED                                           0
  AMP PEAK  9(7P11.2) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  9(7P11.2) MUTATED                                              1
  AMP PEAK  9(7P11.2) WILD-TYPE                                           16
D9V7, multiclass
                                               clus
vv                                              AMP PEAK  9(7P11.2) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              AMP PEAK  9(7P11.2) WILD-TYPE
  ADENOSQUAMOUS                                                             6
  CERVICAL SQUAMOUS CELL CARCINOMA                                        193
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(7P11.2) MUTATED                                  1     2
  AMP PEAK  9(7P11.2) WILD-TYPE                                7    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(7P11.2) MUTATED                           8
  AMP PEAK  9(7P11.2) WILD-TYPE                        20
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(7P11.2) MUTATED                                           0    35
  AMP PEAK  9(7P11.2) WILD-TYPE                                         2   167
D9V10, multiclass
                                           clus
vv                                          AMP PEAK  9(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              35
                                           clus
vv                                          AMP PEAK  9(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               167
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
                               cls
clus                              0   1
  AMP PEAK  9(7P11.2) MUTATED     4  27
  AMP PEAK  9(7P11.2) WILD-TYPE  19 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED      4   27
  AMP PEAK  9(7P11.2) WILD-TYPE   19  136
                        clus
vv                       AMP PEAK  9(7P11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          27
                        clus
vv                       AMP PEAK  9(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           136
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                               cls
clus                              0   1
  AMP PEAK  9(7P11.2) MUTATED    29  21
  AMP PEAK  9(7P11.2) WILD-TYPE 164  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED     29   21
  AMP PEAK  9(7P11.2) WILD-TYPE  164   55
            clus
vv           AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  TUMOR FREE                          29                           164
  WITH TUMOR                          21                            55
[1] 2 2
[1] FALSE
                               vv
clus                             G1  G2  G3  G4  GX
  AMP PEAK  9(7P11.2) MUTATED     1  19  24   1   5
  AMP PEAK  9(7P11.2) WILD-TYPE  17 110  91   0  19
D9V14, multiclass
    clus
vv   AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  G1                           1                            17
  G2                          19                           110
  G3                          24                            91
  G4                           1                             0
  GX                           5                            19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, continuous
D9V16, continuous
D9V17, continuous
D9V18, continuous
D9V19, binary
                               cls
clus                             0  1
  AMP PEAK  9(7P11.2) MUTATED    6  2
  AMP PEAK  9(7P11.2) WILD-TYPE 19  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED      6    2
  AMP PEAK  9(7P11.2) WILD-TYPE   19    1
                         clus
vv                        AMP PEAK  9(7P11.2) MUTATED
  COMPLETED AS PLANNED                              6
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        AMP PEAK  9(7P11.2) WILD-TYPE
  COMPLETED AS PLANNED                               19
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
D9V20, continuous
D9V21, continuous
D9V22, continuous
D9V23, continuous
D9V24, continuous
D9V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  9(7P11.2) MUTATED                                     0
  AMP PEAK  9(7P11.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  9(7P11.2) MUTATED                                     1
  AMP PEAK  9(7P11.2) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  9(7P11.2) MUTATED                         3                       1
  AMP PEAK  9(7P11.2) WILD-TYPE                      33                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  9(7P11.2) MUTATED                         2
  AMP PEAK  9(7P11.2) WILD-TYPE                       8
D9V26, multiclass
                                     clus
vv                                    AMP PEAK  9(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  9(7P11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                        33
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  9(7P11.2) MUTATED                                               0
  AMP PEAK  9(7P11.2) WILD-TYPE                                             3
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  9(7P11.2) MUTATED                                                3
  AMP PEAK  9(7P11.2) WILD-TYPE                                             22
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  9(7P11.2) MUTATED                                                                                  16
  AMP PEAK  9(7P11.2) WILD-TYPE                                                                                66
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  9(7P11.2) MUTATED                                                                                             23
  AMP PEAK  9(7P11.2) WILD-TYPE                                                                                           98
D9V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  9(7P11.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          23
                                                                                              clus
vv                                                                                             AMP PEAK  9(7P11.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       66
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V28, binary
                               cls
clus                             0  1
  AMP PEAK  9(7P11.2) MUTATED    6 16
  AMP PEAK  9(7P11.2) WILD-TYPE 65 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED      6   16
  AMP PEAK  9(7P11.2) WILD-TYPE   65   58
         clus
vv        AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  ABSENT                            6                            65
  PRESENT                          16                            58
[1] 2 2
[1] FALSE
D9V29, continuous
D9V30, continuous
D9V31, binary
                               cls
clus                             0  1
  AMP PEAK  9(7P11.2) MUTATED   11 20
  AMP PEAK  9(7P11.2) WILD-TYPE 38 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED     11   20
  AMP PEAK  9(7P11.2) WILD-TYPE   38   97
                                          clus
vv                                         AMP PEAK  9(7P11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          20
                                          clus
vv                                         AMP PEAK  9(7P11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            97
[1] 2 2
[1] FALSE
D9V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  9(7P11.2) MUTATED              2           8         14
  AMP PEAK  9(7P11.2) WILD-TYPE           13          46         71
D9V33, multiclass
              clus
vv             AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  CURRENT USER                           2                            13
  FORMER USER                            8                            46
  NEVER USED                            14                            71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V34, continuous
D9V35, binary
                               cls
clus                             0  1
  AMP PEAK  9(7P11.2) MUTATED   14  2
  AMP PEAK  9(7P11.2) WILD-TYPE 78 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED     14    2
  AMP PEAK  9(7P11.2) WILD-TYPE   78   16
         clus
vv        AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  ABSENT                           14                            78
  PRESENT                           2                            16
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  AMP PEAK  9(7P11.2) MUTATED             1        26     0
  AMP PEAK  9(7P11.2) WILD-TYPE           4        74     2
D9V36, multiclass
             clus
vv            AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            26                            74
  OTHER                                 0                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V37, continuous
[1] "Remove cluster labels:"      "AMP PEAK  9(7P11.2) MUTATED"
clus
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                            2                            15 
                   TCGA-C5-A1BN                    TCGA-C5-A1MH 
"AMP PEAK  9(7P11.2) WILD-TYPE" "AMP PEAK  9(7P11.2) WILD-TYPE" 
                   TCGA-C5-A1ML                    TCGA-C5-A1MP 
"AMP PEAK  9(7P11.2) WILD-TYPE" "AMP PEAK  9(7P11.2) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-GH-A9DA 
"AMP PEAK  9(7P11.2) WILD-TYPE" "AMP PEAK  9(7P11.2) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-JW-A852 
"AMP PEAK  9(7P11.2) WILD-TYPE" "AMP PEAK  9(7P11.2) WILD-TYPE" 
                   TCGA-JX-A3Q8                    TCGA-MA-AA3W 
"AMP PEAK  9(7P11.2) WILD-TYPE" "AMP PEAK  9(7P11.2) WILD-TYPE" 
                   TCGA-MA-AA3Z                    TCGA-MA-AA42 
"AMP PEAK  9(7P11.2) WILD-TYPE" "AMP PEAK  9(7P11.2) WILD-TYPE" 
                   TCGA-MU-A51Y                    TCGA-MU-A8JM 
"AMP PEAK  9(7P11.2) WILD-TYPE" "AMP PEAK  9(7P11.2) WILD-TYPE" 
                   TCGA-ZX-AA5X 
"AMP PEAK  9(7P11.2) WILD-TYPE" 
D9V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK  9(7P11.2) MUTATED         1        0         0         0        7
  AMP PEAK  9(7P11.2) WILD-TYPE       4        1         1         1       27
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK  9(7P11.2) MUTATED           6         5        0         2
  AMP PEAK  9(7P11.2) WILD-TYPE        71        32        4         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK  9(7P11.2) MUTATED            3          1         8         0
  AMP PEAK  9(7P11.2) WILD-TYPE          2          6        36         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK  9(7P11.2) MUTATED            1         10         5         2
  AMP PEAK  9(7P11.2) WILD-TYPE          2         32         2        10
D9V39, multiclass
            clus
vv           AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             7                            27
  STAGE IB1                            6                            71
  STAGE IB2                            5                            32
  STAGE II                             0                             4
  STAGE IIA                            2                             6
  STAGE IIA1                           3                             2
  STAGE IIA2                           1                             6
  STAGE IIB                            8                            36
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          10                            32
  STAGE IVA                            5                             2
  STAGE IVB                            2                            10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(8Q24.21) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(8Q24.21) MUTATED    90  29
  AMP PEAK 10(8Q24.21) WILD-TYPE 124  39
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           119                            163 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                            29                             39 
$`AMP PEAK 10(8Q24.21) MUTATED`
TCGA-EX-A69M TCGA-VS-A9V4 TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ 
        8.32         4.34        57.04       177.04        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       67.46        31.40        35.01        53.16        38.99        35.61 
TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD 
        2.43         3.58        73.45       100.14        38.43        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X5 
       18.02        17.85       210.67       154.32       131.11        13.61 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-DG-A2KH 
       50.99         8.35        23.51        27.52        20.91         1.12 
TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT 
       95.11        87.75        55.63       117.99        22.98        40.87 
TCGA-EA-A3HQ TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E 
       37.35        13.05        36.89        24.56        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       14.89        25.91         0.36        60.72         6.64         1.51 
TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.39         0.59         0.43         2.33         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3HY 
        0.49         0.89        15.55        12.23        23.84        31.36 
TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-HG-A9SC TCGA-HM-A6W2 
       20.98        28.31        14.01        35.44        16.57         9.44 
TCGA-IR-A3LA TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 
      137.16        29.85        36.36        21.44        15.58         8.28 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       44.61        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       13.35        20.28        17.82         9.17         8.52        11.38 
TCGA-MU-A5YI TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       34.62        20.84        17.23        16.41         9.04        17.56 
TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-VS-A8EB 
        9.34        22.62        19.59        14.60        12.16        10.03 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 
       32.42        19.96        16.64        40.14        15.68        56.35 
TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UM 
       50.14        50.47        43.40        29.95        27.12        27.25 
TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V2 
       41.52        14.53         3.42        18.25        18.84        18.25 
TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       17.75        26.01        29.26        67.59         1.41 

$`AMP PEAK 10(8Q24.21) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        12.59        14.70         1.48         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       17.82        49.48        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M7 TCGA-C5-A1M8 
       36.56       144.16       173.29         5.46        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
       57.73         0.46        20.91        40.93        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       83.05        78.35        33.24        20.42       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A907 
        9.34         2.73        45.83        99.91        20.81        14.73 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VN 
       82.06        44.94        63.98        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        39.55        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B 
       31.53        31.36        25.02        26.40        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.13        26.79        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       13.48        26.27        19.27         0.43         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        40.96         0.30         4.24         0.07         1.87 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        1.74        47.77         1.64        20.35         7.92        15.22 
TCGA-EX-A69L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
       19.79        19.04        16.11        36.26        26.14        16.14 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       10.55         1.12        17.75        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
       14.93       147.39        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B 
       81.96        27.42         3.29        24.56        20.48        28.37 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-MA-AA3W TCGA-MA-AA3Z 
       18.15        21.11       209.59        20.91        22.52        19.56 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 
       28.08        19.96        54.81        35.05         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        18.64        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL 
       93.99        69.50        46.52        45.57        23.97        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 
       31.27        40.87         4.73        33.37        58.45        55.50 
TCGA-VS-A959 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       51.32        48.39        28.50        24.30        46.92        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UT 
        1.71        14.53        47.87        47.47        26.07        15.85 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       67.20         5.16        16.24        15.42        19.13         0.16 
TCGA-ZX-AA5X 
        3.91 

  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                        210.67                         209.59 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                         19.96                          25.02 
[1] "0.1 - 210.7 (20.0)" "0.1 - 209.6 (25.0)"
[1] "hr=" "1.2"
D10V2, continuous
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 10(8Q24.21) MUTATED   57 26 13  6
  AMP PEAK 10(8Q24.21) WILD-TYPE 78 44  8  2
D10V3, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  T1                           57                             78
  T2                           26                             44
  T3                           13                              8
  T4                            6                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                                cls
clus                              0  1
  AMP PEAK 10(8Q24.21) MUTATED   53 27
  AMP PEAK 10(8Q24.21) WILD-TYPE 76 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED     53   27
  AMP PEAK 10(8Q24.21) WILD-TYPE   76   29
   clus
vv  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  0                           53                             76
  1                           27                             29
[1] 2 2
[1] FALSE
D10V5, binary
                                cls
clus                              0  1
  AMP PEAK 10(8Q24.21) MUTATED   44  6
  AMP PEAK 10(8Q24.21) WILD-TYPE 64  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED     44    6
  AMP PEAK 10(8Q24.21) WILD-TYPE   64    4
   clus
vv  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  0                           44                             64
  1                            6                              4
[1] 2 2
[1] FALSE
D10V6, binary
                                cls
clus                              0  1
  AMP PEAK 10(8Q24.21) MUTATED   21 56
  AMP PEAK 10(8Q24.21) WILD-TYPE 32 69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED     21   56
  AMP PEAK 10(8Q24.21) WILD-TYPE   32   69
     clus
vv    AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  NO                            21                             32
  YES                           56                             69
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED               4                              108
  AMP PEAK 10(8Q24.21) WILD-TYPE             2                              134
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 10(8Q24.21) MUTATED                                               1
  AMP PEAK 10(8Q24.21) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                                     8
  AMP PEAK 10(8Q24.21) WILD-TYPE                                  13
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 10(8Q24.21) MUTATED                                           2
  AMP PEAK 10(8Q24.21) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 10(8Q24.21) MUTATED                                              4
  AMP PEAK 10(8Q24.21) WILD-TYPE                                           13
D10V7, multiclass
                                               clus
vv                                              AMP PEAK 10(8Q24.21) MUTATED
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       108
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              AMP PEAK 10(8Q24.21) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         134
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
D10V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(8Q24.21) MUTATED                                  3     9
  AMP PEAK 10(8Q24.21) WILD-TYPE                                5    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(8Q24.21) MUTATED                          14
  AMP PEAK 10(8Q24.21) WILD-TYPE                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 10(8Q24.21) MUTATED                                           1
  AMP PEAK 10(8Q24.21) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 10(8Q24.21) MUTATED      81
  AMP PEAK 10(8Q24.21) WILD-TYPE   121
D10V10, multiclass
                                           clus
vv                                          AMP PEAK 10(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               81
                                           clus
vv                                          AMP PEAK 10(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 10
  BLACK OR AFRICAN AMERICAN                                             14
  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"
D10V11, binary
                                cls
clus                              0  1
  AMP PEAK 10(8Q24.21) MUTATED   10 71
  AMP PEAK 10(8Q24.21) WILD-TYPE 13 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED     10   71
  AMP PEAK 10(8Q24.21) WILD-TYPE   13   92
                        clus
vv                       AMP PEAK 10(8Q24.21) MUTATED
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       AMP PEAK 10(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                             92
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED    75  36
  AMP PEAK 10(8Q24.21) WILD-TYPE 118  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED     75   36
  AMP PEAK 10(8Q24.21) WILD-TYPE  118   40
            clus
vv           AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  TUMOR FREE                           75                            118
  WITH TUMOR                           36                             40
[1] 2 2
[1] FALSE
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 10(8Q24.21) MUTATED    7 47 58  0 10
  AMP PEAK 10(8Q24.21) WILD-TYPE 11 82 57  1 14
D10V14, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  G1                            7                             11
  G2                           47                             82
  G3                           58                             57
  G4                            0                              1
  GX                           10                             14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, continuous
D10V16, continuous
D10V17, continuous
D10V18, continuous
D10V19, binary
                                cls
clus                              0  1
  AMP PEAK 10(8Q24.21) MUTATED    9  2
  AMP PEAK 10(8Q24.21) WILD-TYPE 16  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED      9    2
  AMP PEAK 10(8Q24.21) WILD-TYPE   16    1
                         clus
vv                        AMP PEAK 10(8Q24.21) MUTATED
  COMPLETED AS PLANNED                               9
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        AMP PEAK 10(8Q24.21) WILD-TYPE
  COMPLETED AS PLANNED                                16
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
D10V20, continuous
D10V21, continuous
D10V22, continuous
D10V23, continuous
D10V24, continuous
D10V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 10(8Q24.21) MUTATED                                     0
  AMP PEAK 10(8Q24.21) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 10(8Q24.21) MUTATED                                     2
  AMP PEAK 10(8Q24.21) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 10(8Q24.21) MUTATED                        16
  AMP PEAK 10(8Q24.21) WILD-TYPE                      20
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 10(8Q24.21) MUTATED                         1
  AMP PEAK 10(8Q24.21) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 10(8Q24.21) MUTATED                         2
  AMP PEAK 10(8Q24.21) WILD-TYPE                       8
D10V26, multiclass
                                     clus
vv                                    AMP PEAK 10(8Q24.21) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       16
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK 10(8Q24.21) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         20
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 10(8Q24.21) MUTATED                                               2
  AMP PEAK 10(8Q24.21) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 10(8Q24.21) MUTATED                                               11
  AMP PEAK 10(8Q24.21) WILD-TYPE                                             14
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 10(8Q24.21) MUTATED                                                                                  39
  AMP PEAK 10(8Q24.21) WILD-TYPE                                                                                43
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 10(8Q24.21) MUTATED                                                                                             50
  AMP PEAK 10(8Q24.21) WILD-TYPE                                                                                           71
D10V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 10(8Q24.21) 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)                                      39
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           50
                                                                                              clus
vv                                                                                             AMP PEAK 10(8Q24.21) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        43
  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"
D10V28, binary
                                cls
clus                              0  1
  AMP PEAK 10(8Q24.21) MUTATED   23 30
  AMP PEAK 10(8Q24.21) WILD-TYPE 48 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED     23   30
  AMP PEAK 10(8Q24.21) WILD-TYPE   48   44
         clus
vv        AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  ABSENT                            23                             48
  PRESENT                           30                             44
[1] 2 2
[1] FALSE
D10V29, continuous
D10V30, continuous
D10V31, binary
                                cls
clus                              0  1
  AMP PEAK 10(8Q24.21) MUTATED   22 55
  AMP PEAK 10(8Q24.21) WILD-TYPE 27 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED     22   55
  AMP PEAK 10(8Q24.21) WILD-TYPE   27   62
                                          clus
vv                                         AMP PEAK 10(8Q24.21) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           55
                                          clus
vv                                         AMP PEAK 10(8Q24.21) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             62
[1] 2 2
[1] FALSE
D10V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 10(8Q24.21) MUTATED              3          23         35
  AMP PEAK 10(8Q24.21) WILD-TYPE           12          31         50
D10V33, multiclass
              clus
vv             AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                            23                             31
  NEVER USED                             35                             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"
D10V34, continuous
D10V35, binary
                                cls
clus                              0  1
  AMP PEAK 10(8Q24.21) MUTATED   36  4
  AMP PEAK 10(8Q24.21) WILD-TYPE 56 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED     36    4
  AMP PEAK 10(8Q24.21) WILD-TYPE   56   14
         clus
vv        AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  ABSENT                            36                             56
  PRESENT                            4                             14
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 10(8Q24.21) MUTATED             3        47     0
  AMP PEAK 10(8Q24.21) WILD-TYPE           2        53     2
D10V36, multiclass
             clus
vv            AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  CARBOPLATIN                            3                              2
  CISPLATIN                             47                             53
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V37, continuous
D10V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 10(8Q24.21) MUTATED         3        1         1         1       15
  AMP PEAK 10(8Q24.21) WILD-TYPE       2        0         0         0       19
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 10(8Q24.21) MUTATED          26        14        2         1
  AMP PEAK 10(8Q24.21) WILD-TYPE        51        23        2         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 10(8Q24.21) MUTATED            1          1        24         0
  AMP PEAK 10(8Q24.21) WILD-TYPE          4          6        20         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 10(8Q24.21) MUTATED            1         22         4         6
  AMP PEAK 10(8Q24.21) WILD-TYPE          2         20         3         6
D10V39, multiclass
            clus
vv           AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                              1                              0
  STAGE IA1                             1                              0
  STAGE IA2                             1                              0
  STAGE IB                             15                             19
  STAGE IB1                            26                             51
  STAGE IB2                            14                             23
  STAGE II                              2                              2
  STAGE IIA                             1                              7
  STAGE IIA1                            1                              4
  STAGE IIA2                            1                              6
  STAGE IIB                            24                             20
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                           22                             20
  STAGE IVA                             4                              3
  STAGE IVB                             6                              6
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(9P24.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(9P24.1) MUTATED    46  12
  AMP PEAK 11(9P24.1) WILD-TYPE 168  56
  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE 
                           58                           224 
  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE 
                           12                            56 
$`AMP PEAK 11(9P24.1) MUTATED`
TCGA-C5-A8XJ TCGA-VS-A9V4 TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1MP TCGA-C5-A2LT 
      146.86         4.34        49.48       177.04         3.58        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CK 
       73.45        83.05        33.24        52.01       210.67       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-DG-A2KL TCGA-DG-A2KM 
       15.48       147.35       155.77         2.73        44.94        63.98 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZE 
      117.99        22.98        16.83        13.05        25.91        27.25 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A3L1 
       26.27         1.51         0.39         1.64         2.33        15.22 
TCGA-FU-A23K TCGA-FU-A40J TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VL TCGA-JW-A69B 
       12.23        14.01        78.71        36.36        15.58        28.37 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE TCGA-MY-A913 
       21.11        44.61        11.28         0.30        35.05        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EL 
        2.96        16.41        11.67        93.99        12.16        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A9U5 
       32.15        11.51        40.87        16.64        40.14        50.47 
TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-A9UU TCGA-ZJ-A8QR 
       29.95        46.92        14.53        19.13 

$`AMP PEAK 11(9P24.1) WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
       12.59        14.70         8.32         1.48         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       17.82        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HE 
       40.93        44.22        78.35       100.14        38.43        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC 
       17.85        20.42       154.32       101.82        20.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
      131.11        94.95         9.34        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM 
       14.73         1.12        95.11        82.06        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       36.76        55.63       118.65        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        36.89        26.40        24.56        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       12.13        24.82         7.46        14.89        26.79        27.29 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP 
       27.22        24.00        13.48         0.36        60.72         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.43         0.59         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       40.96         0.30         4.24         0.07         1.87         1.74 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.43        47.77         0.07         0.10         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A2QG 
       20.35         7.92        19.79        15.55        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81       129.37        96.95        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 
       27.42         3.29        24.56        21.44        20.48         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       18.15       209.59        20.91         0.89        12.49         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       13.35        22.52        20.28        17.82        19.56         9.17 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84        15.58        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       14.60        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       23.97        19.96        53.59        36.13        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       31.27         4.73        33.37        58.45        15.68        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       55.50        50.14        51.32        43.40        48.39        28.50 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       27.12        24.30        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV 
       47.87        47.47        41.52        26.07        15.85         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       16.24        15.42        26.01        29.26        67.59         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE 
                         0.30                          0.07 
  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE 
                       210.67                        209.59 
  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE 
                        26.76                         21.21 
[1] "0.3 - 210.7 (26.8)" "0.1 - 209.6 (21.2)"
[1] "hr=" "1.5"
D11V2, continuous
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(9P24.1) MUTATED    21  19   5   2
  AMP PEAK 11(9P24.1) WILD-TYPE 114  51  16   6
D11V3, multiclass
    clus
vv   AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  T1                          21                           114
  T2                          19                            51
  T3                           5                            16
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                               cls
clus                              0   1
  AMP PEAK 11(9P24.1) MUTATED    19  19
  AMP PEAK 11(9P24.1) WILD-TYPE 110  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED     19   19
  AMP PEAK 11(9P24.1) WILD-TYPE  110   37
   clus
vv  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  0                          19                           110
  1                          19                            37
[1] 2 2
[1] FALSE
D11V5, binary
                               cls
clus                             0  1
  AMP PEAK 11(9P24.1) MUTATED   22  1
  AMP PEAK 11(9P24.1) WILD-TYPE 86  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED     22    1
  AMP PEAK 11(9P24.1) WILD-TYPE   86    9
   clus
vv  AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  0                          22                            86
  1                           1                             9
[1] 2 2
[1] FALSE
D11V6, binary
                               cls
clus                             0  1
  AMP PEAK 11(9P24.1) MUTATED    9 30
  AMP PEAK 11(9P24.1) WILD-TYPE 44 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED      9   30
  AMP PEAK 11(9P24.1) WILD-TYPE   44   95
     clus
vv    AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  NO                            9                            44
  YES                          30                            95
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(9P24.1) MUTATED               0                               56
  AMP PEAK 11(9P24.1) WILD-TYPE             6                              186
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 11(9P24.1) MUTATED                                               1
  AMP PEAK 11(9P24.1) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 11(9P24.1) MUTATED                                     4
  AMP PEAK 11(9P24.1) WILD-TYPE                                  17
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 11(9P24.1) MUTATED                                           0
  AMP PEAK 11(9P24.1) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 11(9P24.1) MUTATED                                              2
  AMP PEAK 11(9P24.1) WILD-TYPE                                           15
D11V7, multiclass
                                               clus
vv                                              AMP PEAK 11(9P24.1) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       56
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              AMP PEAK 11(9P24.1) WILD-TYPE
  ADENOSQUAMOUS                                                             6
  CERVICAL SQUAMOUS CELL CARCINOMA                                        186
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, continuous
D11V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(9P24.1) MUTATED                                  2     4
  AMP PEAK 11(9P24.1) WILD-TYPE                                6    15
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(9P24.1) MUTATED                          11
  AMP PEAK 11(9P24.1) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(9P24.1) MUTATED                                           1    34
  AMP PEAK 11(9P24.1) WILD-TYPE                                         1   168
D11V10, multiclass
                                           clus
vv                                          AMP PEAK 11(9P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              34
                                           clus
vv                                          AMP PEAK 11(9P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               168
[1] 5 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(9P24.1) MUTATED     3  30
  AMP PEAK 11(9P24.1) WILD-TYPE  20 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED      3   30
  AMP PEAK 11(9P24.1) WILD-TYPE   20  133
                        clus
vv                       AMP PEAK 11(9P24.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          30
                        clus
vv                       AMP PEAK 11(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           133
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                               cls
clus                              0   1
  AMP PEAK 11(9P24.1) MUTATED    42  12
  AMP PEAK 11(9P24.1) WILD-TYPE 151  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED     42   12
  AMP PEAK 11(9P24.1) WILD-TYPE  151   64
            clus
vv           AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  TUMOR FREE                          42                           151
  WITH TUMOR                          12                            64
[1] 2 2
[1] FALSE
                               vv
clus                             G1  G2  G3  G4  GX
  AMP PEAK 11(9P24.1) MUTATED     4  25  26   1   3
  AMP PEAK 11(9P24.1) WILD-TYPE  14 104  89   0  21
D11V14, multiclass
    clus
vv   AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  G1                           4                            14
  G2                          25                           104
  G3                          26                            89
  G4                           1                             0
  GX                           3                            21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, continuous
D11V16, continuous
D11V17, continuous
D11V18, continuous
D11V19, binary
                               cls
clus                             0  1
  AMP PEAK 11(9P24.1) MUTATED    4  0
  AMP PEAK 11(9P24.1) WILD-TYPE 21  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED      4    0
  AMP PEAK 11(9P24.1) WILD-TYPE   21    3
                         clus
vv                        AMP PEAK 11(9P24.1) MUTATED
  COMPLETED AS PLANNED                              4
  TREATMENT NOT COMPLETED                           0
                         clus
vv                        AMP PEAK 11(9P24.1) WILD-TYPE
  COMPLETED AS PLANNED                               21
  TREATMENT NOT COMPLETED                             3
[1] 2 2
[1] FALSE
D11V20, continuous
D11V21, continuous
D11V22, continuous
D11V23, continuous
D11V24, continuous
D11V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 11(9P24.1) MUTATED                                     0
  AMP PEAK 11(9P24.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 11(9P24.1) MUTATED                                     0
  AMP PEAK 11(9P24.1) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 11(9P24.1) MUTATED                        10                       0
  AMP PEAK 11(9P24.1) WILD-TYPE                      26                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK 11(9P24.1) MUTATED                         3
  AMP PEAK 11(9P24.1) WILD-TYPE                       7
D11V26, multiclass
                                     clus
vv                                    AMP PEAK 11(9P24.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                      10
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    AMP PEAK 11(9P24.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        26
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 11(9P24.1) MUTATED                                               1
  AMP PEAK 11(9P24.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 11(9P24.1) MUTATED                                                3
  AMP PEAK 11(9P24.1) WILD-TYPE                                             22
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 11(9P24.1) MUTATED                                                                                  15
  AMP PEAK 11(9P24.1) WILD-TYPE                                                                                67
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 11(9P24.1) MUTATED                                                                                             28
  AMP PEAK 11(9P24.1) WILD-TYPE                                                                                           93
D11V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 11(9P24.1) 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)                                     15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          28
                                                                                              clus
vv                                                                                             AMP PEAK 11(9P24.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       67
  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"
D11V28, binary
                               cls
clus                             0  1
  AMP PEAK 11(9P24.1) MUTATED   12 19
  AMP PEAK 11(9P24.1) WILD-TYPE 59 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED     12   19
  AMP PEAK 11(9P24.1) WILD-TYPE   59   55
         clus
vv        AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  ABSENT                           12                            59
  PRESENT                          19                            55
[1] 2 2
[1] FALSE
D11V29, continuous
D11V30, continuous
D11V31, binary
                               cls
clus                             0  1
  AMP PEAK 11(9P24.1) MUTATED   13 19
  AMP PEAK 11(9P24.1) WILD-TYPE 36 98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED     13   19
  AMP PEAK 11(9P24.1) WILD-TYPE   36   98
                                          clus
vv                                         AMP PEAK 11(9P24.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          19
                                          clus
vv                                         AMP PEAK 11(9P24.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            98
[1] 2 2
[1] FALSE
D11V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK 11(9P24.1) MUTATED              3          15         12
  AMP PEAK 11(9P24.1) WILD-TYPE           12          39         73
D11V33, multiclass
              clus
vv             AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           15                            39
  NEVER USED                            12                            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"
D11V34, continuous
D11V35, binary
                               cls
clus                             0  1
  AMP PEAK 11(9P24.1) MUTATED   17  2
  AMP PEAK 11(9P24.1) WILD-TYPE 75 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(9P24.1) MUTATED     17    2
  AMP PEAK 11(9P24.1) WILD-TYPE   75   16
         clus
vv        AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  ABSENT                           17                            75
  PRESENT                           2                            16
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 11(9P24.1) MUTATED             0        28     1
  AMP PEAK 11(9P24.1) WILD-TYPE           5        72     1
D11V36, multiclass
             clus
vv            AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  CARBOPLATIN                           0                             5
  CISPLATIN                            28                            72
  OTHER                                 1                             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"
D11V37, continuous
D11V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 11(9P24.1) MUTATED         1        0         0         0       10
  AMP PEAK 11(9P24.1) WILD-TYPE       4        1         1         1       24
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 11(9P24.1) MUTATED          12         7        0         2
  AMP PEAK 11(9P24.1) WILD-TYPE        65        30        4         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 11(9P24.1) MUTATED            2          0        10         0
  AMP PEAK 11(9P24.1) WILD-TYPE          3          7        34         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 11(9P24.1) MUTATED            1         11         4         0
  AMP PEAK 11(9P24.1) WILD-TYPE          2         31         3        12
D11V39, multiclass
            clus
vv           AMP PEAK 11(9P24.1) MUTATED AMP PEAK 11(9P24.1) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            10                            24
  STAGE IB1                           12                            65
  STAGE IB2                            7                            30
  STAGE II                             0                             4
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           10                            34
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          11                            31
  STAGE IVA                            4                             3
  STAGE IVB                            0                            12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(11P12) MUTATION ANALYSIS
D12V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 12(11P12) MUTATED    18   4
  AMP PEAK 12(11P12) WILD-TYPE 196  64
  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                          22                          260 
  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                           4                           64 
$`AMP PEAK 12(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        63.98        60.72 
TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-FU-A40J TCGA-FU-A770 TCGA-JW-A5VI TCGA-JW-A5VJ 
       26.27        19.27        14.01         1.12        24.56        21.44 
TCGA-MA-AA3W TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A6DW TCGA-VS-A8EC TCGA-VS-A8EI 
       22.52        17.23         2.96        17.56        46.52        23.97 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A9V2 TCGA-ZJ-A8QQ 
       32.15        53.59        18.25        67.59 

$`AMP PEAK 12(11P12) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A 
        0.69        17.52        17.82        49.48        57.04        23.67 
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       11.44        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85        19.86        67.46        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-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-A2LV TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       94.95         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZL 
       14.73         1.12        95.11        82.06        44.94        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76        55.63       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        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2IP 
       27.25        27.22        24.00        13.48         0.36         6.64 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.51         0.39         0.43         0.59         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        40.96         0.30         4.24         0.07         1.87 
TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        1.74         0.43        47.77         1.64         2.33         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.49         0.89        20.35         7.92        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79        15.55        12.23        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        20.98        26.14        16.14        28.31 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44        10.55        17.75        25.41        16.57        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 
      129.37        96.95        78.71        81.96        29.85        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        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3X 
        0.89        12.49         0.30         0.82        13.35        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         9.17         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       34.62        19.96        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95         9.04        16.14        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        12.16        69.50        10.03        45.57        32.42 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       19.96        65.49        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 
        3.42        18.25        67.20        18.84         5.16        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       16.24        15.42        26.01        29.26        19.13         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                        1.12                         0.07 
  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                       73.18                       210.67 
  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                      24.265                       21.390 
[1] "1.1 - 73.2 (24.3)"  "0.1 - 210.7 (21.4)"
[1] "hr=" "1.3"
D12V2, continuous
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 12(11P12) MUTATED     6   5   3   0
  AMP PEAK 12(11P12) WILD-TYPE 129  65  18   8
D12V3, multiclass
    clus
vv   AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  T1                          6                          129
  T2                          5                           65
  T3                          3                           18
  T4                          0                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                              cls
clus                             0   1
  AMP PEAK 12(11P12) MUTATED     6   5
  AMP PEAK 12(11P12) WILD-TYPE 123  51
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED      6    5
  AMP PEAK 12(11P12) WILD-TYPE  123   51
   clus
vv  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  0                          6                          123
  1                          5                           51
[1] 2 2
[1] FALSE
D12V5, binary
                              cls
clus                             0   1
  AMP PEAK 12(11P12) MUTATED     8   1
  AMP PEAK 12(11P12) WILD-TYPE 100   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED      8    1
  AMP PEAK 12(11P12) WILD-TYPE  100    9
   clus
vv  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  0                          8                          100
  1                          1                            9
[1] 2 2
[1] FALSE
D12V6, binary
                              cls
clus                             0   1
  AMP PEAK 12(11P12) MUTATED     3  12
  AMP PEAK 12(11P12) WILD-TYPE  50 113
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED      3   12
  AMP PEAK 12(11P12) WILD-TYPE   50  113
     clus
vv    AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  NO                           3                           50
  YES                         12                          113
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(11P12) MUTATED               0                               20
  AMP PEAK 12(11P12) WILD-TYPE             6                              222
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 12(11P12) MUTATED                                               1
  AMP PEAK 12(11P12) WILD-TYPE                                             5
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 12(11P12) MUTATED                                     2
  AMP PEAK 12(11P12) WILD-TYPE                                  19
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 12(11P12) MUTATED                                           0
  AMP PEAK 12(11P12) WILD-TYPE                                         3
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 12(11P12) MUTATED                                              0
  AMP PEAK 12(11P12) WILD-TYPE                                           17
D12V7, multiclass
                                               clus
vv                                              AMP PEAK 12(11P12) MUTATED
  ADENOSQUAMOUS                                                          0
  CERVICAL SQUAMOUS CELL CARCINOMA                                      20
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           0
                                               clus
vv                                              AMP PEAK 12(11P12) WILD-TYPE
  ADENOSQUAMOUS                                                            6
  CERVICAL SQUAMOUS CELL CARCINOMA                                       222
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, continuous
D12V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(11P12) MUTATED                                  2     0
  AMP PEAK 12(11P12) WILD-TYPE                                6    19
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(11P12) MUTATED                           2
  AMP PEAK 12(11P12) WILD-TYPE                        26
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(11P12) MUTATED                                           0    17
  AMP PEAK 12(11P12) WILD-TYPE                                         2   185
D12V10, multiclass
                                           clus
vv                                          AMP PEAK 12(11P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              0
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             17
                                           clus
vv                                          AMP PEAK 12(11P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                           26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                              185
[1] 5 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(11P12) MUTATED     4   8
  AMP PEAK 12(11P12) WILD-TYPE  19 155
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED      4    8
  AMP PEAK 12(11P12) WILD-TYPE   19  155
                        clus
vv                       AMP PEAK 12(11P12) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                          8
                        clus
vv                       AMP PEAK 12(11P12) WILD-TYPE
  HISPANIC OR LATINO                               19
  NOT HISPANIC OR LATINO                          155
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                              cls
clus                             0   1
  AMP PEAK 12(11P12) MUTATED    13   8
  AMP PEAK 12(11P12) WILD-TYPE 180  68
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED     13    8
  AMP PEAK 12(11P12) WILD-TYPE  180   68
            clus
vv           AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  TUMOR FREE                         13                          180
  WITH TUMOR                          8                           68
[1] 2 2
[1] FALSE
                              vv
clus                            G1  G2  G3  G4  GX
  AMP PEAK 12(11P12) MUTATED     0   7  12   0   3
  AMP PEAK 12(11P12) WILD-TYPE  18 122 103   1  21
D12V14, multiclass
    clus
vv   AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  G1                          0                           18
  G2                          7                          122
  G3                         12                          103
  G4                          0                            1
  GX                          3                           21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, continuous
[1] "Remove cluster labels:"     "AMP PEAK 12(11P12) MUTATED"
clus
  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                           1                           42 
                  TCGA-EX-A69M                   TCGA-FU-A3TX 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-VS-A9V4                   TCGA-ZJ-AAX4 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-2W-A8YY                   TCGA-BI-A0VR 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A1BJ                   TCGA-C5-A1BL 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A1BQ                   TCGA-C5-A1ME 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A1MF                   TCGA-C5-A1MH 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A2M2                   TCGA-C5-A3HD 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A7CM                   TCGA-C5-A7CO 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A8XH                   TCGA-C5-A907 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-DG-A2KK                   TCGA-DS-A3LQ 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-EK-A2RA                   TCGA-FU-A2QG 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-FU-A3WB                   TCGA-HM-A3JK 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-HM-A4S6                   TCGA-IR-A3L7 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-IR-A3LB                   TCGA-IR-A3LH 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-JX-A3Q0                   TCGA-MA-AA43 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-MU-A5YI                   TCGA-MU-A8JM 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-Q1-A73S                   TCGA-RA-A741 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-VS-A8QF                   TCGA-VS-A94Z 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-VS-A9V0                   TCGA-WL-A834 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-ZJ-A8QR                   TCGA-ZJ-AAXA 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-ZJ-AAXT                   TCGA-ZJ-AB0I 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
D12V16, continuous
D12V17, continuous
D12V18, continuous
D12V19, binary
                              cls
clus                            0  1
  AMP PEAK 12(11P12) MUTATED    4  1
  AMP PEAK 12(11P12) WILD-TYPE 21  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED      4    1
  AMP PEAK 12(11P12) WILD-TYPE   21    2
                         clus
vv                        AMP PEAK 12(11P12) MUTATED
  COMPLETED AS PLANNED                             4
  TREATMENT NOT COMPLETED                          1
                         clus
vv                        AMP PEAK 12(11P12) WILD-TYPE
  COMPLETED AS PLANNED                              21
  TREATMENT NOT COMPLETED                            2
[1] 2 2
[1] FALSE
D12V20, continuous
D12V21, continuous
D12V22, continuous
D12V23, continuous
D12V24, continuous
D12V25, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 12(11P12) MUTATED                                     0
  AMP PEAK 12(11P12) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 12(11P12) MUTATED                                     0
  AMP PEAK 12(11P12) WILD-TYPE                                   7
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 12(11P12) MUTATED                         2                       0
  AMP PEAK 12(11P12) WILD-TYPE                      34                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 12(11P12) MUTATED                         0
  AMP PEAK 12(11P12) WILD-TYPE                      10
D12V26, multiclass
[1] "Remove cluster labels:"     "AMP PEAK 12(11P12) MUTATED"
clus
  AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE 
                           2                           54 
                  TCGA-EX-A449                   TCGA-ZJ-AAX4 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-2W-A8YY                   TCGA-BI-A20A 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A0TN                   TCGA-C5-A1BE 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A1BK                   TCGA-C5-A1BM 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A1M5                   TCGA-C5-A1M7 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A1M8                   TCGA-C5-A1ME 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A1MF                   TCGA-C5-A1MJ 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A1MP                   TCGA-C5-A2LS 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A2LV                   TCGA-C5-A2LX 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A2M1                   TCGA-C5-A3HE 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A3HL                   TCGA-C5-A7CG 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A7CJ                   TCGA-C5-A7UC 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A7UI                   TCGA-C5-A7X8 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A7XC                   TCGA-C5-A8XH 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-C5-A8XI                   TCGA-DG-A2KK 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-DG-A2KL                   TCGA-DR-A0ZM 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-DS-A0VK                   TCGA-DS-A0VL 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-DS-A0VM                   TCGA-DS-A0VN 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-DS-A3LQ                   TCGA-EA-A50E 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-EK-A2RC                   TCGA-EK-A2RK 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-EK-A2RN                   TCGA-EX-A1H5 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-FU-A3EO                   TCGA-HM-A4S6 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-IR-A3LH                   TCGA-IR-A3LI 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-IR-A3LK                   TCGA-MU-A51Y 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-MU-A8JM                   TCGA-UC-A7PD 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-VS-A8QA                   TCGA-VS-A9UT 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                  TCGA-WL-A834                   TCGA-XS-A8TJ 
"AMP PEAK 12(11P12) WILD-TYPE" "AMP PEAK 12(11P12) WILD-TYPE" 
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 12(11P12) MUTATED                                               0
  AMP PEAK 12(11P12) WILD-TYPE                                             3
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 12(11P12) MUTATED                                                2
  AMP PEAK 12(11P12) WILD-TYPE                                             23
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 12(11P12) MUTATED                                                                                   5
  AMP PEAK 12(11P12) WILD-TYPE                                                                                77
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 12(11P12) MUTATED                                                                                             13
  AMP PEAK 12(11P12) WILD-TYPE                                                                                          108
D12V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 12(11P12) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         13
                                                                                              clus
vv                                                                                             AMP PEAK 12(11P12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      77
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V28, binary
                              cls
clus                            0  1
  AMP PEAK 12(11P12) MUTATED    6  3
  AMP PEAK 12(11P12) WILD-TYPE 65 71
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED      6    3
  AMP PEAK 12(11P12) WILD-TYPE   65   71
         clus
vv        AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  ABSENT                           6                           65
  PRESENT                          3                           71
[1] 2 2
[1] FALSE
D12V29, continuous
D12V30, continuous
D12V31, binary
                              cls
clus                             0   1
  AMP PEAK 12(11P12) MUTATED     1   9
  AMP PEAK 12(11P12) WILD-TYPE  48 108
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED      1    9
  AMP PEAK 12(11P12) WILD-TYPE   48  108
                                          clus
vv                                         AMP PEAK 12(11P12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              1
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          9
                                          clus
vv                                         AMP PEAK 12(11P12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               48
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          108
[1] 2 2
[1] FALSE
D12V32, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 12(11P12) MUTATED              1           8          5
  AMP PEAK 12(11P12) WILD-TYPE           14          46         80
D12V33, multiclass
              clus
vv             AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  CURRENT USER                          1                           14
  FORMER USER                           8                           46
  NEVER USED                            5                           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"
D12V34, continuous
D12V35, binary
                              cls
clus                            0  1
  AMP PEAK 12(11P12) MUTATED    6  1
  AMP PEAK 12(11P12) WILD-TYPE 86 17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(11P12) MUTATED      6    1
  AMP PEAK 12(11P12) WILD-TYPE   86   17
         clus
vv        AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  ABSENT                           6                           86
  PRESENT                          1                           17
[1] 2 2
[1] FALSE
                              vv
clus                           CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 12(11P12) MUTATED             0        13     1
  AMP PEAK 12(11P12) WILD-TYPE           5        87     1
D12V36, multiclass
             clus
vv            AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  CARBOPLATIN                          0                            5
  CISPLATIN                           13                           87
  OTHER                                1                            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"
D12V37, continuous
D12V38, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 12(11P12) MUTATED         1        0         0         0        2
  AMP PEAK 12(11P12) WILD-TYPE       4        1         1         1       32
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 12(11P12) MUTATED           5         2        0         1
  AMP PEAK 12(11P12) WILD-TYPE        72        35        4         7
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 12(11P12) MUTATED            0          0         7         0
  AMP PEAK 12(11P12) WILD-TYPE          5          7        37         1
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 12(11P12) MUTATED            0          4         0         0
  AMP PEAK 12(11P12) WILD-TYPE          3         38         7        12
D12V39, multiclass
            clus
vv           AMP PEAK 12(11P12) MUTATED AMP PEAK 12(11P12) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                            0                            1
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            2                           32
  STAGE IB1                           5                           72
  STAGE IB2                           2                           35
  STAGE II                            0                            4
  STAGE IIA                           1                            7
  STAGE IIA1                          0                            5
  STAGE IIA2                          0                            7
  STAGE IIB                           7                           37
  STAGE III                           0                            1
  STAGE IIIA                          0                            3
  STAGE IIIB                          4                           38
  STAGE IVA                           0                            7
  STAGE IVB                           0                           12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(11Q13.3) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(11Q13.3) MUTATED    27  11
  AMP PEAK 13(11Q13.3) WILD-TYPE 187  57
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            38                            244 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            11                             57 
$`AMP PEAK 13(11Q13.3) MUTATED`
TCGA-C5-A8XJ TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BN 
      146.86        17.82        11.44        68.84       144.16         5.46 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A7UC 
       35.01        53.16        73.18        73.45       154.32        17.19 
TCGA-DG-A2KJ TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       95.11         8.28        40.87        26.27         6.64        19.27 
TCGA-EK-A2RJ TCGA-FU-A40J TCGA-HG-A9SC TCGA-IR-A3LA TCGA-IR-A3LH TCGA-JW-A5VK 
        1.74        14.01        16.57       137.16        78.71        20.48 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EI TCGA-VS-A8EJ 
       12.49         0.82        17.23         9.04        23.97        19.96 
TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A9U5 TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9UY 
       53.59        59.18        50.47        45.11        47.47        18.25 
TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       19.13         3.91 

$`AMP PEAK 13(11Q13.3) WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 
       12.59        14.70         8.32         1.48         4.34         0.69 
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        49.48        57.04        23.67        18.74        36.56 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29        82.85        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       46.32        30.21        57.73        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX 
        2.43        20.91        40.93         3.58        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        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       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35       155.77       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK 
       13.61         2.73        50.99        45.83         8.35        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       55.63       117.99       118.65        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        39.55        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.13        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
        0.36        60.72         1.51         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.89         1.45         0.13        40.96         0.30         4.24 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.07         1.87         0.43        47.77         1.64         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.49         0.89        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       15.22        19.79        15.55        12.23        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
       21.67        20.78        14.93         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      129.37        96.95        81.96        29.85        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        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.89         0.30        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         9.17         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
       19.96        54.81        35.05        20.84         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        69.50        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH 
       32.42        65.49        32.15        36.13        11.51        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       43.40        48.39        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ 
       46.92         1.71        14.53        27.25        47.87        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 
       26.07        15.85        14.53         3.42        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        18.25        17.75        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59         1.41         0.16 

  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                          0.82                           0.07 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                        154.32                         210.67 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                        22.225                         22.570 
[1] "0.8 - 154.3 (22.2)" "0.1 - 210.7 (22.6)"
[1] "hr=" "1"  
D13V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 13(11Q13.3) MUTATED    17   9   2   0
  AMP PEAK 13(11Q13.3) WILD-TYPE 118  61  19   8
D13V3, multiclass
    clus
vv   AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  T1                           17                            118
  T2                            9                             61
  T3                            2                             19
  T4                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED    13   8
  AMP PEAK 13(11Q13.3) WILD-TYPE 116  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED     13    8
  AMP PEAK 13(11Q13.3) WILD-TYPE  116   48
   clus
vv  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  0                           13                            116
  1                            8                             48
[1] 2 2
[1] FALSE
D13V5, binary
                                cls
clus                              0  1
  AMP PEAK 13(11Q13.3) MUTATED   13  2
  AMP PEAK 13(11Q13.3) WILD-TYPE 95  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED     13    2
  AMP PEAK 13(11Q13.3) WILD-TYPE   95    8
   clus
vv  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  0                           13                             95
  1                            2                              8
[1] 2 2
[1] FALSE
D13V6, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED     6  17
  AMP PEAK 13(11Q13.3) WILD-TYPE  47 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED      6   17
  AMP PEAK 13(11Q13.3) WILD-TYPE   47  108
     clus
vv    AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  NO                             6                             47
  YES                           17                            108
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(11Q13.3) MUTATED               1                               36
  AMP PEAK 13(11Q13.3) WILD-TYPE             5                              206
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 13(11Q13.3) MUTATED                                               0
  AMP PEAK 13(11Q13.3) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 13(11Q13.3) MUTATED                                     2
  AMP PEAK 13(11Q13.3) WILD-TYPE                                  19
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 13(11Q13.3) MUTATED                                           1
  AMP PEAK 13(11Q13.3) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 13(11Q13.3) MUTATED                                              1
  AMP PEAK 13(11Q13.3) WILD-TYPE                                           16
D13V7, multiclass
                                               clus
vv                                              AMP PEAK 13(11Q13.3) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        36
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 13(11Q13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         206
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, continuous
D13V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(11Q13.3) MUTATED                                  0     2
  AMP PEAK 13(11Q13.3) WILD-TYPE                                8    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(11Q13.3) MUTATED                           5
  AMP PEAK 13(11Q13.3) WILD-TYPE                        23
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 13(11Q13.3) MUTATED                                           1
  AMP PEAK 13(11Q13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 13(11Q13.3) MUTATED      28
  AMP PEAK 13(11Q13.3) WILD-TYPE   174
D13V10, multiclass
                                           clus
vv                                          AMP PEAK 13(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               28
                                           clus
vv                                          AMP PEAK 13(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                174
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED     1  21
  AMP PEAK 13(11Q13.3) WILD-TYPE  22 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED      1   21
  AMP PEAK 13(11Q13.3) WILD-TYPE   22  142
                        clus
vv                       AMP PEAK 13(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       AMP PEAK 13(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            142
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED    25  11
  AMP PEAK 13(11Q13.3) WILD-TYPE 168  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED     25   11
  AMP PEAK 13(11Q13.3) WILD-TYPE  168   65
            clus
vv           AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  TUMOR FREE                           25                            168
  WITH TUMOR                           11                             65
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 13(11Q13.3) MUTATED     0  12  21   1   4
  AMP PEAK 13(11Q13.3) WILD-TYPE  18 117  94   0  20
D13V14, multiclass
    clus
vv   AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  G1                            0                             18
  G2                           12                            117
  G3                           21                             94
  G4                            1                              0
  GX                            4                             20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, continuous
D13V16, continuous
D13V17, continuous
D13V18, continuous
D13V19, binary
                                cls
clus                              0  1
  AMP PEAK 13(11Q13.3) MUTATED    6  1
  AMP PEAK 13(11Q13.3) WILD-TYPE 19  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED      6    1
  AMP PEAK 13(11Q13.3) WILD-TYPE   19    2
                         clus
vv                        AMP PEAK 13(11Q13.3) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 13(11Q13.3) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D13V20, continuous
D13V21, continuous
D13V22, continuous
D13V23, continuous
D13V24, continuous
D13V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 13(11Q13.3) MUTATED                                     0
  AMP PEAK 13(11Q13.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 13(11Q13.3) MUTATED                                     1
  AMP PEAK 13(11Q13.3) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 13(11Q13.3) MUTATED                         6
  AMP PEAK 13(11Q13.3) WILD-TYPE                      30
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 13(11Q13.3) MUTATED                         0
  AMP PEAK 13(11Q13.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 13(11Q13.3) MUTATED                         1
  AMP PEAK 13(11Q13.3) WILD-TYPE                       9
D13V26, multiclass
                                     clus
vv                                    AMP PEAK 13(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 13(11Q13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         30
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 13(11Q13.3) MUTATED                                               0
  AMP PEAK 13(11Q13.3) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 13(11Q13.3) MUTATED                                                3
  AMP PEAK 13(11Q13.3) WILD-TYPE                                             22
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 13(11Q13.3) MUTATED                                                                                   8
  AMP PEAK 13(11Q13.3) WILD-TYPE                                                                                74
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 13(11Q13.3) MUTATED                                                                                             19
  AMP PEAK 13(11Q13.3) WILD-TYPE                                                                                          102
D13V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 13(11Q13.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           19
                                                                                              clus
vv                                                                                             AMP PEAK 13(11Q13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        74
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V28, binary
                                cls
clus                              0  1
  AMP PEAK 13(11Q13.3) MUTATED    7 11
  AMP PEAK 13(11Q13.3) WILD-TYPE 64 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED      7   11
  AMP PEAK 13(11Q13.3) WILD-TYPE   64   63
         clus
vv        AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  ABSENT                             7                             64
  PRESENT                           11                             63
[1] 2 2
[1] FALSE
D13V29, continuous
D13V30, continuous
D13V31, binary
                                cls
clus                              0  1
  AMP PEAK 13(11Q13.3) MUTATED    5 18
  AMP PEAK 13(11Q13.3) WILD-TYPE 44 99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED      5   18
  AMP PEAK 13(11Q13.3) WILD-TYPE   44   99
                                          clus
vv                                         AMP PEAK 13(11Q13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           18
                                          clus
vv                                         AMP PEAK 13(11Q13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             99
[1] 2 2
[1] FALSE
D13V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 13(11Q13.3) MUTATED              1           4         12
  AMP PEAK 13(11Q13.3) WILD-TYPE           14          50         73
D13V33, multiclass
              clus
vv             AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  CURRENT USER                            1                             14
  FORMER USER                             4                             50
  NEVER USED                             12                             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"
D13V34, continuous
D13V35, binary
                                cls
clus                              0  1
  AMP PEAK 13(11Q13.3) MUTATED   12  1
  AMP PEAK 13(11Q13.3) WILD-TYPE 80 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED     12    1
  AMP PEAK 13(11Q13.3) WILD-TYPE   80   17
         clus
vv        AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  ABSENT                            12                             80
  PRESENT                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 13(11Q13.3) MUTATED             0        16     1
  AMP PEAK 13(11Q13.3) WILD-TYPE           5        84     1
D13V36, multiclass
             clus
vv            AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  CARBOPLATIN                            0                              5
  CISPLATIN                             16                             84
  OTHER                                  1                              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"
D13V37, continuous
D13V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 13(11Q13.3) MUTATED         2        0         0         0        5
  AMP PEAK 13(11Q13.3) WILD-TYPE       3        1         1         1       29
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 13(11Q13.3) MUTATED           6         9        0         2
  AMP PEAK 13(11Q13.3) WILD-TYPE        71        28        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 13(11Q13.3) MUTATED            1          1         9         0
  AMP PEAK 13(11Q13.3) WILD-TYPE          4          6        35         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 13(11Q13.3) MUTATED            0          4         0         1
  AMP PEAK 13(11Q13.3) WILD-TYPE          3         38         7        11
D13V39, multiclass
            clus
vv           AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              5                             29
  STAGE IB1                             6                             71
  STAGE IB2                             9                             28
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            1                              4
  STAGE IIA2                            1                              6
  STAGE IIB                             9                             35
  STAGE III                             0                              1
  STAGE IIIA                            0                              3
  STAGE IIIB                            4                             38
  STAGE IVA                             0                              7
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(11Q22.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(11Q22.1) MUTATED    32  14
  AMP PEAK 14(11Q22.1) WILD-TYPE 182  54
  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE 
                            46                            236 
  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE 
                            14                             54 
$`AMP PEAK 14(11Q22.1) MUTATED`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BN 
       17.82        23.67        11.44       144.16       177.04         5.46 
TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A7CH TCGA-C5-A7UC 
       35.01        73.18        73.45        78.35       154.32        17.19 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XK TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VK 
       13.61        50.99        99.91        95.11        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A43B TCGA-EA-A5O9 
       55.63         8.28        13.05        25.02        26.01        25.91 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A3L1 
       26.27         6.64         1.74         0.07         0.10        15.22 
TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-LP-A4AX 
       14.01        16.57        21.67        78.71        21.11        12.49 
TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8Q9 TCGA-VS-A8QF 
       17.23        14.60        11.67        10.03        53.59        59.18 
TCGA-VS-A9U5 TCGA-VS-A9UP TCGA-VS-AA62 TCGA-ZJ-A8QR 
       50.47        47.47        15.42        19.13 

$`AMP PEAK 14(11Q22.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF 
        0.69        17.52        49.48        57.04        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
       36.56       173.29        82.85        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-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-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35       155.77       131.11        94.95         9.34 
TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        2.73        45.83         8.35        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91        14.73         1.12        82.06        44.94        63.98 
TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S 
       31.36        36.89        26.40        24.56        31.73        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82         7.46        14.89        26.79        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG 
       27.22        24.00        13.48         0.36        60.72         1.51 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       19.27         0.39         0.43         0.59         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        40.96         0.30         4.24         0.07         1.87 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN 
        0.43        47.77         1.64         2.33         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       20.35         7.92        19.79        15.55        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       16.14        28.31        35.44        10.55         1.12        17.75 
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       129.37        96.95        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       28.37         8.28        18.15       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       11.28         0.89         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       20.28        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       28.08        34.62        19.96        54.81        35.05        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
       19.59        93.99        12.16        69.50        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA 
       32.42        23.97        19.96        65.49        32.15        36.13 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        51.32        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       27.12        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       27.25        47.87        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       17.75        16.24        26.01        29.26        67.59         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE 
                        177.04                         210.67 
  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE 
                         22.67                          22.57 
[1] "0.1 - 177.0 (22.7)" "0.1 - 210.7 (22.6)"
[1] "hr=" "1.2"
D14V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 14(11Q22.1) MUTATED    25   8   2   0
  AMP PEAK 14(11Q22.1) WILD-TYPE 110  62  19   8
D14V3, multiclass
    clus
vv   AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  T1                           25                            110
  T2                            8                             62
  T3                            2                             19
  T4                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q22.1) MUTATED    22  10
  AMP PEAK 14(11Q22.1) WILD-TYPE 107  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED     22   10
  AMP PEAK 14(11Q22.1) WILD-TYPE  107   46
   clus
vv  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  0                           22                            107
  1                           10                             46
[1] 2 2
[1] FALSE
D14V5, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q22.1) MUTATED   21  2
  AMP PEAK 14(11Q22.1) WILD-TYPE 87  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED     21    2
  AMP PEAK 14(11Q22.1) WILD-TYPE   87    8
   clus
vv  AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  0                           21                             87
  1                            2                              8
[1] 2 2
[1] FALSE
D14V6, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q22.1) MUTATED     6  18
  AMP PEAK 14(11Q22.1) WILD-TYPE  47 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED      6   18
  AMP PEAK 14(11Q22.1) WILD-TYPE   47  107
     clus
vv    AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  NO                             6                             47
  YES                           18                            107
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(11Q22.1) MUTATED               1                               43
  AMP PEAK 14(11Q22.1) WILD-TYPE             5                              199
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 14(11Q22.1) MUTATED                                               0
  AMP PEAK 14(11Q22.1) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 14(11Q22.1) MUTATED                                     2
  AMP PEAK 14(11Q22.1) WILD-TYPE                                  19
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 14(11Q22.1) MUTATED                                           0
  AMP PEAK 14(11Q22.1) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 14(11Q22.1) MUTATED                                              1
  AMP PEAK 14(11Q22.1) WILD-TYPE                                           16
D14V7, multiclass
                                               clus
vv                                              AMP PEAK 14(11Q22.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        43
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 14(11Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         199
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, continuous
D14V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(11Q22.1) MUTATED                                  2     2
  AMP PEAK 14(11Q22.1) WILD-TYPE                                6    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(11Q22.1) MUTATED                           8
  AMP PEAK 14(11Q22.1) WILD-TYPE                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 14(11Q22.1) MUTATED                                           2
  AMP PEAK 14(11Q22.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 14(11Q22.1) MUTATED      31
  AMP PEAK 14(11Q22.1) WILD-TYPE   171
D14V10, multiclass
                                           clus
vv                                          AMP PEAK 14(11Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               31
                                           clus
vv                                          AMP PEAK 14(11Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                171
[1] 5 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(11Q22.1) MUTATED     2  28
  AMP PEAK 14(11Q22.1) WILD-TYPE  21 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED      2   28
  AMP PEAK 14(11Q22.1) WILD-TYPE   21  135
                        clus
vv                       AMP PEAK 14(11Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       AMP PEAK 14(11Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            135
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q22.1) MUTATED    31  13
  AMP PEAK 14(11Q22.1) WILD-TYPE 162  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED     31   13
  AMP PEAK 14(11Q22.1) WILD-TYPE  162   63
            clus
vv           AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  TUMOR FREE                           31                            162
  WITH TUMOR                           13                             63
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 14(11Q22.1) MUTATED     1  15  26   1   3
  AMP PEAK 14(11Q22.1) WILD-TYPE  17 114  89   0  21
D14V14, multiclass
    clus
vv   AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  G1                            1                             17
  G2                           15                            114
  G3                           26                             89
  G4                            1                              0
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, continuous
D14V16, continuous
D14V17, continuous
D14V18, continuous
D14V19, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q22.1) MUTATED    6  1
  AMP PEAK 14(11Q22.1) WILD-TYPE 19  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED      6    1
  AMP PEAK 14(11Q22.1) WILD-TYPE   19    2
                         clus
vv                        AMP PEAK 14(11Q22.1) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 14(11Q22.1) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D14V20, continuous
D14V21, continuous
D14V22, continuous
D14V23, continuous
D14V24, continuous
D14V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 14(11Q22.1) MUTATED                                     0
  AMP PEAK 14(11Q22.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 14(11Q22.1) MUTATED                                     2
  AMP PEAK 14(11Q22.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 14(11Q22.1) MUTATED                         8
  AMP PEAK 14(11Q22.1) WILD-TYPE                      28
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 14(11Q22.1) MUTATED                         0
  AMP PEAK 14(11Q22.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 14(11Q22.1) MUTATED                         2
  AMP PEAK 14(11Q22.1) WILD-TYPE                       8
D14V26, multiclass
                                     clus
vv                                    AMP PEAK 14(11Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        8
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK 14(11Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         28
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 14(11Q22.1) MUTATED                                               0
  AMP PEAK 14(11Q22.1) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 14(11Q22.1) MUTATED                                                4
  AMP PEAK 14(11Q22.1) WILD-TYPE                                             21
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 14(11Q22.1) MUTATED                                                                                   4
  AMP PEAK 14(11Q22.1) WILD-TYPE                                                                                78
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 14(11Q22.1) MUTATED                                                                                             28
  AMP PEAK 14(11Q22.1) WILD-TYPE                                                                                           93
D14V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 14(11Q22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           28
                                                                                              clus
vv                                                                                             AMP PEAK 14(11Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        78
  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"
D14V28, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q22.1) MUTATED   11 15
  AMP PEAK 14(11Q22.1) WILD-TYPE 60 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED     11   15
  AMP PEAK 14(11Q22.1) WILD-TYPE   60   59
         clus
vv        AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  ABSENT                            11                             60
  PRESENT                           15                             59
[1] 2 2
[1] FALSE
D14V29, continuous
D14V30, continuous
D14V31, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q22.1) MUTATED   12 19
  AMP PEAK 14(11Q22.1) WILD-TYPE 37 98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED     12   19
  AMP PEAK 14(11Q22.1) WILD-TYPE   37   98
                                          clus
vv                                         AMP PEAK 14(11Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           19
                                          clus
vv                                         AMP PEAK 14(11Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             98
[1] 2 2
[1] FALSE
D14V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 14(11Q22.1) MUTATED              3           7         14
  AMP PEAK 14(11Q22.1) WILD-TYPE           12          47         71
D14V33, multiclass
              clus
vv             AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                             7                             47
  NEVER USED                             14                             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V34, continuous
D14V35, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q22.1) MUTATED   18  1
  AMP PEAK 14(11Q22.1) WILD-TYPE 74 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q22.1) MUTATED     18    1
  AMP PEAK 14(11Q22.1) WILD-TYPE   74   17
         clus
vv        AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  ABSENT                            18                             74
  PRESENT                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 14(11Q22.1) MUTATED             1        15     1
  AMP PEAK 14(11Q22.1) WILD-TYPE           4        85     1
D14V36, multiclass
             clus
vv            AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             15                             85
  OTHER                                  1                              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"
D14V37, continuous
D14V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 14(11Q22.1) MUTATED         1        0         0         0       10
  AMP PEAK 14(11Q22.1) WILD-TYPE       4        1         1         1       24
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 14(11Q22.1) MUTATED          10         7        0         2
  AMP PEAK 14(11Q22.1) WILD-TYPE        67        30        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 14(11Q22.1) MUTATED            2          1         8         0
  AMP PEAK 14(11Q22.1) WILD-TYPE          3          6        36         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 14(11Q22.1) MUTATED            0          4         0         1
  AMP PEAK 14(11Q22.1) WILD-TYPE          3         38         7        11
D14V39, multiclass
            clus
vv           AMP PEAK 14(11Q22.1) MUTATED AMP PEAK 14(11Q22.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             10                             24
  STAGE IB1                            10                             67
  STAGE IB2                             7                             30
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            2                              3
  STAGE IIA2                            1                              6
  STAGE IIB                             8                             36
  STAGE III                             0                              1
  STAGE IIIA                            0                              3
  STAGE IIIB                            4                             38
  STAGE IVA                             0                              7
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(13Q22.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(13Q22.1) MUTATED    46  18
  AMP PEAK 15(13Q22.1) WILD-TYPE 168  50
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                            64                            218 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                            18                             50 
$`AMP PEAK 15(13Q22.1) MUTATED`
TCGA-VS-A9V4 TCGA-4J-AA1J TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MJ 
        4.34        17.82        82.85         5.46        35.01         0.46 
TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CG 
        3.58       100.14        38.43        52.01        17.85       210.67 
TCGA-C5-A7CH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8YR TCGA-DG-A2KH 
      154.32        13.61         2.73        50.99        27.52         1.12 
TCGA-DS-A0VM TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 
      117.99        31.36        13.05        12.13         7.46        25.91 
TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RE TCGA-EK-A2RJ 
       27.22         0.36        60.72         1.51         1.87         1.74 
TCGA-EK-A2RM TCGA-EK-A3GN TCGA-EX-A8YF TCGA-FU-A3HY TCGA-FU-A40J TCGA-FU-A5XV 
        1.64         0.89        15.55        31.36        14.01        10.55 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LK TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q0 
      147.39        66.81        29.85        21.44        21.11       209.59 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       20.91         0.89        35.05         2.96        16.41         9.04 
TCGA-Q1-A73R TCGA-VS-A8EC TCGA-VS-A8Q8 TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A950 
       18.64        46.52        32.15        59.18        39.78        40.14 
TCGA-VS-A954 TCGA-VS-A959 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UQ TCGA-VS-A9UV 
       56.35        51.32        28.50        27.12        41.52         3.42 
TCGA-VS-A9V2 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       18.25        26.01        67.59        19.13 

$`AMP PEAK 15(13Q22.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 
      146.86        12.59        14.70         8.32         1.48         0.69 
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BQ 
       18.74        36.56       144.16       177.04       173.29        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-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS 
       38.99        35.61         2.43        20.91        40.93        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HE 
       73.18        73.45        83.05        78.35        33.24        18.02 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       20.42       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XH 
       17.19       155.77       131.11        94.95         9.34        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        20.81        20.91        14.73 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       95.11        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76        55.63       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       31.53        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       26.01        24.82        14.89        26.79        27.29        27.25 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK 
       24.00        13.48        26.27         6.64        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.89         1.45         0.13        40.96 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
        0.30         4.24         0.07         0.43        47.77         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.10         0.49        20.35         7.92        15.22 
TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
       19.79        12.23        23.84        19.04        16.11        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 
       20.98        26.14        16.14        28.31        35.44         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
        9.44       137.16       129.37        96.95        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX 
       28.37         8.28        18.15        44.61        11.28        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         9.17         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       19.96        54.81        20.84        17.23        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         9.34        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59        14.60        11.67        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        45.57        32.42        23.97        19.96        65.49 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       53.59        36.13        11.51        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 
        4.73        33.37        58.45        15.68        55.50        50.14 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH 
       50.47        43.40        48.39        29.95        24.30        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       45.11         1.71        14.53        27.25        47.87        47.47 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       26.07        15.85        14.53        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-AAXA 
        5.16        17.75        16.24        15.42        29.26         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                          0.36                           0.07 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                        210.67                         177.04 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                        23.675                         22.570 
[1] "0.4 - 210.7 (23.7)" "0.1 - 177.0 (22.6)"
[1] "hr=" "1.2"
D15V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 15(13Q22.1) MUTATED    29  10   7   3
  AMP PEAK 15(13Q22.1) WILD-TYPE 106  60  14   5
D15V3, multiclass
    clus
vv   AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  T1                           29                            106
  T2                           10                             60
  T3                            7                             14
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED    26  13
  AMP PEAK 15(13Q22.1) WILD-TYPE 103  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     26   13
  AMP PEAK 15(13Q22.1) WILD-TYPE  103   43
   clus
vv  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  0                           26                            103
  1                           13                             43
[1] 2 2
[1] FALSE
D15V5, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   26  0
  AMP PEAK 15(13Q22.1) WILD-TYPE 82 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     26    0
  AMP PEAK 15(13Q22.1) WILD-TYPE   82   10
   clus
vv  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  0                           26                             82
  1                            0                             10
[1] 2 2
[1] FALSE
D15V6, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   13 27
  AMP PEAK 15(13Q22.1) WILD-TYPE 40 98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     13   27
  AMP PEAK 15(13Q22.1) WILD-TYPE   40   98
     clus
vv    AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  NO                            13                             40
  YES                           27                             98
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(13Q22.1) MUTATED               1                               53
  AMP PEAK 15(13Q22.1) WILD-TYPE             5                              189
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 15(13Q22.1) MUTATED                                               0
  AMP PEAK 15(13Q22.1) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 15(13Q22.1) MUTATED                                     6
  AMP PEAK 15(13Q22.1) WILD-TYPE                                  15
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 15(13Q22.1) MUTATED                                           0
  AMP PEAK 15(13Q22.1) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 15(13Q22.1) MUTATED                                              5
  AMP PEAK 15(13Q22.1) WILD-TYPE                                           12
D15V7, multiclass
                                               clus
vv                                              AMP PEAK 15(13Q22.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        53
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             5
                                               clus
vv                                              AMP PEAK 15(13Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         189
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, continuous
D15V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(13Q22.1) MUTATED                                  1     3
  AMP PEAK 15(13Q22.1) WILD-TYPE                                7    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(13Q22.1) MUTATED                           7
  AMP PEAK 15(13Q22.1) WILD-TYPE                        21
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 15(13Q22.1) MUTATED                                           1
  AMP PEAK 15(13Q22.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 15(13Q22.1) MUTATED      45
  AMP PEAK 15(13Q22.1) WILD-TYPE   157
D15V10, multiclass
                                           clus
vv                                          AMP PEAK 15(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               45
                                           clus
vv                                          AMP PEAK 15(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                157
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED     1  40
  AMP PEAK 15(13Q22.1) WILD-TYPE  22 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED      1   40
  AMP PEAK 15(13Q22.1) WILD-TYPE   22  123
                        clus
vv                       AMP PEAK 15(13Q22.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       AMP PEAK 15(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            123
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED    38  22
  AMP PEAK 15(13Q22.1) WILD-TYPE 155  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     38   22
  AMP PEAK 15(13Q22.1) WILD-TYPE  155   54
            clus
vv           AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  TUMOR FREE                           38                            155
  WITH TUMOR                           22                             54
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 15(13Q22.1) MUTATED     2  29  28   0   6
  AMP PEAK 15(13Q22.1) WILD-TYPE  16 100  87   1  18
D15V14, multiclass
    clus
vv   AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  G1                            2                             16
  G2                           29                            100
  G3                           28                             87
  G4                            0                              1
  GX                            6                             18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, continuous
D15V16, continuous
D15V17, continuous
D15V18, continuous
D15V19, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED    5  1
  AMP PEAK 15(13Q22.1) WILD-TYPE 20  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED      5    1
  AMP PEAK 15(13Q22.1) WILD-TYPE   20    2
                         clus
vv                        AMP PEAK 15(13Q22.1) MUTATED
  COMPLETED AS PLANNED                               5
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 15(13Q22.1) WILD-TYPE
  COMPLETED AS PLANNED                                20
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D15V20, continuous
D15V21, continuous
D15V22, continuous
D15V23, continuous
D15V24, continuous
D15V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 15(13Q22.1) MUTATED                                     0
  AMP PEAK 15(13Q22.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 15(13Q22.1) MUTATED                                     2
  AMP PEAK 15(13Q22.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 15(13Q22.1) MUTATED                         8
  AMP PEAK 15(13Q22.1) WILD-TYPE                      28
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 15(13Q22.1) MUTATED                         1
  AMP PEAK 15(13Q22.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 15(13Q22.1) MUTATED                         1
  AMP PEAK 15(13Q22.1) WILD-TYPE                       9
D15V26, multiclass
                                     clus
vv                                    AMP PEAK 15(13Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        8
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 15(13Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         28
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 15(13Q22.1) MUTATED                                               0
  AMP PEAK 15(13Q22.1) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 15(13Q22.1) MUTATED                                                6
  AMP PEAK 15(13Q22.1) WILD-TYPE                                             19
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 15(13Q22.1) MUTATED                                                                                  21
  AMP PEAK 15(13Q22.1) WILD-TYPE                                                                                61
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 15(13Q22.1) MUTATED                                                                                             27
  AMP PEAK 15(13Q22.1) WILD-TYPE                                                                                           94
D15V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 15(13Q22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           27
                                                                                              clus
vv                                                                                             AMP PEAK 15(13Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           19
  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)                             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"
D15V28, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   11 21
  AMP PEAK 15(13Q22.1) WILD-TYPE 60 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     11   21
  AMP PEAK 15(13Q22.1) WILD-TYPE   60   53
         clus
vv        AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  ABSENT                            11                             60
  PRESENT                           21                             53
[1] 2 2
[1] FALSE
D15V29, continuous
D15V30, continuous
D15V31, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   11 22
  AMP PEAK 15(13Q22.1) WILD-TYPE 38 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     11   22
  AMP PEAK 15(13Q22.1) WILD-TYPE   38   95
                                          clus
vv                                         AMP PEAK 15(13Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           22
                                          clus
vv                                         AMP PEAK 15(13Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             95
[1] 2 2
[1] FALSE
D15V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 15(13Q22.1) MUTATED              1          14         21
  AMP PEAK 15(13Q22.1) WILD-TYPE           14          40         64
D15V33, multiclass
              clus
vv             AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  CURRENT USER                            1                             14
  FORMER USER                            14                             40
  NEVER USED                             21                             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"
D15V34, continuous
D15V35, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   19  2
  AMP PEAK 15(13Q22.1) WILD-TYPE 73 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     19    2
  AMP PEAK 15(13Q22.1) WILD-TYPE   73   16
         clus
vv        AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  ABSENT                            19                             73
  PRESENT                            2                             16
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 15(13Q22.1) MUTATED             1        16     1
  AMP PEAK 15(13Q22.1) WILD-TYPE           4        84     1
D15V36, multiclass
             clus
vv            AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             16                             84
  OTHER                                  1                              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"
D15V37, continuous
[1] "Remove cluster labels:"       "AMP PEAK 15(13Q22.1) MUTATED"
clus
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1MH                     TCGA-C5-A1ML 
"AMP PEAK 15(13Q22.1) WILD-TYPE" "AMP PEAK 15(13Q22.1) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-EK-A2RO 
"AMP PEAK 15(13Q22.1) WILD-TYPE" "AMP PEAK 15(13Q22.1) WILD-TYPE" 
                    TCGA-GH-A9DA                     TCGA-HM-A3JK 
"AMP PEAK 15(13Q22.1) WILD-TYPE" "AMP PEAK 15(13Q22.1) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-JX-A3Q8 
"AMP PEAK 15(13Q22.1) WILD-TYPE" "AMP PEAK 15(13Q22.1) WILD-TYPE" 
                    TCGA-MA-AA3W                     TCGA-MA-AA3Z 
"AMP PEAK 15(13Q22.1) WILD-TYPE" "AMP PEAK 15(13Q22.1) WILD-TYPE" 
                    TCGA-MA-AA42                     TCGA-MU-A51Y 
"AMP PEAK 15(13Q22.1) WILD-TYPE" "AMP PEAK 15(13Q22.1) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-MY-A913 
"AMP PEAK 15(13Q22.1) WILD-TYPE" "AMP PEAK 15(13Q22.1) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"AMP PEAK 15(13Q22.1) WILD-TYPE" 
D15V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 15(13Q22.1) MUTATED         3        1         0         0        9
  AMP PEAK 15(13Q22.1) WILD-TYPE       2        0         1         1       25
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 15(13Q22.1) MUTATED          14         9        0         1
  AMP PEAK 15(13Q22.1) WILD-TYPE        63        28        4         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 15(13Q22.1) MUTATED            0          0         9         1
  AMP PEAK 15(13Q22.1) WILD-TYPE          5          7        35         0
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 15(13Q22.1) MUTATED            2          9         3         1
  AMP PEAK 15(13Q22.1) WILD-TYPE          1         33         4        11
D15V39, multiclass
            clus
vv           AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              9                             25
  STAGE IB1                            14                             63
  STAGE IB2                             9                             28
  STAGE II                              0                              4
  STAGE IIA                             1                              7
  STAGE IIA1                            0                              5
  STAGE IIA2                            0                              7
  STAGE IIB                             9                             35
  STAGE III                             1                              0
  STAGE IIIA                            2                              1
  STAGE IIIB                            9                             33
  STAGE IVA                             3                              4
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(13Q34) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 16(13Q34) MUTATED    49  19
  AMP PEAK 16(13Q34) WILD-TYPE 165  49
  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE 
                          68                          214 
  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE 
                          19                           49 
$`AMP PEAK 16(13Q34) MUTATED`
TCGA-EX-A69M TCGA-VS-A9V4 TCGA-4J-AA1J TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MK 
        8.32         4.34        17.82        35.01         0.46         2.43 
TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X5 
      100.14        17.85       210.67       154.32       131.11        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-DS-A0VM TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A5O9 
      117.99         8.28        37.35        31.36        13.05        25.91 
TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RE 
       27.22         0.36        60.72         1.51         0.59         1.87 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EX-A1H6 TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3NI 
        1.74         1.64         7.92        15.55        23.84        20.98 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       14.01        10.55       147.39        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AW 
       27.42        21.44        21.11       209.59        11.28         0.89 
TCGA-MA-AA3Z TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73Q TCGA-Q1-A73R 
       19.56        35.05         2.96        16.41         9.34        18.64 
TCGA-R2-A69V TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QH TCGA-VS-A954 TCGA-VS-A959 
       19.59        19.96        32.15        39.78        56.35        51.32 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UQ TCGA-VS-A9V2 TCGA-WL-A834 
       48.39        28.50        27.12        41.52        18.25        26.01 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       67.59        19.13 

$`AMP PEAK 16(13Q34) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        12.59        14.70         1.48         0.69        17.52 
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99        35.61        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       33.24        52.01        18.02        20.42       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
        9.34         8.35        99.91        20.81        20.91        14.73 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       95.11        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76        55.63       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QE 
       17.52        39.55        40.87        30.90        31.53        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82         7.46        14.89        26.79        27.29        27.25 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK 
       24.00        13.48        26.27         6.64        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        4.24         0.07         0.43        47.77         2.33         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L 
        0.10         0.49         0.89        20.35        15.22        19.79 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
       12.23        19.04        16.11        31.36        36.26        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       16.14        28.31        35.44         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA 
       16.57        21.67        20.78        14.93         9.44       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI 
       66.81       129.37        96.95        36.36         3.29        24.56 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 
       20.48        15.58        28.37         8.28        18.15        44.61 
TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       20.91        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       20.28        17.82         9.17         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
       34.62        19.96        54.81        20.84        17.23        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       22.62        14.60        11.67        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL 
       10.03        46.52        45.57        32.42        23.97        65.49 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        36.13        11.51        59.18        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       16.64         4.73        33.37        40.14        58.45        15.68 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UD 
       55.50        50.14        50.47        43.40        29.95        24.30 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       46.92        45.11         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       47.47        26.07        15.85        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       67.20        18.84         5.16        17.75        16.24        15.42 
TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26         1.41         0.16         3.91 

  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE 
                        0.36                         0.07 
  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE 
                      210.67                       177.04 
  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE 
                      21.275                       22.800 
[1] "0.4 - 210.7 (21.3)" "0.1 - 177.0 (22.8)"
[1] "hr=" "1.2"
D16V2, continuous
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 16(13Q34) MUTATED    31  16   5   1
  AMP PEAK 16(13Q34) WILD-TYPE 104  54  16   7
D16V3, multiclass
    clus
vv   AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  T1                         31                          104
  T2                         16                           54
  T3                          5                           16
  T4                          1                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                              cls
clus                            0  1
  AMP PEAK 16(13Q34) MUTATED   31 13
  AMP PEAK 16(13Q34) WILD-TYPE 98 43
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED     31   13
  AMP PEAK 16(13Q34) WILD-TYPE   98   43
   clus
vv  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  0                         31                           98
  1                         13                           43
[1] 2 2
[1] FALSE
D16V5, binary
                              cls
clus                            0  1
  AMP PEAK 16(13Q34) MUTATED   28  2
  AMP PEAK 16(13Q34) WILD-TYPE 80  8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED     28    2
  AMP PEAK 16(13Q34) WILD-TYPE   80    8
   clus
vv  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  0                         28                           80
  1                          2                            8
[1] 2 2
[1] FALSE
D16V6, binary
                              cls
clus                            0  1
  AMP PEAK 16(13Q34) MUTATED   15 33
  AMP PEAK 16(13Q34) WILD-TYPE 38 92
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED     15   33
  AMP PEAK 16(13Q34) WILD-TYPE   38   92
     clus
vv    AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  NO                          15                           38
  YES                         33                           92
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(13Q34) MUTATED               1                               57
  AMP PEAK 16(13Q34) WILD-TYPE             5                              185
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 16(13Q34) MUTATED                                               0
  AMP PEAK 16(13Q34) WILD-TYPE                                             6
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 16(13Q34) MUTATED                                     6
  AMP PEAK 16(13Q34) WILD-TYPE                                  15
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 16(13Q34) MUTATED                                           0
  AMP PEAK 16(13Q34) WILD-TYPE                                         3
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 16(13Q34) MUTATED                                              5
  AMP PEAK 16(13Q34) WILD-TYPE                                           12
D16V7, multiclass
                                               clus
vv                                              AMP PEAK 16(13Q34) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      57
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           5
                                               clus
vv                                              AMP PEAK 16(13Q34) WILD-TYPE
  ADENOSQUAMOUS                                                            5
  CERVICAL SQUAMOUS CELL CARCINOMA                                       185
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, continuous
D16V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(13Q34) MUTATED                                  2     3
  AMP PEAK 16(13Q34) WILD-TYPE                                6    16
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(13Q34) MUTATED                           6
  AMP PEAK 16(13Q34) WILD-TYPE                        22
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 16(13Q34) MUTATED                                           1    51
  AMP PEAK 16(13Q34) WILD-TYPE                                         1   151
D16V10, multiclass
                                           clus
vv                                          AMP PEAK 16(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              3
  BLACK OR AFRICAN AMERICAN                                          6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             51
                                           clus
vv                                          AMP PEAK 16(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                           22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              151
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                              cls
clus                             0   1
  AMP PEAK 16(13Q34) MUTATED     3  39
  AMP PEAK 16(13Q34) WILD-TYPE  20 124
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED      3   39
  AMP PEAK 16(13Q34) WILD-TYPE   20  124
                        clus
vv                       AMP PEAK 16(13Q34) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         39
                        clus
vv                       AMP PEAK 16(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               20
  NOT HISPANIC OR LATINO                          124
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                              cls
clus                             0   1
  AMP PEAK 16(13Q34) MUTATED    43  21
  AMP PEAK 16(13Q34) WILD-TYPE 150  55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED     43   21
  AMP PEAK 16(13Q34) WILD-TYPE  150   55
            clus
vv           AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  TUMOR FREE                         43                          150
  WITH TUMOR                         21                           55
[1] 2 2
[1] FALSE
                              vv
clus                            G1  G2  G3  G4  GX
  AMP PEAK 16(13Q34) MUTATED     3  25  32   1   6
  AMP PEAK 16(13Q34) WILD-TYPE  15 104  83   0  18
D16V14, multiclass
    clus
vv   AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  G1                          3                           15
  G2                         25                          104
  G3                         32                           83
  G4                          1                            0
  GX                          6                           18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, continuous
D16V16, continuous
D16V17, continuous
D16V18, continuous
D16V19, binary
                              cls
clus                            0  1
  AMP PEAK 16(13Q34) MUTATED    2  2
  AMP PEAK 16(13Q34) WILD-TYPE 23  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED      2    2
  AMP PEAK 16(13Q34) WILD-TYPE   23    1
                         clus
vv                        AMP PEAK 16(13Q34) MUTATED
  COMPLETED AS PLANNED                             2
  TREATMENT NOT COMPLETED                          2
                         clus
vv                        AMP PEAK 16(13Q34) WILD-TYPE
  COMPLETED AS PLANNED                              23
  TREATMENT NOT COMPLETED                            1
[1] 2 2
[1] FALSE
D16V20, continuous
D16V21, continuous
D16V22, continuous
D16V23, continuous
D16V24, continuous
D16V25, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 16(13Q34) MUTATED                                     0
  AMP PEAK 16(13Q34) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 16(13Q34) MUTATED                                     3
  AMP PEAK 16(13Q34) WILD-TYPE                                   4
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 16(13Q34) MUTATED                         7                       0
  AMP PEAK 16(13Q34) WILD-TYPE                      29                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 16(13Q34) MUTATED                         1
  AMP PEAK 16(13Q34) WILD-TYPE                       9
D16V26, multiclass
                                     clus
vv                                    AMP PEAK 16(13Q34) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          3
  OTHER LOCATION, SPECIFY                                      7
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      1
                                     clus
vv                                    AMP PEAK 16(13Q34) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                       29
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 16(13Q34) MUTATED                                               0
  AMP PEAK 16(13Q34) WILD-TYPE                                             3
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 16(13Q34) MUTATED                                                7
  AMP PEAK 16(13Q34) WILD-TYPE                                             18
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 16(13Q34) MUTATED                                                                                  24
  AMP PEAK 16(13Q34) WILD-TYPE                                                                                58
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 16(13Q34) MUTATED                                                                                             27
  AMP PEAK 16(13Q34) WILD-TYPE                                                                                           94
D16V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 16(13Q34) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    24
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         27
                                                                                              clus
vv                                                                                             AMP PEAK 16(13Q34) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         18
  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)                           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"
D16V28, binary
                              cls
clus                            0  1
  AMP PEAK 16(13Q34) MUTATED   11 19
  AMP PEAK 16(13Q34) WILD-TYPE 60 55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED     11   19
  AMP PEAK 16(13Q34) WILD-TYPE   60   55
         clus
vv        AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  ABSENT                          11                           60
  PRESENT                         19                           55
[1] 2 2
[1] FALSE
D16V29, continuous
D16V30, continuous
D16V31, binary
                              cls
clus                            0  1
  AMP PEAK 16(13Q34) MUTATED   15 23
  AMP PEAK 16(13Q34) WILD-TYPE 34 94
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED     15   23
  AMP PEAK 16(13Q34) WILD-TYPE   34   94
                                          clus
vv                                         AMP PEAK 16(13Q34) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         23
                                          clus
vv                                         AMP PEAK 16(13Q34) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           94
[1] 2 2
[1] FALSE
D16V32, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 16(13Q34) MUTATED              3          12         20
  AMP PEAK 16(13Q34) WILD-TYPE           12          42         65
D16V33, multiclass
              clus
vv             AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  CURRENT USER                          3                           12
  FORMER USER                          12                           42
  NEVER USED                           20                           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"
D16V34, continuous
D16V35, binary
                              cls
clus                            0  1
  AMP PEAK 16(13Q34) MUTATED   19  1
  AMP PEAK 16(13Q34) WILD-TYPE 73 17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(13Q34) MUTATED     19    1
  AMP PEAK 16(13Q34) WILD-TYPE   73   17
         clus
vv        AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  ABSENT                          19                           73
  PRESENT                          1                           17
[1] 2 2
[1] FALSE
                              vv
clus                           CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 16(13Q34) MUTATED             2        21     1
  AMP PEAK 16(13Q34) WILD-TYPE           3        79     1
D16V36, multiclass
             clus
vv            AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  CARBOPLATIN                          2                            3
  CISPLATIN                           21                           79
  OTHER                                1                            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"
D16V37, continuous
[1] "Remove cluster labels:"     "AMP PEAK 16(13Q34) MUTATED"
clus
  AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE 
                           1                           16 
                  TCGA-C5-A1BN                   TCGA-C5-A1MH 
"AMP PEAK 16(13Q34) WILD-TYPE" "AMP PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-C5-A1ML                   TCGA-C5-A1MN 
"AMP PEAK 16(13Q34) WILD-TYPE" "AMP PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-C5-A1MP                   TCGA-EK-A2RO 
"AMP PEAK 16(13Q34) WILD-TYPE" "AMP PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GH-A9DA                   TCGA-HM-A3JK 
"AMP PEAK 16(13Q34) WILD-TYPE" "AMP PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-JW-A852                   TCGA-JX-A3Q8 
"AMP PEAK 16(13Q34) WILD-TYPE" "AMP PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-MA-AA3W                   TCGA-MA-AA42 
"AMP PEAK 16(13Q34) WILD-TYPE" "AMP PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-MU-A51Y                   TCGA-MU-A8JM 
"AMP PEAK 16(13Q34) WILD-TYPE" "AMP PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-MY-A913                   TCGA-ZX-AA5X 
"AMP PEAK 16(13Q34) WILD-TYPE" "AMP PEAK 16(13Q34) WILD-TYPE" 
D16V38, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 16(13Q34) MUTATED         3        1         0         0        9
  AMP PEAK 16(13Q34) WILD-TYPE       2        0         1         1       25
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 16(13Q34) MUTATED          16         8        1         2
  AMP PEAK 16(13Q34) WILD-TYPE        61        29        3         6
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 16(13Q34) MUTATED            2          1         9         1
  AMP PEAK 16(13Q34) WILD-TYPE          3          6        35         0
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 16(13Q34) MUTATED            1          9         1         2
  AMP PEAK 16(13Q34) WILD-TYPE          2         33         6        10
D16V39, multiclass
            clus
vv           AMP PEAK 16(13Q34) MUTATED AMP PEAK 16(13Q34) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                            1                            0
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            9                           25
  STAGE IB1                          16                           61
  STAGE IB2                           8                           29
  STAGE II                            1                            3
  STAGE IIA                           2                            6
  STAGE IIA1                          2                            3
  STAGE IIA2                          1                            6
  STAGE IIB                           9                           35
  STAGE III                           1                            0
  STAGE IIIA                          1                            2
  STAGE IIIB                          9                           33
  STAGE IVA                           1                            6
  STAGE IVB                           2                           10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(15Q26.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(15Q26.1) MUTATED    56  16
  AMP PEAK 17(15Q26.1) WILD-TYPE 158  52
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            72                            210 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            16                             52 
$`AMP PEAK 17(15Q26.1) MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1M6 TCGA-C5-A1M8 
       17.82        49.48        18.74       177.04        31.40        30.21 
TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ 
       57.73        35.61         2.43         3.58        73.18       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UI 
       33.24        52.01        18.02       101.82        20.35        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KL 
        9.34         2.73        20.91        14.73         1.12        44.94 
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A50E TCGA-EA-A556 
       87.75        55.63         8.28        37.35         7.46        14.89 
TCGA-EA-A5O9 TCGA-EK-A2PI TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EX-A3L1 
       25.91        19.27         4.24         0.07         1.64        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A9SC 
       19.79        15.55        23.84        10.55        17.75        16.57 
TCGA-HM-A3JK TCGA-IR-A3LA TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A5QV 
       20.78       137.16        27.42        21.44        15.58        20.91 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MA-AA3W TCGA-MA-AA43 TCGA-MY-A5BE TCGA-Q1-A73S 
       11.28         0.30        22.52        11.38        35.05        22.62 
TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q9 
       19.59        12.16        46.52        32.42        23.97        53.59 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A950 TCGA-VS-A959 TCGA-VS-A9UB TCGA-VS-A9UC 
       11.51        59.18        40.14        51.32        29.95        27.12 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-ZJ-A8QR 
       14.53        47.87        47.47        41.52        14.53        19.13 

$`AMP PEAK 17(15Q26.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
        0.69        17.52        57.04        23.67        11.44        68.84 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       67.46        46.32        35.01        53.16        38.99         0.46 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       20.91        40.93        44.22        73.45        83.05        78.35 
TCGA-C5-A2M1 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK 
       38.43        17.85        20.42       210.67       154.32       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X5 
       15.48       147.35        17.19       155.77       131.11        13.61 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99        45.83         8.35        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK 
       20.81        95.11        82.06        63.98        58.88        36.76 
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-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        40.87        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        36.89        26.40        24.56        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       12.13        24.82        26.79        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       24.00        13.48         0.36        60.72        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.51         0.39         0.43         0.59         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK 
        0.13        40.96         0.30         1.87         1.74         0.43 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       47.77         2.33         0.07         0.10         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       20.35         7.92        12.23        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26        20.98        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
       35.44         1.12        25.41        21.67        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      147.39        66.81       129.37        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B 
       29.85        36.36         3.29        24.56        20.48        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AW 
        8.28        18.15        21.11       209.59        44.61         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
       12.49         0.82        13.35        20.28        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        9.17         8.52        28.08        34.62        19.96        54.81 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       20.84        17.23         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB 
       18.64        14.60        11.67        93.99        69.50        10.03 
TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QH 
       45.57        19.96        65.49        32.15        36.13        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       31.27        40.87        16.64         4.73        33.37        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 
       15.68        56.35        55.50        50.14        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       48.39        28.50        24.30        46.92        45.11         1.71 
TCGA-VS-A9UM TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       27.25        26.07        15.85         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       18.84         5.16        18.25        17.75        16.24        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       26.01        29.26        67.59         1.41         0.16         3.91 

  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                        177.04                         210.67 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                        21.175                         23.590 
[1] "0.1 - 177.0 (21.2)" "0.1 - 210.7 (23.6)"
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 17(15Q26.1) MUTATED    27  22   8   1
  AMP PEAK 17(15Q26.1) WILD-TYPE 108  48  13   7
D17V3, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  T1                           27                            108
  T2                           22                             48
  T3                            8                             13
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   30 16
  AMP PEAK 17(15Q26.1) WILD-TYPE 99 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     30   16
  AMP PEAK 17(15Q26.1) WILD-TYPE   99   40
   clus
vv  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  0                           30                             99
  1                           16                             40
[1] 2 2
[1] FALSE
D17V5, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   28  0
  AMP PEAK 17(15Q26.1) WILD-TYPE 80 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     28    0
  AMP PEAK 17(15Q26.1) WILD-TYPE   80   10
   clus
vv  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  0                           28                             80
  1                            0                             10
[1] 2 2
[1] FALSE
D17V6, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   10 37
  AMP PEAK 17(15Q26.1) WILD-TYPE 43 88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     10   37
  AMP PEAK 17(15Q26.1) WILD-TYPE   43   88
     clus
vv    AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  NO                            10                             43
  YES                           37                             88
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED               3                               61
  AMP PEAK 17(15Q26.1) WILD-TYPE             3                              181
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 17(15Q26.1) MUTATED                                               3
  AMP PEAK 17(15Q26.1) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                                     3
  AMP PEAK 17(15Q26.1) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 17(15Q26.1) MUTATED                                           2
  AMP PEAK 17(15Q26.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 17(15Q26.1) MUTATED                                              4
  AMP PEAK 17(15Q26.1) WILD-TYPE                                           13
D17V7, multiclass
                                               clus
vv                                              AMP PEAK 17(15Q26.1) MUTATED
  ADENOSQUAMOUS                                                            3
  CERVICAL SQUAMOUS CELL CARCINOMA                                        61
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              AMP PEAK 17(15Q26.1) WILD-TYPE
  ADENOSQUAMOUS                                                              3
  CERVICAL SQUAMOUS CELL CARCINOMA                                         181
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, continuous
D17V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(15Q26.1) MUTATED                                  4     5
  AMP PEAK 17(15Q26.1) WILD-TYPE                                4    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(15Q26.1) MUTATED                           4
  AMP PEAK 17(15Q26.1) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 17(15Q26.1) MUTATED                                           1
  AMP PEAK 17(15Q26.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 17(15Q26.1) MUTATED      50
  AMP PEAK 17(15Q26.1) WILD-TYPE   152
D17V10, multiclass
                                           clus
vv                                          AMP PEAK 17(15Q26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               50
                                           clus
vv                                          AMP PEAK 17(15Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                152
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED     7  42
  AMP PEAK 17(15Q26.1) WILD-TYPE  16 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      7   42
  AMP PEAK 17(15Q26.1) WILD-TYPE   16  121
                        clus
vv                       AMP PEAK 17(15Q26.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       AMP PEAK 17(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            121
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    51  17
  AMP PEAK 17(15Q26.1) WILD-TYPE 142  59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     51   17
  AMP PEAK 17(15Q26.1) WILD-TYPE  142   59
            clus
vv           AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  TUMOR FREE                           51                            142
  WITH TUMOR                           17                             59
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 17(15Q26.1) MUTATED     6  29  36   0   3
  AMP PEAK 17(15Q26.1) WILD-TYPE  12 100  79   1  21
D17V14, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  G1                            6                             12
  G2                           29                            100
  G3                           36                             79
  G4                            0                              1
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, continuous
D17V16, continuous
D17V17, continuous
D17V18, continuous
D17V19, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED    6  1
  AMP PEAK 17(15Q26.1) WILD-TYPE 19  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      6    1
  AMP PEAK 17(15Q26.1) WILD-TYPE   19    2
                         clus
vv                        AMP PEAK 17(15Q26.1) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        AMP PEAK 17(15Q26.1) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D17V20, continuous
D17V21, continuous
D17V22, continuous
D17V23, continuous
D17V24, continuous
D17V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 17(15Q26.1) MUTATED                                     0
  AMP PEAK 17(15Q26.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 17(15Q26.1) MUTATED                                     0
  AMP PEAK 17(15Q26.1) WILD-TYPE                                   7
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 17(15Q26.1) MUTATED                        10
  AMP PEAK 17(15Q26.1) WILD-TYPE                      26
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 17(15Q26.1) MUTATED                         1
  AMP PEAK 17(15Q26.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 17(15Q26.1) MUTATED                         2
  AMP PEAK 17(15Q26.1) WILD-TYPE                       8
D17V26, multiclass
                                     clus
vv                                    AMP PEAK 17(15Q26.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  OTHER LOCATION, SPECIFY                                       10
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK 17(15Q26.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              7
  OTHER LOCATION, SPECIFY                                         26
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 17(15Q26.1) MUTATED                                               1
  AMP PEAK 17(15Q26.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 17(15Q26.1) MUTATED                                               10
  AMP PEAK 17(15Q26.1) WILD-TYPE                                             15
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 17(15Q26.1) MUTATED                                                                                  20
  AMP PEAK 17(15Q26.1) WILD-TYPE                                                                                62
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 17(15Q26.1) MUTATED                                                                                             29
  AMP PEAK 17(15Q26.1) WILD-TYPE                                                                                           92
D17V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 17(15Q26.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           29
                                                                                              clus
vv                                                                                             AMP PEAK 17(15Q26.1) 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)                                        62
  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"
D17V28, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   16 19
  AMP PEAK 17(15Q26.1) WILD-TYPE 55 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     16   19
  AMP PEAK 17(15Q26.1) WILD-TYPE   55   55
         clus
vv        AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  ABSENT                            16                             55
  PRESENT                           19                             55
[1] 2 2
[1] FALSE
D17V29, continuous
D17V30, continuous
D17V31, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   11 26
  AMP PEAK 17(15Q26.1) WILD-TYPE 38 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     11   26
  AMP PEAK 17(15Q26.1) WILD-TYPE   38   91
                                          clus
vv                                         AMP PEAK 17(15Q26.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           26
                                          clus
vv                                         AMP PEAK 17(15Q26.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             91
[1] 2 2
[1] FALSE
D17V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 17(15Q26.1) MUTATED              4           8         27
  AMP PEAK 17(15Q26.1) WILD-TYPE           11          46         58
D17V33, multiclass
              clus
vv             AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  CURRENT USER                            4                             11
  FORMER USER                             8                             46
  NEVER USED                             27                             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"
D17V34, continuous
D17V35, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   20  5
  AMP PEAK 17(15Q26.1) WILD-TYPE 72 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     20    5
  AMP PEAK 17(15Q26.1) WILD-TYPE   72   13
         clus
vv        AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  ABSENT                            20                             72
  PRESENT                            5                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 17(15Q26.1) MUTATED             1        29     0
  AMP PEAK 17(15Q26.1) WILD-TYPE           4        71     2
D17V36, multiclass
             clus
vv            AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             29                             71
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V37, continuous
D17V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 17(15Q26.1) MUTATED         1        0         0         0        8
  AMP PEAK 17(15Q26.1) WILD-TYPE       4        1         1         1       26
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 17(15Q26.1) MUTATED          18         9        1         5
  AMP PEAK 17(15Q26.1) WILD-TYPE        59        28        3         3
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 17(15Q26.1) MUTATED            2          2        13         0
  AMP PEAK 17(15Q26.1) WILD-TYPE          3          5        31         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 17(15Q26.1) MUTATED            1         14         2         0
  AMP PEAK 17(15Q26.1) WILD-TYPE          2         28         5        12
D17V39, multiclass
            clus
vv           AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              8                             26
  STAGE IB1                            18                             59
  STAGE IB2                             9                             28
  STAGE II                              1                              3
  STAGE IIA                             5                              3
  STAGE IIA1                            2                              3
  STAGE IIA2                            2                              5
  STAGE IIB                            13                             31
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                           14                             28
  STAGE IVA                             2                              5
  STAGE IVB                             0                             12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(16P13.13) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 18(16P13.13) MUTATED    45  16
  AMP PEAK 18(16P13.13) WILD-TYPE 169  52
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                             61                             221 
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                             16                              52 
$`AMP PEAK 18(16P13.13) MUTATED`
TCGA-FU-A3TX TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MI 
        1.48        57.04        31.40        46.32        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7X8 TCGA-C5-A8YR 
        0.46        44.22        17.85       154.32         2.73        27.52 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HQ 
        1.12        95.11        44.94        22.98         8.28        37.35 
TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H1 
       13.05        31.73        25.91        27.22         0.36        26.27 
TCGA-EK-A2PI TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GN 
       19.27         4.24         0.07        47.77         0.10         0.89 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HM-A3JK 
       23.84        16.11        20.98        26.14        14.01        20.78 
TCGA-IR-A3LI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-MA-AA3X 
       81.96        21.44        15.58       209.59        20.91        20.28 
TCGA-PN-A8MA TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA 
        2.96        93.99        12.16        19.96        32.15        36.13 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC 
       58.45        15.68        50.47        43.40        29.95        27.12 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UU TCGA-XS-A8TJ 
       46.92        45.11        14.53        47.47        14.53        29.26 
TCGA-ZJ-AAXA 
        1.41 

$`AMP PEAK 18(16P13.13) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-VS-A9V4 TCGA-ZJ-AAX4 
      146.86        12.59        14.70         8.32         4.34         0.69 
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
        5.46        19.86        67.46        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT 
       53.16         2.43        20.91        40.93         3.58        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        18.02        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34        13.61        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK 
       99.91        23.51        20.81        20.91        14.73        82.06 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT 
      118.65        16.83        16.18        17.52        39.55        40.87 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       30.90        31.53        31.36        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       24.56        26.01        12.13        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       26.79        27.29        27.25        24.00        13.48        60.72 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51         0.39         0.43         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ 
        1.45         0.13        40.96         0.30         1.87         1.74 
TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EX-A1H5 
        0.43         1.64         2.33         0.07         0.49        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
        7.92        15.22        19.79        15.55        12.23        19.04 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
       31.36        36.26        16.14        28.31        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 
        1.12        17.75        25.41        16.57        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       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        29.85        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        28.37         8.28        18.15        21.11        44.61 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       22.52        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       28.08        34.62        19.96        54.81        35.05        20.84 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       17.23        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59        14.60        11.67        69.50        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QC 
       45.57        32.42        23.97        65.49        53.59        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       59.18        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       33.37        40.14        56.35        55.50        50.14        51.32 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO 
       48.39        28.50        24.30         1.71        27.25        47.87 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.52        26.07        15.85         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       18.84         5.16        18.25        17.75        16.24        15.42 
TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       26.01        67.59        19.13         0.16         3.91 

  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                         209.59                          210.67 
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                          25.91                           21.11 
[1] "0.1 - 209.6 (25.9)" "0.1 - 210.7 (21.1)"
[1] "hr=" "1.2"
D18V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 18(16P13.13) MUTATED    25  22   6   3
  AMP PEAK 18(16P13.13) WILD-TYPE 110  48  15   5
D18V3, multiclass
    clus
vv   AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  T1                            25                             110
  T2                            22                              48
  T3                             6                              15
  T4                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                                 cls
clus                                0   1
  AMP PEAK 18(16P13.13) MUTATED    26  16
  AMP PEAK 18(16P13.13) WILD-TYPE 103  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     26   16
  AMP PEAK 18(16P13.13) WILD-TYPE  103   40
   clus
vv  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  0                            26                             103
  1                            16                              40
[1] 2 2
[1] FALSE
D18V5, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED   23  3
  AMP PEAK 18(16P13.13) WILD-TYPE 85  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     23    3
  AMP PEAK 18(16P13.13) WILD-TYPE   85    7
   clus
vv  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  0                            23                              85
  1                             3                               7
[1] 2 2
[1] FALSE
D18V6, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED    8 28
  AMP PEAK 18(16P13.13) WILD-TYPE 45 97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED      8   28
  AMP PEAK 18(16P13.13) WILD-TYPE   45   97
     clus
vv    AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  NO                              8                              45
  YES                            28                              97
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 18(16P13.13) MUTATED               1
  AMP PEAK 18(16P13.13) WILD-TYPE             5
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(16P13.13) MUTATED                                 54
  AMP PEAK 18(16P13.13) WILD-TYPE                              188
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 18(16P13.13) MUTATED                                               1
  AMP PEAK 18(16P13.13) WILD-TYPE                                             5
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 18(16P13.13) MUTATED                                     5
  AMP PEAK 18(16P13.13) WILD-TYPE                                  16
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 18(16P13.13) MUTATED                                           0
  AMP PEAK 18(16P13.13) WILD-TYPE                                         3
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 18(16P13.13) MUTATED                                              4
  AMP PEAK 18(16P13.13) WILD-TYPE                                           13
D18V7, multiclass
                                               clus
vv                                              AMP PEAK 18(16P13.13) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         54
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
                                               clus
vv                                              AMP PEAK 18(16P13.13) WILD-TYPE
  ADENOSQUAMOUS                                                               5
  CERVICAL SQUAMOUS CELL CARCINOMA                                          188
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, continuous
D18V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(16P13.13) MUTATED                                  3     2
  AMP PEAK 18(16P13.13) WILD-TYPE                                5    17
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(16P13.13) MUTATED                           6
  AMP PEAK 18(16P13.13) WILD-TYPE                        22
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 18(16P13.13) MUTATED                                           1
  AMP PEAK 18(16P13.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 18(16P13.13) MUTATED      37
  AMP PEAK 18(16P13.13) WILD-TYPE   165
D18V10, multiclass
                                           clus
vv                                          AMP PEAK 18(16P13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 2
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                37
                                           clus
vv                                          AMP PEAK 18(16P13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        5
  ASIAN                                                                  17
  BLACK OR AFRICAN AMERICAN                                              22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 165
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                                 cls
clus                                0   1
  AMP PEAK 18(16P13.13) MUTATED     3  30
  AMP PEAK 18(16P13.13) WILD-TYPE  20 133
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED      3   30
  AMP PEAK 18(16P13.13) WILD-TYPE   20  133
                        clus
vv                       AMP PEAK 18(16P13.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            30
                        clus
vv                       AMP PEAK 18(16P13.13) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             133
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
                                 cls
clus                                0   1
  AMP PEAK 18(16P13.13) MUTATED    37  19
  AMP PEAK 18(16P13.13) WILD-TYPE 156  57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     37   19
  AMP PEAK 18(16P13.13) WILD-TYPE  156   57
            clus
vv           AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  TUMOR FREE                            37                             156
  WITH TUMOR                            19                              57
[1] 2 2
[1] FALSE
                                 vv
clus                               G1  G2  G3  G4  GX
  AMP PEAK 18(16P13.13) MUTATED     5  27  25   0   6
  AMP PEAK 18(16P13.13) WILD-TYPE  13 102  90   1  18
D18V14, multiclass
    clus
vv   AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  G1                             5                              13
  G2                            27                             102
  G3                            25                              90
  G4                             0                               1
  GX                             6                              18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, continuous
D18V16, continuous
D18V17, continuous
D18V18, continuous
D18V19, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED    5  0
  AMP PEAK 18(16P13.13) WILD-TYPE 20  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED      5    0
  AMP PEAK 18(16P13.13) WILD-TYPE   20    3
                         clus
vv                        AMP PEAK 18(16P13.13) MUTATED
  COMPLETED AS PLANNED                                5
  TREATMENT NOT COMPLETED                             0
                         clus
vv                        AMP PEAK 18(16P13.13) WILD-TYPE
  COMPLETED AS PLANNED                                 20
  TREATMENT NOT COMPLETED                               3
[1] 2 2
[1] FALSE
D18V20, continuous
D18V21, continuous
D18V22, continuous
D18V23, continuous
D18V24, continuous
D18V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 18(16P13.13) MUTATED                                     0
  AMP PEAK 18(16P13.13) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 18(16P13.13) MUTATED                                     1
  AMP PEAK 18(16P13.13) WILD-TYPE                                   6
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 18(16P13.13) MUTATED                         6
  AMP PEAK 18(16P13.13) WILD-TYPE                      30
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 18(16P13.13) MUTATED                         0
  AMP PEAK 18(16P13.13) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 18(16P13.13) MUTATED                         4
  AMP PEAK 18(16P13.13) WILD-TYPE                       6
D18V26, multiclass
                                     clus
vv                                    AMP PEAK 18(16P13.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         6
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         4
                                     clus
vv                                    AMP PEAK 18(16P13.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               6
  OTHER LOCATION, SPECIFY                                          30
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 18(16P13.13) MUTATED                                               0
  AMP PEAK 18(16P13.13) WILD-TYPE                                             3
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 18(16P13.13) MUTATED                                                7
  AMP PEAK 18(16P13.13) WILD-TYPE                                             18
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 18(16P13.13) MUTATED                                                                                  21
  AMP PEAK 18(16P13.13) WILD-TYPE                                                                                61
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 18(16P13.13) MUTATED                                                                                             21
  AMP PEAK 18(16P13.13) WILD-TYPE                                                                                          100
D18V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 18(16P13.13) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            21
                                                                                              clus
vv                                                                                             AMP PEAK 18(16P13.13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            18
  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)                             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V28, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED   19 16
  AMP PEAK 18(16P13.13) WILD-TYPE 52 58
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     19   16
  AMP PEAK 18(16P13.13) WILD-TYPE   52   58
         clus
vv        AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  ABSENT                             19                              52
  PRESENT                            16                              58
[1] 2 2
[1] FALSE
D18V29, continuous
D18V30, continuous
D18V31, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED   10 25
  AMP PEAK 18(16P13.13) WILD-TYPE 39 92
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     10   25
  AMP PEAK 18(16P13.13) WILD-TYPE   39   92
                                          clus
vv                                         AMP PEAK 18(16P13.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            25
                                          clus
vv                                         AMP PEAK 18(16P13.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              92
[1] 2 2
[1] FALSE
D18V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 18(16P13.13) MUTATED              1           8         21
  AMP PEAK 18(16P13.13) WILD-TYPE           14          46         64
D18V33, multiclass
              clus
vv             AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  CURRENT USER                             1                              14
  FORMER USER                              8                              46
  NEVER USED                              21                              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"
D18V34, continuous
D18V35, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED   17  5
  AMP PEAK 18(16P13.13) WILD-TYPE 75 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     17    5
  AMP PEAK 18(16P13.13) WILD-TYPE   75   13
         clus
vv        AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  ABSENT                             17                              75
  PRESENT                             5                              13
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 18(16P13.13) MUTATED             0        20     1
  AMP PEAK 18(16P13.13) WILD-TYPE           5        80     1
D18V36, multiclass
             clus
vv            AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  CARBOPLATIN                             0                               5
  CISPLATIN                              20                              80
  OTHER                                   1                               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"
D18V37, continuous
[1] "Remove cluster labels:"        "AMP PEAK 18(16P13.13) MUTATED"
clus
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                              2                              15 
                     TCGA-C5-A1BN                      TCGA-C5-A1ML 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-C5-A1MN                      TCGA-C5-A1MP 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-EK-A2RO                      TCGA-GH-A9DA 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-JW-A852                      TCGA-JX-A3Q8 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-MA-AA3W                      TCGA-MA-AA3Z 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-MA-AA42                      TCGA-MU-A51Y 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-MU-A8JM                      TCGA-MY-A913 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-ZX-AA5X 
"AMP PEAK 18(16P13.13) WILD-TYPE" 
D18V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 18(16P13.13) MUTATED         0        0         0         0        5
  AMP PEAK 18(16P13.13) WILD-TYPE       5        1         1         1       29
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 18(16P13.13) MUTATED          15         7        1         2
  AMP PEAK 18(16P13.13) WILD-TYPE        62        30        3         6
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 18(16P13.13) MUTATED            2          2        13         1
  AMP PEAK 18(16P13.13) WILD-TYPE          3          5        31         0
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 18(16P13.13) MUTATED            0         12         2         2
  AMP PEAK 18(16P13.13) WILD-TYPE          3         30         5        10
D18V39, multiclass
            clus
vv           AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  STAGE I                                0                               5
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               5                              29
  STAGE IB1                             15                              62
  STAGE IB2                              7                              30
  STAGE II                               1                               3
  STAGE IIA                              2                               6
  STAGE IIA1                             2                               3
  STAGE IIA2                             2                               5
  STAGE IIB                             13                              31
  STAGE III                              1                               0
  STAGE IIIA                             0                               3
  STAGE IIIB                            12                              30
  STAGE IVA                              2                               5
  STAGE IVB                              2                              10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(17Q12) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(17Q12) MUTATED    40  13
  AMP PEAK 19(17Q12) WILD-TYPE 174  55
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          53                          229 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          13                           55 
$`AMP PEAK 19(17Q12) MUTATED`
TCGA-C5-A8XJ TCGA-EX-A69M TCGA-VS-A9V4 TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1M6 
      146.86         8.32         4.34        17.82        23.67        31.40 
TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7CO 
       35.01        35.61         3.58       100.14       154.32       147.35 
TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VM 
      155.77         2.73        20.81         1.12        95.11       117.99 
TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A3HR TCGA-EA-A5ZF TCGA-EK-A2R9 
       22.98        16.18        17.52        30.90        27.22         0.13 
TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-FU-A40J 
       40.96         0.07         1.64         0.49        15.22        14.01 
TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U3 TCGA-MA-AA43 
       28.37        44.61        20.91        11.28         0.82        11.38 
TCGA-MU-A51Y TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73R TCGA-UC-A7PF 
       28.08        17.23        16.41        15.95        18.64        93.99 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A959 
       69.50        46.52        23.97        19.96        16.64        51.32 
TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9V0 TCGA-VS-A9V5 
       50.47        24.30        14.53        18.84        16.24 

$`AMP PEAK 19(17Q12) WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-BI-A0VR 
       12.59        14.70         1.48         0.69        17.52        49.48 
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       46.32        30.21        57.73        53.16        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        33.24        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       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       20.35        17.19       131.11        94.95         9.34        13.61 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99        45.83         8.35        99.91        23.51        27.52 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        14.73        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WI 
       58.88        36.76        55.63       118.65        16.83         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        40.87        37.35        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        36.89        26.40        24.56        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.13        24.82         7.46        14.89        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 
       27.29        27.25        24.00        13.48         0.36        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       26.27         6.64         1.51        19.27         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
        0.59         0.89         1.45         0.30         4.24         1.87 
TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.74         0.43        47.77         2.33         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        0.89        20.35         7.92        19.79        15.55        12.23 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       26.14        16.14        28.31        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        20.48        15.58         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU 
       21.11       209.59         0.89        12.49         0.30        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        20.28        17.82        19.56         9.17         8.52 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58         9.04        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-A7PG 
        9.34        22.62        19.59        14.60        11.67        12.16 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       10.03        45.57        32.42        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       36.13        11.51        59.18        39.78        31.27        40.87 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
        4.73        33.37        40.14        58.45        15.68        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       55.50        50.14        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO 
       27.12        46.92        45.11         1.71        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 
       18.25        67.20         5.16        18.25        17.75        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       26.01        29.26        67.59        19.13         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                      155.77                       210.67 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                       20.81                        23.51 
[1] "0.1 - 155.8 (20.8)" "0.1 - 210.7 (23.5)"
[1] "hr=" "1"  
D19V2, continuous
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 19(17Q12) MUTATED    21  13   7   1
  AMP PEAK 19(17Q12) WILD-TYPE 114  57  14   7
D19V3, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  T1                         21                          114
  T2                         13                           57
  T3                          7                           14
  T4                          1                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED    19  10
  AMP PEAK 19(17Q12) WILD-TYPE 110  46
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     19   10
  AMP PEAK 19(17Q12) WILD-TYPE  110   46
   clus
vv  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  0                         19                          110
  1                         10                           46
[1] 2 2
[1] FALSE
D19V5, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED   19  2
  AMP PEAK 19(17Q12) WILD-TYPE 89  8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     19    2
  AMP PEAK 19(17Q12) WILD-TYPE   89    8
   clus
vv  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  0                         19                           89
  1                          2                            8
[1] 2 2
[1] FALSE
D19V6, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED   10 29
  AMP PEAK 19(17Q12) WILD-TYPE 43 96
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     10   29
  AMP PEAK 19(17Q12) WILD-TYPE   43   96
     clus
vv    AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  NO                          10                           43
  YES                         29                           96
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(17Q12) MUTATED               2                               40
  AMP PEAK 19(17Q12) WILD-TYPE             4                              202
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 19(17Q12) MUTATED                                               0
  AMP PEAK 19(17Q12) WILD-TYPE                                             6
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                                     7
  AMP PEAK 19(17Q12) WILD-TYPE                                  14
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 19(17Q12) MUTATED                                           1
  AMP PEAK 19(17Q12) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 19(17Q12) MUTATED                                              5
  AMP PEAK 19(17Q12) WILD-TYPE                                           12
D19V7, multiclass
                                               clus
vv                                              AMP PEAK 19(17Q12) MUTATED
  ADENOSQUAMOUS                                                          2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      40
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           5
                                               clus
vv                                              AMP PEAK 19(17Q12) WILD-TYPE
  ADENOSQUAMOUS                                                            4
  CERVICAL SQUAMOUS CELL CARCINOMA                                       202
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, continuous
D19V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(17Q12) MUTATED                                  1     4
  AMP PEAK 19(17Q12) WILD-TYPE                                7    15
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(17Q12) MUTATED                           3
  AMP PEAK 19(17Q12) WILD-TYPE                        25
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 19(17Q12) MUTATED                                           0    38
  AMP PEAK 19(17Q12) WILD-TYPE                                         2   164
D19V10, multiclass
                                           clus
vv                                          AMP PEAK 19(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              4
  BLACK OR AFRICAN AMERICAN                                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             38
                                           clus
vv                                          AMP PEAK 19(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     7
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                              164
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED     6  28
  AMP PEAK 19(17Q12) WILD-TYPE  17 135
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      6   28
  AMP PEAK 19(17Q12) WILD-TYPE   17  135
                        clus
vv                       AMP PEAK 19(17Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                         28
                        clus
vv                       AMP PEAK 19(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          135
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED    35  16
  AMP PEAK 19(17Q12) WILD-TYPE 158  60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     35   16
  AMP PEAK 19(17Q12) WILD-TYPE  158   60
            clus
vv           AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  TUMOR FREE                         35                          158
  WITH TUMOR                         16                           60
[1] 2 2
[1] FALSE
                              vv
clus                            G1  G2  G3  G4  GX
  AMP PEAK 19(17Q12) MUTATED     1  19  29   0   4
  AMP PEAK 19(17Q12) WILD-TYPE  17 110  86   1  20
D19V14, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  G1                          1                           17
  G2                         19                          110
  G3                         29                           86
  G4                          0                            1
  GX                          4                           20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, continuous
D19V16, continuous
D19V17, continuous
D19V18, continuous
D19V19, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED    4  0
  AMP PEAK 19(17Q12) WILD-TYPE 21  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      4    0
  AMP PEAK 19(17Q12) WILD-TYPE   21    3
                         clus
vv                        AMP PEAK 19(17Q12) MUTATED
  COMPLETED AS PLANNED                             4
  TREATMENT NOT COMPLETED                          0
                         clus
vv                        AMP PEAK 19(17Q12) WILD-TYPE
  COMPLETED AS PLANNED                              21
  TREATMENT NOT COMPLETED                            3
[1] 2 2
[1] FALSE
D19V20, continuous
D19V21, continuous
D19V22, continuous
D19V23, continuous
D19V24, continuous
D19V25, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 19(17Q12) MUTATED                                     0
  AMP PEAK 19(17Q12) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 19(17Q12) MUTATED                                     1
  AMP PEAK 19(17Q12) WILD-TYPE                                   6
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 19(17Q12) MUTATED                         6                       0
  AMP PEAK 19(17Q12) WILD-TYPE                      30                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 19(17Q12) MUTATED                         0
  AMP PEAK 19(17Q12) WILD-TYPE                      10
D19V26, multiclass
                                     clus
vv                                    AMP PEAK 19(17Q12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          1
  OTHER LOCATION, SPECIFY                                      6
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      0
                                     clus
vv                                    AMP PEAK 19(17Q12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            6
  OTHER LOCATION, SPECIFY                                       30
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                       10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 19(17Q12) MUTATED                                               0
  AMP PEAK 19(17Q12) WILD-TYPE                                             3
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 19(17Q12) MUTATED                                                5
  AMP PEAK 19(17Q12) WILD-TYPE                                             20
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 19(17Q12) MUTATED                                                                                  15
  AMP PEAK 19(17Q12) WILD-TYPE                                                                                67
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 19(17Q12) MUTATED                                                                                             22
  AMP PEAK 19(17Q12) WILD-TYPE                                                                                           99
D19V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 19(17Q12) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         22
                                                                                              clus
vv                                                                                             AMP PEAK 19(17Q12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V28, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED   11 14
  AMP PEAK 19(17Q12) WILD-TYPE 60 60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     11   14
  AMP PEAK 19(17Q12) WILD-TYPE   60   60
         clus
vv        AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  ABSENT                          11                           60
  PRESENT                         14                           60
[1] 2 2
[1] FALSE
D19V29, continuous
D19V30, continuous
D19V31, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED    5 18
  AMP PEAK 19(17Q12) WILD-TYPE 44 99
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      5   18
  AMP PEAK 19(17Q12) WILD-TYPE   44   99
                                          clus
vv                                         AMP PEAK 19(17Q12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         18
                                          clus
vv                                         AMP PEAK 19(17Q12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           99
[1] 2 2
[1] FALSE
D19V32, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 19(17Q12) MUTATED              2          11         16
  AMP PEAK 19(17Q12) WILD-TYPE           13          43         69
D19V33, multiclass
              clus
vv             AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  CURRENT USER                          2                           13
  FORMER USER                          11                           43
  NEVER USED                           16                           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"
D19V34, continuous
D19V35, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED   17  3
  AMP PEAK 19(17Q12) WILD-TYPE 75 15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     17    3
  AMP PEAK 19(17Q12) WILD-TYPE   75   15
         clus
vv        AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  ABSENT                          17                           75
  PRESENT                          3                           15
[1] 2 2
[1] FALSE
                              vv
clus                           CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 19(17Q12) MUTATED             1        23     0
  AMP PEAK 19(17Q12) WILD-TYPE           4        77     2
D19V36, multiclass
             clus
vv            AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  CARBOPLATIN                          1                            4
  CISPLATIN                           23                           77
  OTHER                                0                            2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V37, continuous
D19V38, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 19(17Q12) MUTATED         1        0         0         0        4
  AMP PEAK 19(17Q12) WILD-TYPE       4        1         1         1       30
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 19(17Q12) MUTATED          17         6        1         2
  AMP PEAK 19(17Q12) WILD-TYPE        60        31        3         6
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 19(17Q12) MUTATED            2          1         9         0
  AMP PEAK 19(17Q12) WILD-TYPE          3          6        35         1
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 19(17Q12) MUTATED            1          8         1         0
  AMP PEAK 19(17Q12) WILD-TYPE          2         34         6        12
D19V39, multiclass
            clus
vv           AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                            0                            1
  STAGE IA1                           0                            1
  STAGE IA2                           0                            1
  STAGE IB                            4                           30
  STAGE IB1                          17                           60
  STAGE IB2                           6                           31
  STAGE II                            1                            3
  STAGE IIA                           2                            6
  STAGE IIA1                          2                            3
  STAGE IIA2                          1                            6
  STAGE IIB                           9                           35
  STAGE III                           0                            1
  STAGE IIIA                          1                            2
  STAGE IIIB                          8                           34
  STAGE IVA                           1                            6
  STAGE IVB                           0                           12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(17Q25.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(17Q25.1) MUTATED    54  16
  AMP PEAK 20(17Q25.1) WILD-TYPE 160  52
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            70                            212 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            16                             52 
$`AMP PEAK 20(17Q25.1) MUTATED`
TCGA-EX-A69M TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI 
        8.32        23.67        31.40        35.01        53.16        35.61 
TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7CO 
        3.58       100.14       154.32       134.33        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DG-A2KJ 
      155.77        13.61        45.83        23.51         1.12        95.11 
TCGA-DS-A0VK TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A439 
       36.76        22.98        37.35        30.90        13.05        31.73 
TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PM 
       14.89        25.91        27.22         6.64        19.27         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A3L1 
        0.13        40.96         0.07         1.64         0.49        15.22 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A4S6 
       31.36        20.98        26.14        14.01        16.57        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV 
      147.39       129.37        24.56        28.37        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y 
       11.28         0.89         0.30         9.17        11.38        28.08 
TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73Q TCGA-UC-A7PF TCGA-UC-A7PI 
       17.23        16.41        15.95         9.34        93.99        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A9U5 
       10.03        46.52        23.97        19.96        16.64        50.47 
TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9V0 
       29.95        24.30        14.53        18.84 

$`AMP PEAK 20(17Q25.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 
      146.86        12.59        14.70         1.48         4.34         0.69 
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
        5.46        19.86        67.46        46.32        30.21        57.73 
TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS 
       38.99         0.46         2.43        20.91        40.93        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        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       210.67       101.82 
TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
       15.48        17.19       131.11        94.95         9.34         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       50.99         8.35        99.91        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       14.73        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       55.63       117.99       118.65        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
        8.28        39.55        40.87        31.53        31.36        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       36.89        26.40        24.56        26.01        12.13        24.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        7.46        26.79        27.29        27.25        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL 
        0.36        60.72        26.27         1.51         0.39         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.89         1.45         0.30         4.24         1.87         1.74 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
        0.43        47.77         2.33         0.07         0.10         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       20.35         7.92        19.79        15.55        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
       19.04        16.11        36.26        16.14        28.31        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       10.55         1.12        17.75        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 
       29.85        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         8.28        18.15        21.11       209.59        12.49 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        20.28        17.82        19.56 
TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        8.52        34.62        19.96        54.81        35.05        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        2.96        15.58         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       15.88        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PG TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       12.16        45.57        32.42        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       36.13        11.51        59.18        39.78        31.27        40.87 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
        4.73        33.37        40.14        58.45        15.68        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       55.50        50.14        51.32        43.40        48.39        28.50 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO 
       27.12        46.92        45.11         1.71        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 
       18.25        67.20         5.16        18.25        17.75        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       15.42        26.01        29.26        67.59        19.13         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                        155.77                         210.67 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                        23.245                         22.095 
[1] "0.1 - 155.8 (23.2)" "0.1 - 210.7 (22.1)"
[1] "hr=" "1.1"
D20V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 20(17Q25.1) MUTATED    30  19   8   0
  AMP PEAK 20(17Q25.1) WILD-TYPE 105  51  13   8
D20V3, multiclass
    clus
vv   AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  T1                           30                            105
  T2                           19                             51
  T3                            8                             13
  T4                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q25.1) MUTATED    28  17
  AMP PEAK 20(17Q25.1) WILD-TYPE 101  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     28   17
  AMP PEAK 20(17Q25.1) WILD-TYPE  101   39
   clus
vv  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  0                           28                            101
  1                           17                             39
[1] 2 2
[1] FALSE
D20V5, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED   25  4
  AMP PEAK 20(17Q25.1) WILD-TYPE 83  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     25    4
  AMP PEAK 20(17Q25.1) WILD-TYPE   83    6
   clus
vv  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  0                           25                             83
  1                            4                              6
[1] 2 2
[1] FALSE
D20V6, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED   13 33
  AMP PEAK 20(17Q25.1) WILD-TYPE 40 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     13   33
  AMP PEAK 20(17Q25.1) WILD-TYPE   40   92
     clus
vv    AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  NO                            13                             40
  YES                           33                             92
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(17Q25.1) MUTATED               2                               60
  AMP PEAK 20(17Q25.1) WILD-TYPE             4                              182
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 20(17Q25.1) MUTATED                                               3
  AMP PEAK 20(17Q25.1) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 20(17Q25.1) MUTATED                                     6
  AMP PEAK 20(17Q25.1) WILD-TYPE                                  15
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 20(17Q25.1) MUTATED                                           2
  AMP PEAK 20(17Q25.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 20(17Q25.1) MUTATED                                              1
  AMP PEAK 20(17Q25.1) WILD-TYPE                                           16
D20V7, multiclass
                                               clus
vv                                              AMP PEAK 20(17Q25.1) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        60
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 20(17Q25.1) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         182
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, continuous
D20V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(17Q25.1) MUTATED                                  2     6
  AMP PEAK 20(17Q25.1) WILD-TYPE                                6    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(17Q25.1) MUTATED                           4
  AMP PEAK 20(17Q25.1) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 20(17Q25.1) MUTATED                                           0
  AMP PEAK 20(17Q25.1) WILD-TYPE                                         2
                                vv
clus                             WHITE
  AMP PEAK 20(17Q25.1) MUTATED      54
  AMP PEAK 20(17Q25.1) WILD-TYPE   148
D20V10, multiclass
                                           clus
vv                                          AMP PEAK 20(17Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               54
                                           clus
vv                                          AMP PEAK 20(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  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"
D20V11, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q25.1) MUTATED     8  41
  AMP PEAK 20(17Q25.1) WILD-TYPE  15 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED      8   41
  AMP PEAK 20(17Q25.1) WILD-TYPE   15  122
                        clus
vv                       AMP PEAK 20(17Q25.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       AMP PEAK 20(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            122
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q25.1) MUTATED    46  21
  AMP PEAK 20(17Q25.1) WILD-TYPE 147  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     46   21
  AMP PEAK 20(17Q25.1) WILD-TYPE  147   55
            clus
vv           AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  TUMOR FREE                           46                            147
  WITH TUMOR                           21                             55
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 20(17Q25.1) MUTATED     2  26  38   0   5
  AMP PEAK 20(17Q25.1) WILD-TYPE  16 103  77   1  19
D20V14, multiclass
    clus
vv   AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  G1                            2                             16
  G2                           26                            103
  G3                           38                             77
  G4                            0                              1
  GX                            5                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V15, continuous
D20V16, continuous
D20V17, continuous
D20V18, continuous
D20V19, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED    5  0
  AMP PEAK 20(17Q25.1) WILD-TYPE 20  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED      5    0
  AMP PEAK 20(17Q25.1) WILD-TYPE   20    3
                         clus
vv                        AMP PEAK 20(17Q25.1) MUTATED
  COMPLETED AS PLANNED                               5
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        AMP PEAK 20(17Q25.1) WILD-TYPE
  COMPLETED AS PLANNED                                20
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
D20V20, continuous
D20V21, continuous
D20V22, continuous
D20V23, continuous
D20V24, continuous
D20V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 20(17Q25.1) MUTATED                                     0
  AMP PEAK 20(17Q25.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 20(17Q25.1) MUTATED                                     1
  AMP PEAK 20(17Q25.1) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 20(17Q25.1) MUTATED                         7
  AMP PEAK 20(17Q25.1) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 20(17Q25.1) MUTATED                         0
  AMP PEAK 20(17Q25.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 20(17Q25.1) MUTATED                         1
  AMP PEAK 20(17Q25.1) WILD-TYPE                       9
D20V26, multiclass
                                     clus
vv                                    AMP PEAK 20(17Q25.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        7
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 20(17Q25.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 20(17Q25.1) MUTATED                                               0
  AMP PEAK 20(17Q25.1) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 20(17Q25.1) MUTATED                                                6
  AMP PEAK 20(17Q25.1) WILD-TYPE                                             19
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 20(17Q25.1) MUTATED                                                                                  18
  AMP PEAK 20(17Q25.1) WILD-TYPE                                                                                64
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 20(17Q25.1) MUTATED                                                                                             32
  AMP PEAK 20(17Q25.1) WILD-TYPE                                                                                           89
D20V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 20(17Q25.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           32
                                                                                              clus
vv                                                                                             AMP PEAK 20(17Q25.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D20V28, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED   12 22
  AMP PEAK 20(17Q25.1) WILD-TYPE 59 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     12   22
  AMP PEAK 20(17Q25.1) WILD-TYPE   59   52
         clus
vv        AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  ABSENT                            12                             59
  PRESENT                           22                             52
[1] 2 2
[1] FALSE
D20V29, continuous
D20V30, continuous
D20V31, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED   15 22
  AMP PEAK 20(17Q25.1) WILD-TYPE 34 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     15   22
  AMP PEAK 20(17Q25.1) WILD-TYPE   34   95
                                          clus
vv                                         AMP PEAK 20(17Q25.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           22
                                          clus
vv                                         AMP PEAK 20(17Q25.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             95
[1] 2 2
[1] FALSE
D20V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 20(17Q25.1) MUTATED              3          17         18
  AMP PEAK 20(17Q25.1) WILD-TYPE           12          37         67
D20V33, multiclass
              clus
vv             AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                            17                             37
  NEVER USED                             18                             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"
D20V34, continuous
D20V35, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED   23  5
  AMP PEAK 20(17Q25.1) WILD-TYPE 69 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     23    5
  AMP PEAK 20(17Q25.1) WILD-TYPE   69   13
         clus
vv        AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  ABSENT                            23                             69
  PRESENT                            5                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 20(17Q25.1) MUTATED             1        26     0
  AMP PEAK 20(17Q25.1) WILD-TYPE           4        74     2
D20V36, multiclass
             clus
vv            AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             26                             74
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V37, continuous
D20V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 20(17Q25.1) MUTATED         1        1         0         0        3
  AMP PEAK 20(17Q25.1) WILD-TYPE       4        0         1         1       31
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 20(17Q25.1) MUTATED          20         9        2         2
  AMP PEAK 20(17Q25.1) WILD-TYPE        57        28        2         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 20(17Q25.1) MUTATED            3          1        13         0
  AMP PEAK 20(17Q25.1) WILD-TYPE          2          6        31         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 20(17Q25.1) MUTATED            1         14         1         1
  AMP PEAK 20(17Q25.1) WILD-TYPE          2         28         6        11
D20V39, multiclass
            clus
vv           AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              3                             31
  STAGE IB1                            20                             57
  STAGE IB2                             9                             28
  STAGE II                              2                              2
  STAGE IIA                             2                              6
  STAGE IIA1                            3                              2
  STAGE IIA2                            1                              6
  STAGE IIB                            13                             31
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                           14                             28
  STAGE IVA                             1                              6
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(19P13.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(19P13.3) MUTATED    29   7
  AMP PEAK 21(19P13.3) WILD-TYPE 185  61
  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE 
                            36                            246 
  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE 
                             7                             61 
$`AMP PEAK 21(19P13.3) MUTATED`
TCGA-C5-A1BE TCGA-C5-A1BK TCGA-C5-A1MH TCGA-C5-A7CG TCGA-C5-A7CH TCGA-DG-A2KJ 
       68.84       177.04        38.99       210.67       154.32        95.11 
TCGA-DG-A2KL TCGA-DS-A0VL TCGA-EK-A2IP TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-FU-A3NI 
       44.94        55.63         6.64         0.59         0.13        20.98 
TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A852 
       14.01        20.78       129.37        36.36        24.56         8.28 
TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BE TCGA-Q1-A5R2 
      209.59        11.28         0.30        13.35        35.05        16.41 
TCGA-Q1-A73R TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A9U5 
       18.64        93.99        23.97        15.68        56.35        50.47 
TCGA-VS-A9UD TCGA-VS-A9UU TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-WL-A834 TCGA-ZJ-AAXA 
       24.30        14.53        18.84        18.25        26.01         1.41 

$`AMP PEAK 21(19P13.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A 
        0.69        17.52        17.82        49.48        57.04        23.67 
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM 
       11.44        18.74        36.56       144.16       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       35.01        57.73        53.16        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       18.02        17.85        20.42       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        82.06        63.98        87.75        58.88        36.76 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       31.73        26.01        12.13        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI 
       13.48         0.36        60.72        26.27         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.39         0.43         0.89         1.45        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL 
        4.24         0.07         1.87         1.74         0.43        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        1.64         2.33         0.07         0.10         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
       20.35         7.92        15.22        19.79        15.55        12.23 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
       23.84        19.04        16.11        31.36        36.26        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       16.14        28.31        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        16.57        21.67        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81        96.95        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        21.44        20.48        15.58        28.37 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX 
       18.15        21.11        44.61        20.91         0.89        12.49 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        22.52        20.28        17.82        19.56         9.17 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84        17.23         2.96        15.58        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S 
       16.14        17.56        14.07        15.88         9.34        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
       19.59        14.60        11.67        12.16        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       46.52        45.57        32.42        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       53.59        36.13        11.51        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       40.87        16.64         4.73        33.37        40.14        58.45 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       55.50        50.14        51.32        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       29.95        27.12        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 
        3.42        18.25        67.20         5.16        17.75        16.24 
TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        29.26        67.59        19.13         0.16         3.91 

  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE 
                          0.13                           0.07 
  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE 
                        210.67                         173.29 
  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE 
                        24.135                         22.095 
[1] "0.1 - 210.7 (24.1)" "0.1 - 173.3 (22.1)"
[1] "hr=" "1.6"
D21V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 21(19P13.3) MUTATED    16  12   5   1
  AMP PEAK 21(19P13.3) WILD-TYPE 119  58  16   7
D21V3, multiclass
    clus
vv   AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  T1                           16                            119
  T2                           12                             58
  T3                            5                             16
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.3) MUTATED    16  10
  AMP PEAK 21(19P13.3) WILD-TYPE 113  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED     16   10
  AMP PEAK 21(19P13.3) WILD-TYPE  113   46
   clus
vv  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  0                           16                            113
  1                           10                             46
[1] 2 2
[1] FALSE
D21V5, binary
                                cls
clus                              0  1
  AMP PEAK 21(19P13.3) MUTATED   12  0
  AMP PEAK 21(19P13.3) WILD-TYPE 96 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED     12    0
  AMP PEAK 21(19P13.3) WILD-TYPE   96   10
   clus
vv  AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  0                           12                             96
  1                            0                             10
[1] 2 2
[1] FALSE
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.3) MUTATED     7  17
  AMP PEAK 21(19P13.3) WILD-TYPE  46 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED      7   17
  AMP PEAK 21(19P13.3) WILD-TYPE   46  108
     clus
vv    AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  NO                             7                             46
  YES                           17                            108
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(19P13.3) MUTATED               0                               34
  AMP PEAK 21(19P13.3) WILD-TYPE             6                              208
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 21(19P13.3) MUTATED                                               1
  AMP PEAK 21(19P13.3) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 21(19P13.3) MUTATED                                     3
  AMP PEAK 21(19P13.3) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 21(19P13.3) MUTATED                                           0
  AMP PEAK 21(19P13.3) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 21(19P13.3) MUTATED                                              1
  AMP PEAK 21(19P13.3) WILD-TYPE                                           16
D21V7, multiclass
                                               clus
vv                                              AMP PEAK 21(19P13.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        34
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 21(19P13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         208
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, continuous
D21V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(19P13.3) MUTATED                                  1     3
  AMP PEAK 21(19P13.3) WILD-TYPE                                7    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(19P13.3) MUTATED                           3
  AMP PEAK 21(19P13.3) WILD-TYPE                        25
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 21(19P13.3) MUTATED                                           0
  AMP PEAK 21(19P13.3) WILD-TYPE                                         2
                                vv
clus                             WHITE
  AMP PEAK 21(19P13.3) MUTATED      22
  AMP PEAK 21(19P13.3) WILD-TYPE   180
D21V10, multiclass
                                           clus
vv                                          AMP PEAK 21(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               22
                                           clus
vv                                          AMP PEAK 21(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                180
[1] 5 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(19P13.3) MUTATED     2  16
  AMP PEAK 21(19P13.3) WILD-TYPE  21 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED      2   16
  AMP PEAK 21(19P13.3) WILD-TYPE   21  147
                        clus
vv                       AMP PEAK 21(19P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       AMP PEAK 21(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            147
[1] 2 2
[1] FALSE
D21V12, continuous
D21V13, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.3) MUTATED    25   8
  AMP PEAK 21(19P13.3) WILD-TYPE 168  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED     25    8
  AMP PEAK 21(19P13.3) WILD-TYPE  168   68
            clus
vv           AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  TUMOR FREE                           25                            168
  WITH TUMOR                            8                             68
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 21(19P13.3) MUTATED     2  15  18   0   3
  AMP PEAK 21(19P13.3) WILD-TYPE  16 114  97   1  21
D21V14, multiclass
    clus
vv   AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  G1                            2                             16
  G2                           15                            114
  G3                           18                             97
  G4                            0                              1
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, continuous
D21V16, continuous
D21V17, continuous
D21V18, continuous
D21V19, binary
                                cls
clus                              0  1
  AMP PEAK 21(19P13.3) MUTATED    2  0
  AMP PEAK 21(19P13.3) WILD-TYPE 23  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED      2    0
  AMP PEAK 21(19P13.3) WILD-TYPE   23    3
                         clus
vv                        AMP PEAK 21(19P13.3) MUTATED
  COMPLETED AS PLANNED                               2
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        AMP PEAK 21(19P13.3) WILD-TYPE
  COMPLETED AS PLANNED                                23
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
D21V20, continuous
D21V21, continuous
D21V22, continuous
D21V23, continuous
D21V24, continuous
D21V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 21(19P13.3) MUTATED                                     0
  AMP PEAK 21(19P13.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 21(19P13.3) MUTATED                                     1
  AMP PEAK 21(19P13.3) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 21(19P13.3) MUTATED                         4
  AMP PEAK 21(19P13.3) WILD-TYPE                      32
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 21(19P13.3) MUTATED                         0
  AMP PEAK 21(19P13.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 21(19P13.3) MUTATED                         1
  AMP PEAK 21(19P13.3) WILD-TYPE                       9
D21V26, multiclass
                                     clus
vv                                    AMP PEAK 21(19P13.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        4
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 21(19P13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         32
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 21(19P13.3) MUTATED                                               0
  AMP PEAK 21(19P13.3) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 21(19P13.3) MUTATED                                                2
  AMP PEAK 21(19P13.3) WILD-TYPE                                             23
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 21(19P13.3) MUTATED                                                                                  13
  AMP PEAK 21(19P13.3) WILD-TYPE                                                                                69
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 21(19P13.3) MUTATED                                                                                             15
  AMP PEAK 21(19P13.3) WILD-TYPE                                                                                          106
D21V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 21(19P13.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           15
                                                                                              clus
vv                                                                                             AMP PEAK 21(19P13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        69
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V28, binary
                                cls
clus                              0  1
  AMP PEAK 21(19P13.3) MUTATED    4 11
  AMP PEAK 21(19P13.3) WILD-TYPE 67 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED      4   11
  AMP PEAK 21(19P13.3) WILD-TYPE   67   63
         clus
vv        AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  ABSENT                             4                             67
  PRESENT                           11                             63
[1] 2 2
[1] FALSE
D21V29, continuous
D21V30, continuous
D21V31, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.3) MUTATED    11  10
  AMP PEAK 21(19P13.3) WILD-TYPE  38 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED     11   10
  AMP PEAK 21(19P13.3) WILD-TYPE   38  107
                                          clus
vv                                         AMP PEAK 21(19P13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           10
                                          clus
vv                                         AMP PEAK 21(19P13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            107
[1] 2 2
[1] FALSE
D21V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 21(19P13.3) MUTATED              2           3         13
  AMP PEAK 21(19P13.3) WILD-TYPE           13          51         72
D21V33, multiclass
              clus
vv             AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                             3                             51
  NEVER USED                             13                             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"
D21V34, continuous
D21V35, binary
                                cls
clus                              0  1
  AMP PEAK 21(19P13.3) MUTATED   10  2
  AMP PEAK 21(19P13.3) WILD-TYPE 82 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.3) MUTATED     10    2
  AMP PEAK 21(19P13.3) WILD-TYPE   82   16
         clus
vv        AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  ABSENT                            10                             82
  PRESENT                            2                             16
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 21(19P13.3) MUTATED             0        13     0
  AMP PEAK 21(19P13.3) WILD-TYPE           5        87     2
D21V36, multiclass
             clus
vv            AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  CARBOPLATIN                            0                              5
  CISPLATIN                             13                             87
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V37, continuous
D21V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 21(19P13.3) MUTATED         1        0         0         0        4
  AMP PEAK 21(19P13.3) WILD-TYPE       4        1         1         1       30
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 21(19P13.3) MUTATED           9         1        1         1
  AMP PEAK 21(19P13.3) WILD-TYPE        68        36        3         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 21(19P13.3) MUTATED            0          1         9         1
  AMP PEAK 21(19P13.3) WILD-TYPE          5          6        35         0
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 21(19P13.3) MUTATED            1          7         1         0
  AMP PEAK 21(19P13.3) WILD-TYPE          2         35         6        12
D21V39, multiclass
            clus
vv           AMP PEAK 21(19P13.3) MUTATED AMP PEAK 21(19P13.3) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              4                             30
  STAGE IB1                             9                             68
  STAGE IB2                             1                             36
  STAGE II                              1                              3
  STAGE IIA                             1                              7
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             9                             35
  STAGE III                             1                              0
  STAGE IIIA                            1                              2
  STAGE IIIB                            7                             35
  STAGE IVA                             1                              6
  STAGE IVB                             0                             12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(19P13.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(19P13.2) MUTATED    34   6
  AMP PEAK 22(19P13.2) WILD-TYPE 180  62
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                            40                            242 
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                             6                             62 
$`AMP PEAK 22(19P13.2) MUTATED`
TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A2LY TCGA-C5-A7CG 
       18.74       177.04        53.16        38.99        78.35       210.67 
TCGA-C5-A7CH TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VL 
      154.32        13.61        50.99        95.11        44.94        55.63 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A5O9 TCGA-EA-A97N TCGA-EK-A2PM TCGA-EK-A2RN 
       22.98        16.83        25.91         0.36         0.59         2.33 
TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LA TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JX-A3Q0 
       14.01        20.78       137.16        36.36        24.56       209.59 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BE TCGA-MY-A913 
       11.28        12.49         0.30        13.35        35.05        17.23 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       23.97        32.15        53.59        58.45        15.68        56.35 
TCGA-VS-A9U5 TCGA-VS-A9UU TCGA-WL-A834 TCGA-ZJ-AAXA 
       50.47        14.53        26.01         1.41 

$`AMP PEAK 22(19P13.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A 
        0.69        17.52        17.82        49.48        57.04        23.67 
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM 
       11.44        68.84        36.56       144.16       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       35.01        57.73        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       20.42       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
       17.19       155.77       131.11        94.95         9.34         2.73 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        14.73         1.12        82.06        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH 
       58.88        36.76       117.99       118.65        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       31.73        26.01        12.13        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       26.79        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       60.72        26.27         6.64         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL 
        4.24         0.07         1.87         1.74         0.43        47.77 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        1.64         0.07         0.10         0.49         0.89        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        7.92        15.22        19.79        15.55        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       16.14        28.31        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        16.57        21.67        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       129.37        96.95        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW 
        8.28        18.15        21.11        44.61        20.91         0.89 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        22.52        20.28        17.82        19.56         9.17 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       22.62        19.59        14.60        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ 
       69.50        10.03        46.52        45.57        32.42        19.96 
TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       65.49        36.13        11.51        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A957 
       40.87        16.64         4.73        33.37        40.14        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        51.32        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       27.12        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       17.75        16.24        15.42        29.26        67.59        19.13 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                          0.30                           0.07 
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                        210.67                         173.29 
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                        25.960                         21.045 
[1] "0.3 - 210.7 (26.0)" "0.1 - 173.3 (21.0)"
[1] "hr=" "2.2"
D22V2, continuous
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 22(19P13.2) MUTATED    18  12   5   1
  AMP PEAK 22(19P13.2) WILD-TYPE 117  58  16   7
D22V3, multiclass
    clus
vv   AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  T1                           18                            117
  T2                           12                             58
  T3                            5                             16
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.2) MUTATED    24   8
  AMP PEAK 22(19P13.2) WILD-TYPE 105  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED     24    8
  AMP PEAK 22(19P13.2) WILD-TYPE  105   48
   clus
vv  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  0                           24                            105
  1                            8                             48
[1] 2 2
[1] FALSE
D22V5, binary
                                cls
clus                              0  1
  AMP PEAK 22(19P13.2) MUTATED   17  1
  AMP PEAK 22(19P13.2) WILD-TYPE 91  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED     17    1
  AMP PEAK 22(19P13.2) WILD-TYPE   91    9
   clus
vv  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  0                           17                             91
  1                            1                              9
[1] 2 2
[1] FALSE
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.2) MUTATED     9  20
  AMP PEAK 22(19P13.2) WILD-TYPE  44 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED      9   20
  AMP PEAK 22(19P13.2) WILD-TYPE   44  105
     clus
vv    AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  NO                             9                             44
  YES                           20                            105
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(19P13.2) MUTATED               0                               38
  AMP PEAK 22(19P13.2) WILD-TYPE             6                              204
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 22(19P13.2) MUTATED                                               1
  AMP PEAK 22(19P13.2) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 22(19P13.2) MUTATED                                     2
  AMP PEAK 22(19P13.2) WILD-TYPE                                  19
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 22(19P13.2) MUTATED                                           1
  AMP PEAK 22(19P13.2) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 22(19P13.2) MUTATED                                              1
  AMP PEAK 22(19P13.2) WILD-TYPE                                           16
D22V7, multiclass
                                               clus
vv                                              AMP PEAK 22(19P13.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        38
  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 22(19P13.2) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         204
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, continuous
D22V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(19P13.2) MUTATED                                  1     4
  AMP PEAK 22(19P13.2) WILD-TYPE                                7    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(19P13.2) MUTATED                           5
  AMP PEAK 22(19P13.2) WILD-TYPE                        23
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 22(19P13.2) MUTATED                                           0
  AMP PEAK 22(19P13.2) WILD-TYPE                                         2
                                vv
clus                             WHITE
  AMP PEAK 22(19P13.2) MUTATED      24
  AMP PEAK 22(19P13.2) WILD-TYPE   178
D22V10, multiclass
                                           clus
vv                                          AMP PEAK 22(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               24
                                           clus
vv                                          AMP PEAK 22(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                178
[1] 5 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(19P13.2) MUTATED     2  22
  AMP PEAK 22(19P13.2) WILD-TYPE  21 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED      2   22
  AMP PEAK 22(19P13.2) WILD-TYPE   21  141
                        clus
vv                       AMP PEAK 22(19P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           22
                        clus
vv                       AMP PEAK 22(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            141
[1] 2 2
[1] FALSE
D22V12, continuous
D22V13, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.2) MUTATED    31   8
  AMP PEAK 22(19P13.2) WILD-TYPE 162  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED     31    8
  AMP PEAK 22(19P13.2) WILD-TYPE  162   68
            clus
vv           AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  TUMOR FREE                           31                            162
  WITH TUMOR                            8                             68
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  AMP PEAK 22(19P13.2) MUTATED     3  19  18   0   2
  AMP PEAK 22(19P13.2) WILD-TYPE  15 110  97   1  22
D22V14, multiclass
    clus
vv   AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  G1                            3                             15
  G2                           19                            110
  G3                           18                             97
  G4                            0                              1
  GX                            2                             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, continuous
D22V16, continuous
D22V17, continuous
D22V18, continuous
D22V19, binary
                                cls
clus                              0  1
  AMP PEAK 22(19P13.2) MUTATED    5  0
  AMP PEAK 22(19P13.2) WILD-TYPE 20  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED      5    0
  AMP PEAK 22(19P13.2) WILD-TYPE   20    3
                         clus
vv                        AMP PEAK 22(19P13.2) MUTATED
  COMPLETED AS PLANNED                               5
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        AMP PEAK 22(19P13.2) WILD-TYPE
  COMPLETED AS PLANNED                                20
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
D22V20, continuous
D22V21, continuous
D22V22, continuous
D22V23, continuous
D22V24, continuous
D22V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 22(19P13.2) MUTATED                                     0
  AMP PEAK 22(19P13.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 22(19P13.2) MUTATED                                     1
  AMP PEAK 22(19P13.2) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 22(19P13.2) MUTATED                         7
  AMP PEAK 22(19P13.2) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 22(19P13.2) MUTATED                         0
  AMP PEAK 22(19P13.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 22(19P13.2) MUTATED                         1
  AMP PEAK 22(19P13.2) WILD-TYPE                       9
D22V26, multiclass
                                     clus
vv                                    AMP PEAK 22(19P13.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        7
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 22(19P13.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 22(19P13.2) MUTATED                                               0
  AMP PEAK 22(19P13.2) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 22(19P13.2) MUTATED                                                2
  AMP PEAK 22(19P13.2) WILD-TYPE                                             23
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 22(19P13.2) MUTATED                                                                                  15
  AMP PEAK 22(19P13.2) WILD-TYPE                                                                                67
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 22(19P13.2) MUTATED                                                                                             16
  AMP PEAK 22(19P13.2) WILD-TYPE                                                                                          105
D22V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 22(19P13.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           16
                                                                                              clus
vv                                                                                             AMP PEAK 22(19P13.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V28, binary
                                cls
clus                              0  1
  AMP PEAK 22(19P13.2) MUTATED    9 11
  AMP PEAK 22(19P13.2) WILD-TYPE 62 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED      9   11
  AMP PEAK 22(19P13.2) WILD-TYPE   62   63
         clus
vv        AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  ABSENT                             9                             62
  PRESENT                           11                             63
[1] 2 2
[1] FALSE
D22V29, continuous
D22V30, continuous
D22V31, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.2) MUTATED    14  10
  AMP PEAK 22(19P13.2) WILD-TYPE  35 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED     14   10
  AMP PEAK 22(19P13.2) WILD-TYPE   35  107
                                          clus
vv                                         AMP PEAK 22(19P13.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           10
                                          clus
vv                                         AMP PEAK 22(19P13.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            107
[1] 2 2
[1] FALSE
D22V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 22(19P13.2) MUTATED              1           6         14
  AMP PEAK 22(19P13.2) WILD-TYPE           14          48         71
D22V33, multiclass
              clus
vv             AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  CURRENT USER                            1                             14
  FORMER USER                             6                             48
  NEVER USED                             14                             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V34, continuous
D22V35, binary
                                cls
clus                              0  1
  AMP PEAK 22(19P13.2) MUTATED   14  0
  AMP PEAK 22(19P13.2) WILD-TYPE 78 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED     14    0
  AMP PEAK 22(19P13.2) WILD-TYPE   78   18
         clus
vv        AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  ABSENT                            14                             78
  PRESENT                            0                             18
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 22(19P13.2) MUTATED             1        13     0
  AMP PEAK 22(19P13.2) WILD-TYPE           4        87     2
D22V36, multiclass
             clus
vv            AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             13                             87
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V37, continuous
D22V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 22(19P13.2) MUTATED         0        0         0         0        5
  AMP PEAK 22(19P13.2) WILD-TYPE       5        1         1         1       29
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 22(19P13.2) MUTATED          11         3        1         2
  AMP PEAK 22(19P13.2) WILD-TYPE        66        34        3         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 22(19P13.2) MUTATED            0          1         8         1
  AMP PEAK 22(19P13.2) WILD-TYPE          5          6        36         0
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 22(19P13.2) MUTATED            0          8         1         1
  AMP PEAK 22(19P13.2) WILD-TYPE          3         34         6        11
D22V39, multiclass
            clus
vv           AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              5                             29
  STAGE IB1                            11                             66
  STAGE IB2                             3                             34
  STAGE II                              1                              3
  STAGE IIA                             2                              6
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             8                             36
  STAGE III                             1                              0
  STAGE IIIA                            0                              3
  STAGE IIIB                            8                             34
  STAGE IVA                             1                              6
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(19Q13.13) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(19Q13.13) MUTATED    61  24
  AMP PEAK 23(19Q13.13) WILD-TYPE 153  44
  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE 
                             85                             197 
  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE 
                             24                              44 
$`AMP PEAK 23(19Q13.13) MUTATED`
TCGA-VS-A9V4 TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M6 
        4.34        23.67        11.44       144.16         5.46        31.40 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A2LT 
       57.73        53.16        38.99        35.61         2.43        73.18 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CM 
       78.35        38.43       210.67       154.32       134.33        20.35 
TCGA-C5-A7CO TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8YR TCGA-C5-A907 
      147.35         9.34        13.61        45.83        27.52        14.73 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WI 
       95.11        44.94        63.98        55.63        22.98         8.28 
TCGA-EA-A3HR TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E 
       30.90        36.89        24.56        31.73        26.01         7.46 
TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       25.91        27.22         0.36         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-FU-A23L 
        0.89        40.96         1.74         1.64         2.33        23.84 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LK 
       20.98        14.01        16.57        21.67        20.78        29.85 
TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-LP-A7HU 
       36.36        24.56        20.48       209.59         0.30        13.35 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73S 
       54.81        35.05         2.96        15.95         9.04        22.62 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A94W TCGA-VS-A94X 
       12.16        10.03        23.97        59.18        40.87        16.64 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA 
       15.68        56.35        50.14        51.32        50.47        28.50 
TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UU TCGA-WL-A834 
       24.30        45.11        47.47        15.85        14.53        26.01 
TCGA-ZJ-AAXA 
        1.41 

$`AMP PEAK 23(19Q13.13) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 
      146.86        12.59        14.70         8.32         1.48         0.69 
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF 
       17.52        17.82        49.48        57.04        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
       36.56       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN 
       46.32        30.21        35.01         0.46        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M2 
        3.58        44.22        73.45        83.05       100.14        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL 
       52.01        18.02        17.85        20.42       101.82        15.48 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A7XC 
       17.19       155.77       131.11        94.95         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH 
        8.35        99.91        23.51        20.81        20.91         1.12 
TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       82.06        87.75        58.88        36.76       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18        17.52        39.55        40.87        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S 
       31.53        31.36        13.05        25.02        26.40        12.13 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       24.82        14.89        26.79        27.29        27.25        24.00 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       13.48        60.72        26.27         6.64         1.51        19.27 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45         0.13         0.30         4.24         0.07         1.87 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.43        47.77         0.07         0.10         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
       20.35         7.92        15.22        19.79        15.55        12.23 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
       19.04        16.11        31.36        36.26        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        25.41 
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       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ 
       96.95        78.71        81.96        27.42         3.29        21.44 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 
       15.58        28.37         8.28        18.15        21.11        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3W 
       20.91        11.28         0.89        12.49         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       20.28        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
       28.08        34.62        19.96        20.84        17.23        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       16.41        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       18.64        19.59        14.60        11.67        93.99        69.50 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       46.52        45.57        32.42        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y 
       53.59        36.13        11.51        39.78        31.27         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A9U6 TCGA-VS-A9U7 
       33.37        40.14        58.45        55.50        43.40        48.39 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       29.95        27.12        46.92         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       47.87        41.52        26.07         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       18.84         5.16        18.25        17.75        16.24        15.42 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        67.59        19.13         0.16         3.91 

  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE 
                           0.30                            0.07 
  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE 
                         210.67                          177.04 
  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE 
                          24.56                           20.84 
[1] "0.3 - 210.7 (24.6)" "0.1 - 177.0 (20.8)"
[1] "hr=" "1.2"
D23V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 23(19Q13.13) MUTATED    33  26  11   3
  AMP PEAK 23(19Q13.13) WILD-TYPE 102  44  10   5
D23V3, multiclass
    clus
vv   AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  T1                            33                             102
  T2                            26                              44
  T3                            11                              10
  T4                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                                 cls
clus                               0  1
  AMP PEAK 23(19Q13.13) MUTATED   34 22
  AMP PEAK 23(19Q13.13) WILD-TYPE 95 34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED     34   22
  AMP PEAK 23(19Q13.13) WILD-TYPE   95   34
   clus
vv  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  0                            34                              95
  1                            22                              34
[1] 2 2
[1] FALSE
D23V5, binary
                                 cls
clus                               0  1
  AMP PEAK 23(19Q13.13) MUTATED   33  1
  AMP PEAK 23(19Q13.13) WILD-TYPE 75  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED     33    1
  AMP PEAK 23(19Q13.13) WILD-TYPE   75    9
   clus
vv  AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  0                            33                              75
  1                             1                               9
[1] 2 2
[1] FALSE
D23V6, binary
                                 cls
clus                               0  1
  AMP PEAK 23(19Q13.13) MUTATED   14 39
  AMP PEAK 23(19Q13.13) WILD-TYPE 39 86
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED     14   39
  AMP PEAK 23(19Q13.13) WILD-TYPE   39   86
     clus
vv    AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  NO                             14                              39
  YES                            39                              86
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 23(19Q13.13) MUTATED               2
  AMP PEAK 23(19Q13.13) WILD-TYPE             4
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(19Q13.13) MUTATED                                 80
  AMP PEAK 23(19Q13.13) WILD-TYPE                              162
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 23(19Q13.13) MUTATED                                               3
  AMP PEAK 23(19Q13.13) WILD-TYPE                                             3
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 23(19Q13.13) MUTATED                                     5
  AMP PEAK 23(19Q13.13) WILD-TYPE                                  16
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 23(19Q13.13) MUTATED                                           0
  AMP PEAK 23(19Q13.13) WILD-TYPE                                         3
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 23(19Q13.13) MUTATED                                              3
  AMP PEAK 23(19Q13.13) WILD-TYPE                                           14
D23V7, multiclass
                                               clus
vv                                              AMP PEAK 23(19Q13.13) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         80
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
                                               clus
vv                                              AMP PEAK 23(19Q13.13) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          162
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, continuous
D23V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(19Q13.13) MUTATED                                  1     6
  AMP PEAK 23(19Q13.13) WILD-TYPE                                7    13
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(19Q13.13) MUTATED                           8
  AMP PEAK 23(19Q13.13) WILD-TYPE                        20
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 23(19Q13.13) MUTATED                                           0
  AMP PEAK 23(19Q13.13) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  AMP PEAK 23(19Q13.13) MUTATED      64
  AMP PEAK 23(19Q13.13) WILD-TYPE   138
D23V10, multiclass
                                           clus
vv                                          AMP PEAK 23(19Q13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                64
                                           clus
vv                                          AMP PEAK 23(19Q13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  WHITE                                                                 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"
D23V11, binary
                                 cls
clus                                0   1
  AMP PEAK 23(19Q13.13) MUTATED     5  53
  AMP PEAK 23(19Q13.13) WILD-TYPE  18 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED      5   53
  AMP PEAK 23(19Q13.13) WILD-TYPE   18  110
                        clus
vv                       AMP PEAK 23(19Q13.13) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       AMP PEAK 23(19Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                  18
  NOT HISPANIC OR LATINO                             110
[1] 2 2
[1] FALSE
D23V12, continuous
D23V13, binary
                                 cls
clus                                0   1
  AMP PEAK 23(19Q13.13) MUTATED    57  26
  AMP PEAK 23(19Q13.13) WILD-TYPE 136  50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED     57   26
  AMP PEAK 23(19Q13.13) WILD-TYPE  136   50
            clus
vv           AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  TUMOR FREE                            57                             136
  WITH TUMOR                            26                              50
[1] 2 2
[1] FALSE
                                 vv
clus                              G1 G2 G3 G4 GX
  AMP PEAK 23(19Q13.13) MUTATED    5 40 39  0  5
  AMP PEAK 23(19Q13.13) WILD-TYPE 13 89 76  1 19
D23V14, multiclass
    clus
vv   AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  G1                             5                              13
  G2                            40                              89
  G3                            39                              76
  G4                             0                               1
  GX                             5                              19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, continuous
D23V16, continuous
D23V17, continuous
D23V18, continuous
D23V19, binary
                                 cls
clus                               0  1
  AMP PEAK 23(19Q13.13) MUTATED   10  2
  AMP PEAK 23(19Q13.13) WILD-TYPE 15  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED     10    2
  AMP PEAK 23(19Q13.13) WILD-TYPE   15    1
                         clus
vv                        AMP PEAK 23(19Q13.13) MUTATED
  COMPLETED AS PLANNED                               10
  TREATMENT NOT COMPLETED                             2
                         clus
vv                        AMP PEAK 23(19Q13.13) WILD-TYPE
  COMPLETED AS PLANNED                                 15
  TREATMENT NOT COMPLETED                               1
[1] 2 2
[1] FALSE
D23V20, continuous
D23V21, continuous
D23V22, continuous
D23V23, continuous
D23V24, continuous
D23V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 23(19Q13.13) MUTATED                                     0
  AMP PEAK 23(19Q13.13) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 23(19Q13.13) MUTATED                                     4
  AMP PEAK 23(19Q13.13) WILD-TYPE                                   3
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 23(19Q13.13) MUTATED                        10
  AMP PEAK 23(19Q13.13) WILD-TYPE                      26
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 23(19Q13.13) MUTATED                         1
  AMP PEAK 23(19Q13.13) WILD-TYPE                       0
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 23(19Q13.13) MUTATED                         1
  AMP PEAK 23(19Q13.13) WILD-TYPE                       9
D23V26, multiclass
                                     clus
vv                                    AMP PEAK 23(19Q13.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                        10
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         1
                                     clus
vv                                    AMP PEAK 23(19Q13.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               3
  OTHER LOCATION, SPECIFY                                          26
  POSITIVE BLADDER MARGIN                                           0
  POSITIVE VAGINAL MARGIN                                           9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 23(19Q13.13) MUTATED                                               1
  AMP PEAK 23(19Q13.13) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 23(19Q13.13) MUTATED                                                4
  AMP PEAK 23(19Q13.13) WILD-TYPE                                             21
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 23(19Q13.13) MUTATED                                                                                  28
  AMP PEAK 23(19Q13.13) WILD-TYPE                                                                                54
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 23(19Q13.13) MUTATED                                                                                             35
  AMP PEAK 23(19Q13.13) WILD-TYPE                                                                                           86
D23V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 23(19Q13.13) 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)                                       28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            35
                                                                                              clus
vv                                                                                             AMP PEAK 23(19Q13.13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              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"
D23V28, binary
                                 cls
clus                               0  1
  AMP PEAK 23(19Q13.13) MUTATED   18 25
  AMP PEAK 23(19Q13.13) WILD-TYPE 53 49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED     18   25
  AMP PEAK 23(19Q13.13) WILD-TYPE   53   49
         clus
vv        AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  ABSENT                             18                              53
  PRESENT                            25                              49
[1] 2 2
[1] FALSE
D23V29, continuous
D23V30, continuous
D23V31, binary
                                 cls
clus                               0  1
  AMP PEAK 23(19Q13.13) MUTATED   20 33
  AMP PEAK 23(19Q13.13) WILD-TYPE 29 84
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED     20   33
  AMP PEAK 23(19Q13.13) WILD-TYPE   29   84
                                          clus
vv                                         AMP PEAK 23(19Q13.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                20
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            33
                                          clus
vv                                         AMP PEAK 23(19Q13.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              84
[1] 2 2
[1] FALSE
D23V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 23(19Q13.13) MUTATED              3          17         29
  AMP PEAK 23(19Q13.13) WILD-TYPE           12          37         56
D23V33, multiclass
              clus
vv             AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  CURRENT USER                             3                              12
  FORMER USER                             17                              37
  NEVER USED                              29                              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"
D23V34, continuous
D23V35, binary
                                 cls
clus                               0  1
  AMP PEAK 23(19Q13.13) MUTATED   23  7
  AMP PEAK 23(19Q13.13) WILD-TYPE 69 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19Q13.13) MUTATED     23    7
  AMP PEAK 23(19Q13.13) WILD-TYPE   69   11
         clus
vv        AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  ABSENT                             23                              69
  PRESENT                             7                              11
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 23(19Q13.13) MUTATED             2        35     0
  AMP PEAK 23(19Q13.13) WILD-TYPE           3        65     2
D23V36, multiclass
             clus
vv            AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  CARBOPLATIN                             2                               3
  CISPLATIN                              35                              65
  OTHER                                   0                               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V37, continuous
D23V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 23(19Q13.13) MUTATED         1        0         0         0        8
  AMP PEAK 23(19Q13.13) WILD-TYPE       4        1         1         1       26
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 23(19Q13.13) MUTATED          18        12        2         3
  AMP PEAK 23(19Q13.13) WILD-TYPE        59        25        2         5
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 23(19Q13.13) MUTATED            2          3        20         1
  AMP PEAK 23(19Q13.13) WILD-TYPE          3          4        24         0
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 23(19Q13.13) MUTATED            2         14         4         1
  AMP PEAK 23(19Q13.13) WILD-TYPE          1         28         3        11
D23V39, multiclass
            clus
vv           AMP PEAK 23(19Q13.13) MUTATED AMP PEAK 23(19Q13.13) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               8                              26
  STAGE IB1                             18                              59
  STAGE IB2                             12                              25
  STAGE II                               2                               2
  STAGE IIA                              3                               5
  STAGE IIA1                             2                               3
  STAGE IIA2                             3                               4
  STAGE IIB                             20                              24
  STAGE III                              1                               0
  STAGE IIIA                             2                               1
  STAGE IIIB                            14                              28
  STAGE IVA                              4                               3
  STAGE IVB                              1                              11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(20Q11.21) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(20Q11.21) MUTATED    98  31
  AMP PEAK 24(20Q11.21) WILD-TYPE 116  37
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                            129                             153 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                             31                              37 
$`AMP PEAK 24(20Q11.21) MUTATED`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-BI-A0VR TCGA-BI-A0VS 
      146.86        12.59         4.34         0.69        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1M6 TCGA-C5-A1M9 
       23.67        68.84       144.16       173.29        31.40        35.01 
TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       57.73        35.61         0.46         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM 
       44.22        73.18       100.14       210.67       154.32        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8YR 
      147.35        17.19       131.11        13.61         2.73        27.52 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VK 
        1.12        95.11        82.06        44.94        63.98        36.76 
TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       22.98        17.52        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF 
       31.53        13.05        31.73        14.89        26.79        27.22 
TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI 
       24.00         0.36        60.72        26.27         1.51        19.27 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
        0.59         0.89         0.13        40.96         1.74         1.64 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
        0.49         0.89        12.23        23.84        16.11        31.36 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       20.98        14.01        17.75        25.41        21.67        20.78 
TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ 
      147.39        96.95        78.71        20.48        28.37        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA43 
      209.59        20.91        12.49        13.35        20.28        11.38 
TCGA-MU-A5YI TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       34.62        17.23         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF 
        9.04        17.56        15.88        22.62        14.60        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QA 
       12.16        69.50        46.52        23.97        19.96        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A959 TCGA-VS-A9U5 
       40.14        58.45        15.68        56.35        51.32        50.47 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP 
       24.30        46.92        45.11        14.53        27.25        47.47 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 
       15.85        14.53        18.25        67.20         5.16        17.75 
TCGA-WL-A834 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       26.01         1.41         0.16 

$`AMP PEAK 24(20Q11.21) WILD-TYPE`
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-2W-A8YY TCGA-4J-AA1J TCGA-C5-A0TN 
       14.70         8.32         1.48        17.52        17.82        11.44 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       18.74        36.56       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1ML 
       67.46        46.32        30.21        53.16        38.99        20.91 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.45        83.05        78.35        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       18.02        17.85        20.42       101.82       134.33        15.48 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
      155.77        94.95         9.34        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DR-A0ZL 
       99.91        23.51        20.81        20.91        14.73        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88        55.63       117.99       118.65        16.83        16.18 
TCGA-DS-A7WI TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        8.28        31.36        25.02        36.89        26.40        24.56 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD 
       26.01        12.13        24.82         7.46        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R8 
       27.25        13.48         6.64         0.39         0.43         1.45 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RL 
        0.30         4.24         0.07         1.87         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        2.33         0.07         0.10        20.35         7.92        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
       19.79        15.55        19.04        36.26        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A9SC TCGA-HM-A4S6 
       28.31        35.44        10.55         1.12        16.57        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK 
        9.44       137.16        66.81       129.37        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
        8.28        18.15        44.61        11.28         0.89         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
        0.82        22.52        17.82        19.56         9.17         8.52 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV 
       28.08        19.96        54.81        35.05        20.84        16.14 
TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB 
       14.07         9.34        18.64        19.59        11.67        10.03 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A94Y 
       45.57        32.42        65.49        32.15        53.59         4.73 
TCGA-VS-A94Z TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       33.37        55.50        50.14        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
       29.95        27.12         1.71        47.87        41.52        26.07 
TCGA-VS-A9UV TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ 
        3.42        18.84        18.25        16.24        15.42        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       67.59        19.13         3.91 

  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                           0.13                            0.07 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                         210.67                          177.04 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                          23.97                           20.84 
[1] "0.1 - 210.7 (24.0)" "0.1 - 177.0 (20.8)"
[1] "hr=" "1.1"
D24V2, continuous
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 24(20Q11.21) MUTATED   59 25 16  4
  AMP PEAK 24(20Q11.21) WILD-TYPE 76 45  5  4
D24V3, multiclass
    clus
vv   AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  T1                            59                              76
  T2                            25                              45
  T3                            16                               5
  T4                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                                 cls
clus                               0  1
  AMP PEAK 24(20Q11.21) MUTATED   52 27
  AMP PEAK 24(20Q11.21) WILD-TYPE 77 29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED     52   27
  AMP PEAK 24(20Q11.21) WILD-TYPE   77   29
   clus
vv  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  0                            52                              77
  1                            27                              29
[1] 2 2
[1] FALSE
D24V5, binary
                                 cls
clus                               0  1
  AMP PEAK 24(20Q11.21) MUTATED   51  3
  AMP PEAK 24(20Q11.21) WILD-TYPE 57  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED     51    3
  AMP PEAK 24(20Q11.21) WILD-TYPE   57    7
   clus
vv  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  0                            51                              57
  1                             3                               7
[1] 2 2
[1] FALSE
D24V6, binary
                                 cls
clus                               0  1
  AMP PEAK 24(20Q11.21) MUTATED   22 59
  AMP PEAK 24(20Q11.21) WILD-TYPE 31 66
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED     22   59
  AMP PEAK 24(20Q11.21) WILD-TYPE   31   66
     clus
vv    AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  NO                             22                              31
  YES                            59                              66
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 24(20Q11.21) MUTATED               2
  AMP PEAK 24(20Q11.21) WILD-TYPE             4
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(20Q11.21) MUTATED                                107
  AMP PEAK 24(20Q11.21) WILD-TYPE                              135
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 24(20Q11.21) MUTATED                                               4
  AMP PEAK 24(20Q11.21) WILD-TYPE                                             2
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 24(20Q11.21) MUTATED                                    10
  AMP PEAK 24(20Q11.21) WILD-TYPE                                  11
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 24(20Q11.21) MUTATED                                           2
  AMP PEAK 24(20Q11.21) WILD-TYPE                                         1
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 24(20Q11.21) MUTATED                                             10
  AMP PEAK 24(20Q11.21) WILD-TYPE                                            7
D24V7, multiclass
                                               clus
vv                                              AMP PEAK 24(20Q11.21) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        107
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             10
                                               clus
vv                                              AMP PEAK 24(20Q11.21) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          135
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, continuous
D24V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(20Q11.21) MUTATED                                  0     7
  AMP PEAK 24(20Q11.21) WILD-TYPE                                8    12
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(20Q11.21) MUTATED                          15
  AMP PEAK 24(20Q11.21) WILD-TYPE                        13
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 24(20Q11.21) MUTATED                                           0
  AMP PEAK 24(20Q11.21) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  AMP PEAK 24(20Q11.21) MUTATED      93
  AMP PEAK 24(20Q11.21) WILD-TYPE   109
D24V10, multiclass
                                           clus
vv                                          AMP PEAK 24(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                93
                                           clus
vv                                          AMP PEAK 24(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  12
  BLACK OR AFRICAN AMERICAN                                              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  WHITE                                                                 109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                                 cls
clus                               0  1
  AMP PEAK 24(20Q11.21) MUTATED    6 73
  AMP PEAK 24(20Q11.21) WILD-TYPE 17 90
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED      6   73
  AMP PEAK 24(20Q11.21) WILD-TYPE   17   90
                        clus
vv                       AMP PEAK 24(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            73
                        clus
vv                       AMP PEAK 24(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  17
  NOT HISPANIC OR LATINO                              90
[1] 2 2
[1] FALSE
D24V12, continuous
D24V13, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q11.21) MUTATED    86  36
  AMP PEAK 24(20Q11.21) WILD-TYPE 107  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED     86   36
  AMP PEAK 24(20Q11.21) WILD-TYPE  107   40
            clus
vv           AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  TUMOR FREE                            86                             107
  WITH TUMOR                            36                              40
[1] 2 2
[1] FALSE
                                 vv
clus                              G1 G2 G3 G4 GX
  AMP PEAK 24(20Q11.21) MUTATED    8 55 58  1 11
  AMP PEAK 24(20Q11.21) WILD-TYPE 10 74 57  0 13
D24V14, multiclass
    clus
vv   AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  G1                             8                              10
  G2                            55                              74
  G3                            58                              57
  G4                             1                               0
  GX                            11                              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, continuous
D24V16, continuous
D24V17, continuous
D24V18, continuous
D24V19, binary
                                 cls
clus                               0  1
  AMP PEAK 24(20Q11.21) MUTATED   10  2
  AMP PEAK 24(20Q11.21) WILD-TYPE 15  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED     10    2
  AMP PEAK 24(20Q11.21) WILD-TYPE   15    1
                         clus
vv                        AMP PEAK 24(20Q11.21) MUTATED
  COMPLETED AS PLANNED                               10
  TREATMENT NOT COMPLETED                             2
                         clus
vv                        AMP PEAK 24(20Q11.21) WILD-TYPE
  COMPLETED AS PLANNED                                 15
  TREATMENT NOT COMPLETED                               1
[1] 2 2
[1] FALSE
D24V20, continuous
D24V21, continuous
D24V22, continuous
D24V23, continuous
D24V24, continuous
D24V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 24(20Q11.21) MUTATED                                     0
  AMP PEAK 24(20Q11.21) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 24(20Q11.21) MUTATED                                     2
  AMP PEAK 24(20Q11.21) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 24(20Q11.21) MUTATED                        13
  AMP PEAK 24(20Q11.21) WILD-TYPE                      23
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 24(20Q11.21) MUTATED                         0
  AMP PEAK 24(20Q11.21) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 24(20Q11.21) MUTATED                         6
  AMP PEAK 24(20Q11.21) WILD-TYPE                       4
D24V26, multiclass
                                     clus
vv                                    AMP PEAK 24(20Q11.21) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        13
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         6
                                     clus
vv                                    AMP PEAK 24(20Q11.21) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                          23
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 24(20Q11.21) MUTATED                                               0
  AMP PEAK 24(20Q11.21) WILD-TYPE                                             3
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 24(20Q11.21) MUTATED                                               12
  AMP PEAK 24(20Q11.21) WILD-TYPE                                             13
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 24(20Q11.21) MUTATED                                                                                  41
  AMP PEAK 24(20Q11.21) WILD-TYPE                                                                                41
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 24(20Q11.21) MUTATED                                                                                             48
  AMP PEAK 24(20Q11.21) WILD-TYPE                                                                                           73
D24V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 24(20Q11.21) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            48
                                                                                              clus
vv                                                                                             AMP PEAK 24(20Q11.21) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              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"
D24V28, binary
                                 cls
clus                               0  1
  AMP PEAK 24(20Q11.21) MUTATED   31 35
  AMP PEAK 24(20Q11.21) WILD-TYPE 40 39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED     31   35
  AMP PEAK 24(20Q11.21) WILD-TYPE   40   39
         clus
vv        AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  ABSENT                             31                              40
  PRESENT                            35                              39
[1] 2 2
[1] FALSE
D24V29, continuous
D24V30, continuous
D24V31, binary
                                 cls
clus                               0  1
  AMP PEAK 24(20Q11.21) MUTATED   17 50
  AMP PEAK 24(20Q11.21) WILD-TYPE 32 67
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED     17   50
  AMP PEAK 24(20Q11.21) WILD-TYPE   32   67
                                          clus
vv                                         AMP PEAK 24(20Q11.21) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            50
                                          clus
vv                                         AMP PEAK 24(20Q11.21) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              67
[1] 2 2
[1] FALSE
D24V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 24(20Q11.21) MUTATED              5          24         37
  AMP PEAK 24(20Q11.21) WILD-TYPE           10          30         48
D24V33, multiclass
              clus
vv             AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  CURRENT USER                             5                              10
  FORMER USER                             24                              30
  NEVER USED                              37                              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"
D24V34, continuous
D24V35, binary
                                 cls
clus                               0  1
  AMP PEAK 24(20Q11.21) MUTATED   39  9
  AMP PEAK 24(20Q11.21) WILD-TYPE 53  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED     39    9
  AMP PEAK 24(20Q11.21) WILD-TYPE   53    9
         clus
vv        AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  ABSENT                             39                              53
  PRESENT                             9                               9
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 24(20Q11.21) MUTATED             2        46     2
  AMP PEAK 24(20Q11.21) WILD-TYPE           3        54     0
D24V36, multiclass
             clus
vv            AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  CARBOPLATIN                             2                               3
  CISPLATIN                              46                              54
  OTHER                                   2                               0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V37, continuous
D24V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 24(20Q11.21) MUTATED         2        0         1         0       15
  AMP PEAK 24(20Q11.21) WILD-TYPE       3        1         0         1       19
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 24(20Q11.21) MUTATED          32        13        4         4
  AMP PEAK 24(20Q11.21) WILD-TYPE        45        24        0         4
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 24(20Q11.21) MUTATED            3          2        19         1
  AMP PEAK 24(20Q11.21) WILD-TYPE          2          5        25         0
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 24(20Q11.21) MUTATED            2         23         4         6
  AMP PEAK 24(20Q11.21) WILD-TYPE          1         19         3         6
D24V39, multiclass
            clus
vv           AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                               0                               1
  STAGE IA1                              1                               0
  STAGE IA2                              0                               1
  STAGE IB                              15                              19
  STAGE IB1                             32                              45
  STAGE IB2                             13                              24
  STAGE II                               4                               0
  STAGE IIA                              4                               4
  STAGE IIA1                             3                               2
  STAGE IIA2                             2                               5
  STAGE IIB                             19                              25
  STAGE III                              1                               0
  STAGE IIIA                             2                               1
  STAGE IIIB                            23                              19
  STAGE IVA                              4                               3
  STAGE IVB                              6                               6
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(21Q22.13) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(21Q22.13) MUTATED    34  12
  AMP PEAK 25(21Q22.13) WILD-TYPE 180  56
  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE 
                             46                             236 
  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE 
                             12                              56 
$`AMP PEAK 25(21Q22.13) MUTATED`
TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1MH 
        1.48         0.69         5.46        19.86        31.40        38.99 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A7X8 TCGA-C5-A8XH 
       35.61         2.43         3.58       100.14         2.73        45.83 
TCGA-DG-A2KH TCGA-DG-A2KL TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A5O9 
        1.12        44.94        39.55        40.87        37.35        25.91 
TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RK TCGA-EK-A2RM TCGA-HG-A9SC 
       19.27         0.59        40.96         0.43         1.64        16.57 
TCGA-HM-A3JK TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU 
       20.78        36.36        21.44        21.11        44.61        11.28 
TCGA-LP-A5U2 TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A73R TCGA-VS-A8EC TCGA-VS-A8EH 
        0.30        35.05        17.23        18.64        46.52        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A9U7 
       23.97        19.96        36.13        59.18         4.73        48.39 
TCGA-VS-A9UI TCGA-VS-A9UU TCGA-VS-A9V3 TCGA-ZJ-AAXA 
       45.11        14.53        17.75         1.41 

$`AMP PEAK 25(21Q22.13) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-VS-A9V4 TCGA-2W-A8YY 
      146.86        12.59        14.70         8.32         4.34        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.82        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        0.46        20.91        40.93        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK 
       94.95         9.34        13.61        50.99         8.35        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
       23.51        27.52        20.81        20.91        14.73        95.11 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       82.06        63.98        87.75        58.88        36.76        55.63 
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        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82         7.46        14.89        26.79        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.22        24.00        13.48         0.36        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64         1.51         0.39         0.43         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.13         0.30         4.24         0.07         1.87         1.74 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       47.77         2.33         0.07         0.10         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
       20.35         7.92        15.22        19.79        15.55        12.23 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        17.75        25.41        21.67        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        29.85        27.42         3.29        24.56        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58        28.37         8.28        18.15       209.59        20.91 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89        12.49         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         9.17         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
       34.62        19.96        54.81        20.84         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       15.88         9.34        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EL 
       93.99        12.16        69.50        10.03        45.57        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       32.15        53.59        11.51        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       16.64        33.37        40.14        58.45        15.68        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA 
       55.50        50.14        51.32        50.47        43.40        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL 
       29.95        27.12        24.30        46.92         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE 
                           0.30                            0.07 
  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE 
                         100.14                          210.67 
  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE 
                         20.945                          23.245 
[1] "0.3 - 100.1 (20.9)" "0.1 - 210.7 (23.2)"
[1] "hr=" "1.4"
D25V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 25(21Q22.13) MUTATED    16  15   4   1
  AMP PEAK 25(21Q22.13) WILD-TYPE 119  55  17   7
D25V3, multiclass
    clus
vv   AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  T1                            16                             119
  T2                            15                              55
  T3                             4                              17
  T4                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                                 cls
clus                                0   1
  AMP PEAK 25(21Q22.13) MUTATED    20   8
  AMP PEAK 25(21Q22.13) WILD-TYPE 109  48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED     20    8
  AMP PEAK 25(21Q22.13) WILD-TYPE  109   48
   clus
vv  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  0                            20                             109
  1                             8                              48
[1] 2 2
[1] FALSE
D25V5, binary
                                 cls
clus                               0  1
  AMP PEAK 25(21Q22.13) MUTATED   19  2
  AMP PEAK 25(21Q22.13) WILD-TYPE 89  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED     19    2
  AMP PEAK 25(21Q22.13) WILD-TYPE   89    8
   clus
vv  AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  0                            19                              89
  1                             2                               8
[1] 2 2
[1] FALSE
D25V6, binary
                                 cls
clus                                0   1
  AMP PEAK 25(21Q22.13) MUTATED    10  20
  AMP PEAK 25(21Q22.13) WILD-TYPE  43 105
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED     10   20
  AMP PEAK 25(21Q22.13) WILD-TYPE   43  105
     clus
vv    AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  NO                             10                              43
  YES                            20                             105
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 25(21Q22.13) MUTATED               2
  AMP PEAK 25(21Q22.13) WILD-TYPE             4
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(21Q22.13) MUTATED                                 42
  AMP PEAK 25(21Q22.13) WILD-TYPE                              200
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 25(21Q22.13) MUTATED                                               1
  AMP PEAK 25(21Q22.13) WILD-TYPE                                             5
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 25(21Q22.13) MUTATED                                     2
  AMP PEAK 25(21Q22.13) WILD-TYPE                                  19
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 25(21Q22.13) MUTATED                                           0
  AMP PEAK 25(21Q22.13) WILD-TYPE                                         3
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 25(21Q22.13) MUTATED                                              1
  AMP PEAK 25(21Q22.13) WILD-TYPE                                           16
D25V7, multiclass
                                               clus
vv                                              AMP PEAK 25(21Q22.13) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         42
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              1
                                               clus
vv                                              AMP PEAK 25(21Q22.13) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          200
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, continuous
D25V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(21Q22.13) MUTATED                                  1     3
  AMP PEAK 25(21Q22.13) WILD-TYPE                                7    16
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(21Q22.13) MUTATED                           3
  AMP PEAK 25(21Q22.13) WILD-TYPE                        25
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 25(21Q22.13) MUTATED                                           0
  AMP PEAK 25(21Q22.13) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  AMP PEAK 25(21Q22.13) MUTATED      32
  AMP PEAK 25(21Q22.13) WILD-TYPE   170
D25V10, multiclass
                                           clus
vv                                          AMP PEAK 25(21Q22.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 3
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                32
                                           clus
vv                                          AMP PEAK 25(21Q22.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  16
  BLACK OR AFRICAN AMERICAN                                              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  WHITE                                                                 170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                                 cls
clus                                0   1
  AMP PEAK 25(21Q22.13) MUTATED     3  23
  AMP PEAK 25(21Q22.13) WILD-TYPE  20 140
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED      3   23
  AMP PEAK 25(21Q22.13) WILD-TYPE   20  140
                        clus
vv                       AMP PEAK 25(21Q22.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            23
                        clus
vv                       AMP PEAK 25(21Q22.13) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             140
[1] 2 2
[1] FALSE
D25V12, continuous
D25V13, binary
                                 cls
clus                                0   1
  AMP PEAK 25(21Q22.13) MUTATED    26  15
  AMP PEAK 25(21Q22.13) WILD-TYPE 167  61
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED     26   15
  AMP PEAK 25(21Q22.13) WILD-TYPE  167   61
            clus
vv           AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  TUMOR FREE                            26                             167
  WITH TUMOR                            15                              61
[1] 2 2
[1] FALSE
                                 vv
clus                               G1  G2  G3  G4  GX
  AMP PEAK 25(21Q22.13) MUTATED     2  15  23   0   6
  AMP PEAK 25(21Q22.13) WILD-TYPE  16 114  92   1  18
D25V14, multiclass
    clus
vv   AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  G1                             2                              16
  G2                            15                             114
  G3                            23                              92
  G4                             0                               1
  GX                             6                              18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, continuous
D25V16, continuous
D25V17, continuous
D25V18, continuous
D25V19, binary
                                 cls
clus                               0  1
  AMP PEAK 25(21Q22.13) MUTATED    4  1
  AMP PEAK 25(21Q22.13) WILD-TYPE 21  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED      4    1
  AMP PEAK 25(21Q22.13) WILD-TYPE   21    2
                         clus
vv                        AMP PEAK 25(21Q22.13) MUTATED
  COMPLETED AS PLANNED                                4
  TREATMENT NOT COMPLETED                             1
                         clus
vv                        AMP PEAK 25(21Q22.13) WILD-TYPE
  COMPLETED AS PLANNED                                 21
  TREATMENT NOT COMPLETED                               2
[1] 2 2
[1] FALSE
D25V20, continuous
D25V21, continuous
D25V22, continuous
D25V23, continuous
D25V24, continuous
D25V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 25(21Q22.13) MUTATED                                     0
  AMP PEAK 25(21Q22.13) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 25(21Q22.13) MUTATED                                     0
  AMP PEAK 25(21Q22.13) WILD-TYPE                                   7
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 25(21Q22.13) MUTATED                         3
  AMP PEAK 25(21Q22.13) WILD-TYPE                      33
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 25(21Q22.13) MUTATED                         0
  AMP PEAK 25(21Q22.13) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 25(21Q22.13) MUTATED                         4
  AMP PEAK 25(21Q22.13) WILD-TYPE                       6
D25V26, multiclass
                                     clus
vv                                    AMP PEAK 25(21Q22.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  OTHER LOCATION, SPECIFY                                         3
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         4
                                     clus
vv                                    AMP PEAK 25(21Q22.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               7
  OTHER LOCATION, SPECIFY                                          33
  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 25(21Q22.13) MUTATED                                               0
  AMP PEAK 25(21Q22.13) WILD-TYPE                                             3
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 25(21Q22.13) MUTATED                                                4
  AMP PEAK 25(21Q22.13) WILD-TYPE                                             21
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 25(21Q22.13) MUTATED                                                                                  18
  AMP PEAK 25(21Q22.13) WILD-TYPE                                                                                64
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 25(21Q22.13) MUTATED                                                                                             16
  AMP PEAK 25(21Q22.13) WILD-TYPE                                                                                          105
D25V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 25(21Q22.13) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            16
                                                                                              clus
vv                                                                                             AMP PEAK 25(21Q22.13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V28, binary
                                 cls
clus                               0  1
  AMP PEAK 25(21Q22.13) MUTATED   11 11
  AMP PEAK 25(21Q22.13) WILD-TYPE 60 63
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED     11   11
  AMP PEAK 25(21Q22.13) WILD-TYPE   60   63
         clus
vv        AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  ABSENT                             11                              60
  PRESENT                            11                              63
[1] 2 2
[1] FALSE
D25V29, continuous
D25V30, continuous
D25V31, binary
                                 cls
clus                                0   1
  AMP PEAK 25(21Q22.13) MUTATED    10  10
  AMP PEAK 25(21Q22.13) WILD-TYPE  39 107
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED     10   10
  AMP PEAK 25(21Q22.13) WILD-TYPE   39  107
                                          clus
vv                                         AMP PEAK 25(21Q22.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            10
                                          clus
vv                                         AMP PEAK 25(21Q22.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             107
[1] 2 2
[1] FALSE
D25V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 25(21Q22.13) MUTATED              3           5         13
  AMP PEAK 25(21Q22.13) WILD-TYPE           12          49         72
D25V33, multiclass
              clus
vv             AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  CURRENT USER                             3                              12
  FORMER USER                              5                              49
  NEVER USED                              13                              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"
D25V34, continuous
D25V35, binary
                                 cls
clus                               0  1
  AMP PEAK 25(21Q22.13) MUTATED   11  1
  AMP PEAK 25(21Q22.13) WILD-TYPE 81 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(21Q22.13) MUTATED     11    1
  AMP PEAK 25(21Q22.13) WILD-TYPE   81   17
         clus
vv        AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  ABSENT                             11                              81
  PRESENT                             1                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 25(21Q22.13) MUTATED             1        16     0
  AMP PEAK 25(21Q22.13) WILD-TYPE           4        84     2
D25V36, multiclass
             clus
vv            AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  CARBOPLATIN                             1                               4
  CISPLATIN                              16                              84
  OTHER                                   0                               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V37, continuous
D25V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 25(21Q22.13) MUTATED         1        0         0         1        3
  AMP PEAK 25(21Q22.13) WILD-TYPE       4        1         1         0       31
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  AMP PEAK 25(21Q22.13) MUTATED          11         4        2         2
  AMP PEAK 25(21Q22.13) WILD-TYPE        66        33        2         6
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  AMP PEAK 25(21Q22.13) MUTATED            0          2        11         0
  AMP PEAK 25(21Q22.13) WILD-TYPE          5          5        33         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 25(21Q22.13) MUTATED            0         10         0         1
  AMP PEAK 25(21Q22.13) WILD-TYPE          3         32         7        11
D25V39, multiclass
            clus
vv           AMP PEAK 25(21Q22.13) MUTATED AMP PEAK 25(21Q22.13) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                               3                              31
  STAGE IB1                             11                              66
  STAGE IB2                              4                              33
  STAGE II                               2                               2
  STAGE IIA                              2                               6
  STAGE IIA1                             0                               5
  STAGE IIA2                             2                               5
  STAGE IIB                             11                              33
  STAGE III                              0                               1
  STAGE IIIA                             0                               3
  STAGE IIIB                            10                              32
  STAGE IVA                              0                               7
  STAGE IVB                              1                              11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = AMP PEAK 26(XQ28) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 26(XQ28) MUTATED    60  12
  AMP PEAK 26(XQ28) WILD-TYPE 154  56
  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE 
                         72                         210 
  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE 
                         12                          56 
$`AMP PEAK 26(XQ28) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MP 
       57.04       144.16       177.04        46.32        53.16         3.58 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UH TCGA-C5-A8XI 
       73.45        83.05       154.32       101.82       131.11         8.35 
TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-EA-A3HQ TCGA-EA-A3QD 
       23.51         1.12        22.98        16.18        37.35        13.05 
TCGA-EA-A3QE TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2H0 
       25.02        31.73        14.89        25.91        27.22        60.72 
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         0.30         0.07 
TCGA-EK-A2RE TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A8YF 
        1.87         0.07         0.10         0.49         0.89        15.55 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LL 
       23.84        20.98       137.16        66.81        78.71        36.36 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A5U2 TCGA-MA-AA3Z TCGA-MY-A5BD TCGA-MY-A5BF 
      209.59        44.61         0.30        19.56        54.81        20.84 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-R2-A69V TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       15.95        16.14        19.59        69.50        10.03        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A950 
       32.42        23.97        11.51        59.18        16.64        40.14 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UM 
       15.68        56.35        48.39        29.95        27.12        27.25 
TCGA-VS-A9UP TCGA-VS-A9UZ TCGA-VS-A9V5 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       47.47        67.20        16.24        67.59        19.13         1.41 

$`AMP PEAK 26(XQ28) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN 
        0.69        17.52        17.82        49.48        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       68.84        18.74        36.56       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       19.86        67.46        31.40        30.21        35.01        57.73 
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-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        73.18        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CK 
       52.01        18.02        17.85        20.42       210.67       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK 
        9.34        13.61         2.73        50.99        45.83        99.91 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK 
       27.52        20.81        20.91        14.73        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
      117.99       118.65        16.83        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 
       40.87        30.90        31.53        31.36        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       24.56        26.01        12.13        24.82         7.46        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 
       27.29        27.25        24.00        13.48         0.36        26.27 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
       19.27         0.39         0.89         1.45         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        4.24         1.74         0.43        47.77         1.64         2.33 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG 
       20.35         7.92        15.22        19.79        12.23        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       16.11        31.36        36.26        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       14.01        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH 
      129.37        96.95        81.96        29.85        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       18.15        21.11        20.91        11.28         0.89        12.49 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 
        0.82        13.35        22.52        20.28        17.82         9.17 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE 
        8.52        11.38        28.08        34.62        19.96        35.05 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       17.23         2.96        15.58        16.41         9.04        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       14.07        15.88         9.34        18.64        22.62        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8EL 
       11.67        93.99        12.16        46.52        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       32.15        53.59        36.13        39.78        31.27        40.87 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
        4.73        33.37        58.45        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       50.47        43.40        28.50        24.30        46.92        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
        1.71        14.53        47.87        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
       14.53         3.42        18.25        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       17.75        15.42        26.01        29.26         0.16         3.91 

  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE 
                       0.07                        0.13 
  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE 
                     209.59                      210.67 
  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE 
                     24.495                      21.010 
[1] "0.1 - 209.6 (24.5)" "0.1 - 210.7 (21.0)"
[1] "hr=" "1.8"
D26V2, continuous
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 26(XQ28) MUTATED    32  17  10   1
  AMP PEAK 26(XQ28) WILD-TYPE 103  53  11   7
D26V3, multiclass
    clus
vv   AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  T1                        32                         103
  T2                        17                          53
  T3                        10                          11
  T4                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                             cls
clus                           0  1
  AMP PEAK 26(XQ28) MUTATED   36 11
  AMP PEAK 26(XQ28) WILD-TYPE 93 45
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED     36   11
  AMP PEAK 26(XQ28) WILD-TYPE   93   45
   clus
vv  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  0                        36                          93
  1                        11                          45
[1] 2 2
[1] FALSE
D26V5, binary
                             cls
clus                           0  1
  AMP PEAK 26(XQ28) MUTATED   27  1
  AMP PEAK 26(XQ28) WILD-TYPE 81  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED     27    1
  AMP PEAK 26(XQ28) WILD-TYPE   81    9
   clus
vv  AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  0                        27                          81
  1                         1                           9
[1] 2 2
[1] FALSE
D26V6, binary
                             cls
clus                           0  1
  AMP PEAK 26(XQ28) MUTATED    7 38
  AMP PEAK 26(XQ28) WILD-TYPE 46 87
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED      7   38
  AMP PEAK 26(XQ28) WILD-TYPE   46   87
     clus
vv    AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  NO                          7                          46
  YES                        38                          87
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(XQ28) MUTATED               2                               62
  AMP PEAK 26(XQ28) WILD-TYPE             4                              180
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 26(XQ28) MUTATED                                               1
  AMP PEAK 26(XQ28) WILD-TYPE                                             5
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 26(XQ28) MUTATED                                     3
  AMP PEAK 26(XQ28) WILD-TYPE                                  18
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 26(XQ28) MUTATED                                           3
  AMP PEAK 26(XQ28) WILD-TYPE                                         0
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 26(XQ28) MUTATED                                              4
  AMP PEAK 26(XQ28) WILD-TYPE                                           13
D26V7, multiclass
                                               clus
vv                                              AMP PEAK 26(XQ28) MUTATED
  ADENOSQUAMOUS                                                         2
  CERVICAL SQUAMOUS CELL CARCINOMA                                     62
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          4
                                               clus
vv                                              AMP PEAK 26(XQ28) WILD-TYPE
  ADENOSQUAMOUS                                                           4
  CERVICAL SQUAMOUS CELL CARCINOMA                                      180
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, continuous
D26V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(XQ28) MUTATED                                  2     5
  AMP PEAK 26(XQ28) WILD-TYPE                                6    14
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(XQ28) MUTATED                           9
  AMP PEAK 26(XQ28) WILD-TYPE                        19
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 26(XQ28) MUTATED                                           2    44
  AMP PEAK 26(XQ28) WILD-TYPE                                         0   158
D26V10, multiclass
                                           clus
vv                                          AMP PEAK 26(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                         9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            44
                                           clus
vv                                          AMP PEAK 26(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                          19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                             cls
clus                            0   1
  AMP PEAK 26(XQ28) MUTATED     4  37
  AMP PEAK 26(XQ28) WILD-TYPE  19 126
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED      4   37
  AMP PEAK 26(XQ28) WILD-TYPE   19  126
                        clus
vv                       AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             4                          19
  NOT HISPANIC OR LATINO                        37                         126
[1] 2 2
[1] FALSE
D26V12, continuous
D26V13, binary
                             cls
clus                            0   1
  AMP PEAK 26(XQ28) MUTATED    50  17
  AMP PEAK 26(XQ28) WILD-TYPE 143  59
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED     50   17
  AMP PEAK 26(XQ28) WILD-TYPE  143   59
            clus
vv           AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  TUMOR FREE                        50                         143
  WITH TUMOR                        17                          59
[1] 2 2
[1] FALSE
                             vv
clus                          G1 G2 G3 G4 GX
  AMP PEAK 26(XQ28) MUTATED    4 30 29  1  8
  AMP PEAK 26(XQ28) WILD-TYPE 14 99 86  0 16
D26V14, multiclass
    clus
vv   AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  G1                         4                          14
  G2                        30                          99
  G3                        29                          86
  G4                         1                           0
  GX                         8                          16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, continuous
D26V16, continuous
D26V17, continuous
D26V18, continuous
D26V19, binary
                             cls
clus                           0  1
  AMP PEAK 26(XQ28) MUTATED    4  1
  AMP PEAK 26(XQ28) WILD-TYPE 21  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED      4    1
  AMP PEAK 26(XQ28) WILD-TYPE   21    2
                         clus
vv                        AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  COMPLETED AS PLANNED                            4                          21
  TREATMENT NOT COMPLETED                         1                           2
[1] 2 2
[1] FALSE
D26V20, continuous
D26V21, continuous
D26V22, continuous
D26V23, continuous
D26V24, continuous
D26V25, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 26(XQ28) MUTATED                                     0
  AMP PEAK 26(XQ28) WILD-TYPE                                   2
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 26(XQ28) MUTATED                                     0
  AMP PEAK 26(XQ28) WILD-TYPE                                   7
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 26(XQ28) MUTATED                         8                       0
  AMP PEAK 26(XQ28) WILD-TYPE                      28                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK 26(XQ28) MUTATED                         2
  AMP PEAK 26(XQ28) WILD-TYPE                       8
D26V26, multiclass
                                     clus
vv                                    AMP PEAK 26(XQ28) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  OTHER LOCATION, SPECIFY                                     8
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     2
                                     clus
vv                                    AMP PEAK 26(XQ28) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           7
  OTHER LOCATION, SPECIFY                                      28
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 26(XQ28) MUTATED                                               0
  AMP PEAK 26(XQ28) WILD-TYPE                                             3
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 26(XQ28) MUTATED                                                9
  AMP PEAK 26(XQ28) WILD-TYPE                                             16
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 26(XQ28) MUTATED                                                                                  21
  AMP PEAK 26(XQ28) WILD-TYPE                                                                                61
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 26(XQ28) MUTATED                                                                                             31
  AMP PEAK 26(XQ28) WILD-TYPE                                                                                           90
D26V27, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 26(XQ28) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        31
                                                                                              clus
vv                                                                                             AMP PEAK 26(XQ28) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        16
  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)                          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"
D26V28, binary
                             cls
clus                           0  1
  AMP PEAK 26(XQ28) MUTATED   17 18
  AMP PEAK 26(XQ28) WILD-TYPE 54 56
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED     17   18
  AMP PEAK 26(XQ28) WILD-TYPE   54   56
         clus
vv        AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  ABSENT                         17                          54
  PRESENT                        18                          56
[1] 2 2
[1] FALSE
D26V29, continuous
D26V30, continuous
D26V31, binary
                             cls
clus                           0  1
  AMP PEAK 26(XQ28) MUTATED   13 25
  AMP PEAK 26(XQ28) WILD-TYPE 36 92
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED     13   25
  AMP PEAK 26(XQ28) WILD-TYPE   36   92
                                          clus
vv                                         AMP PEAK 26(XQ28) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        25
                                          clus
vv                                         AMP PEAK 26(XQ28) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          92
[1] 2 2
[1] FALSE
D26V32, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK 26(XQ28) MUTATED              4          11         25
  AMP PEAK 26(XQ28) WILD-TYPE           11          43         60
D26V33, multiclass
              clus
vv             AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  CURRENT USER                         4                          11
  FORMER USER                         11                          43
  NEVER USED                          25                          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"
D26V34, continuous
D26V35, binary
                             cls
clus                           0  1
  AMP PEAK 26(XQ28) MUTATED   24  3
  AMP PEAK 26(XQ28) WILD-TYPE 68 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(XQ28) MUTATED     24    3
  AMP PEAK 26(XQ28) WILD-TYPE   68   15
         clus
vv        AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  ABSENT                         24                          68
  PRESENT                         3                          15
[1] 2 2
[1] FALSE
                             vv
clus                          CARBOPLATIN CISPLATIN OTHER
  AMP PEAK 26(XQ28) MUTATED             1        24     0
  AMP PEAK 26(XQ28) WILD-TYPE           4        76     2
D26V36, multiclass
             clus
vv            AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  CARBOPLATIN                         1                           4
  CISPLATIN                          24                          76
  OTHER                               0                           2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V37, continuous
D26V38, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  AMP PEAK 26(XQ28) MUTATED         1        0         0         0        6
  AMP PEAK 26(XQ28) WILD-TYPE       4        1         1         1       28
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  AMP PEAK 26(XQ28) MUTATED          21         6        1         3          3
  AMP PEAK 26(XQ28) WILD-TYPE        56        31        3         5          2
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  AMP PEAK 26(XQ28) MUTATED            1        14         1          1
  AMP PEAK 26(XQ28) WILD-TYPE          6        30         0          2
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  AMP PEAK 26(XQ28) MUTATED           11         2         2
  AMP PEAK 26(XQ28) WILD-TYPE         31         5        10
D26V39, multiclass
            clus
vv           AMP PEAK 26(XQ28) MUTATED AMP PEAK 26(XQ28) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                           0                           1
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           6                          28
  STAGE IB1                         21                          56
  STAGE IB2                          6                          31
  STAGE II                           1                           3
  STAGE IIA                          3                           5
  STAGE IIA1                         3                           2
  STAGE IIA2                         1                           6
  STAGE IIB                         14                          30
  STAGE III                          1                           0
  STAGE IIIA                         1                           2
  STAGE IIIB                        11                          31
  STAGE IVA                          2                           5
  STAGE IVB                          2                          10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.23) MUTATED    27  10
  DEL PEAK  1(1P36.23) WILD-TYPE 187  58
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            37                            245 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            10                             58 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-EX-A449 TCGA-VS-A9V4 TCGA-C5-A0TN TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       14.70         4.34        11.44        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CM 
        0.46        73.18        73.45        83.05        52.01        20.35 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A8YQ TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A556 
      131.11         9.34        23.51        30.90        31.73        14.89 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EX-A69L 
        1.51        19.27         0.59         1.74         1.64        19.79 
TCGA-FU-A3EO TCGA-IR-A3LF TCGA-JX-A3Q8 TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EJ 
       16.11        96.95        44.61        17.23         9.04        19.96 
TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A950 TCGA-VS-A9UD TCGA-VS-A9UO TCGA-VS-A9V3 
       53.59        39.78        40.14        24.30        47.87        17.75 
TCGA-VS-A9V5 
       16.24 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        12.59         8.32         1.48         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF 
       17.82        49.48        57.04        23.67        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35       100.14        38.43        33.24        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 
      147.35        17.19       155.77        94.95        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       50.99        45.83         8.35        99.91        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91        14.73         1.12        95.11        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63       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 
       39.55        40.87        37.35        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S 
       25.02        36.89        26.40        24.56        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82         7.46        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.22        24.00        13.48         0.36        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        6.64         0.39         0.43         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK 
       40.96         0.30         4.24         0.07         1.87         0.43 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       47.77         2.33         0.07         0.10         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       20.35         7.92        15.22        15.55        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       19.04        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       28.31        14.01        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        16.57        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
      147.39       137.16        66.81       129.37        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
      209.59        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        20.28        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        9.17         8.52        11.38        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       54.81        35.05        20.84         2.96        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       23.97        65.49        32.15        36.13        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       31.27        40.87        16.64         4.73        33.37        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH 
       43.40        48.39        28.50        29.95        27.12        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ 
       45.11         1.71        14.53        27.25        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       26.07        15.85        14.53         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       18.84         5.16        18.25        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                          0.46                           0.07 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        131.11                         210.67 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         20.35                          22.62 
[1] "0.5 - 131.1 (20.4)" "0.1 - 210.7 (22.6)"
[1] "hr=" "1.2"
D27V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.23) MUTATED    15   7   2   2
  DEL PEAK  1(1P36.23) WILD-TYPE 120  63  19   6
D27V3, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1                           15                            120
  T2                            7                             63
  T3                            2                             19
  T4                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED    15   5
  DEL PEAK  1(1P36.23) WILD-TYPE 114  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     15    5
  DEL PEAK  1(1P36.23) WILD-TYPE  114   51
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           15                            114
  1                            5                             51
[1] 2 2
[1] FALSE
D27V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   10  3
  DEL PEAK  1(1P36.23) WILD-TYPE 98  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     10    3
  DEL PEAK  1(1P36.23) WILD-TYPE   98    7
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           10                             98
  1                            3                              7
[1] 2 2
[1] FALSE
D27V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED     4  17
  DEL PEAK  1(1P36.23) WILD-TYPE  49 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      4   17
  DEL PEAK  1(1P36.23) WILD-TYPE   49  108
     clus
vv    DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  NO                             4                             49
  YES                           17                            108
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.23) MUTATED               0                               26
  DEL PEAK  1(1P36.23) WILD-TYPE             6                              216
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  1(1P36.23) MUTATED                                               3
  DEL PEAK  1(1P36.23) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  1(1P36.23) MUTATED                                     6
  DEL PEAK  1(1P36.23) WILD-TYPE                                  15
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  1(1P36.23) MUTATED                                           1
  DEL PEAK  1(1P36.23) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  1(1P36.23) MUTATED                                              4
  DEL PEAK  1(1P36.23) WILD-TYPE                                           13
D27V7, multiclass
                                               clus
vv                                              DEL PEAK  1(1P36.23) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        26
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              DEL PEAK  1(1P36.23) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         216
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, continuous
D27V9, 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    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.23) MUTATED                           4
  DEL PEAK  1(1P36.23) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  1(1P36.23) MUTATED                                           0
  DEL PEAK  1(1P36.23) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK  1(1P36.23) MUTATED      32
  DEL PEAK  1(1P36.23) WILD-TYPE   170
D27V10, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               32
                                           clus
vv                                          DEL PEAK  1(1P36.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED     3  23
  DEL PEAK  1(1P36.23) WILD-TYPE  20 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      3   23
  DEL PEAK  1(1P36.23) WILD-TYPE   20  140
                        clus
vv                       DEL PEAK  1(1P36.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       DEL PEAK  1(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            140
[1] 2 2
[1] FALSE
D27V12, continuous
D27V13, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED    23  13
  DEL PEAK  1(1P36.23) WILD-TYPE 170  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     23   13
  DEL PEAK  1(1P36.23) WILD-TYPE  170   63
            clus
vv           DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  TUMOR FREE                           23                            170
  WITH TUMOR                           13                             63
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK  1(1P36.23) MUTATED     2  19  17   0   1
  DEL PEAK  1(1P36.23) WILD-TYPE  16 110  98   1  23
D27V14, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  G1                            2                             16
  G2                           19                            110
  G3                           17                             98
  G4                            0                              1
  GX                            1                             23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, continuous
D27V16, continuous
D27V17, continuous
D27V18, continuous
D27V19, 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
D27V20, continuous
D27V21, continuous
D27V22, continuous
D27V23, continuous
D27V24, continuous
D27V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  1(1P36.23) MUTATED                                     1
  DEL PEAK  1(1P36.23) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  1(1P36.23) MUTATED                                     1
  DEL PEAK  1(1P36.23) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK  1(1P36.23) MUTATED                         5
  DEL PEAK  1(1P36.23) WILD-TYPE                      31
                                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                       8
D27V26, multiclass
                                     clus
vv                                    DEL PEAK  1(1P36.23) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        5
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK  1(1P36.23) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         31
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  1(1P36.23) MUTATED                                               0
  DEL PEAK  1(1P36.23) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  1(1P36.23) MUTATED                                                2
  DEL PEAK  1(1P36.23) WILD-TYPE                                             23
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  1(1P36.23) MUTATED                                                                                  15
  DEL PEAK  1(1P36.23) WILD-TYPE                                                                                67
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  1(1P36.23) MUTATED                                                                                             13
  DEL PEAK  1(1P36.23) WILD-TYPE                                                                                          108
D27V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  1(1P36.23) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           13
                                                                                              clus
vv                                                                                             DEL PEAK  1(1P36.23) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V28, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    9  8
  DEL PEAK  1(1P36.23) WILD-TYPE 62 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      9    8
  DEL PEAK  1(1P36.23) WILD-TYPE   62   66
         clus
vv        DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  ABSENT                             9                             62
  PRESENT                            8                             66
[1] 2 2
[1] FALSE
D27V29, continuous
D27V30, continuous
D27V31, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED     6   8
  DEL PEAK  1(1P36.23) WILD-TYPE  43 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      6    8
  DEL PEAK  1(1P36.23) WILD-TYPE   43  109
                                          clus
vv                                         DEL PEAK  1(1P36.23) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            8
                                          clus
vv                                         DEL PEAK  1(1P36.23) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            109
[1] 2 2
[1] FALSE
D27V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK  1(1P36.23) MUTATED              1           8         10
  DEL PEAK  1(1P36.23) WILD-TYPE           14          46         75
D27V33, multiclass
              clus
vv             DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  CURRENT USER                            1                             14
  FORMER USER                             8                             46
  NEVER USED                             10                             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"
D27V34, continuous
D27V35, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   15  1
  DEL PEAK  1(1P36.23) WILD-TYPE 77 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     15    1
  DEL PEAK  1(1P36.23) WILD-TYPE   77   17
         clus
vv        DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  ABSENT                            15                             77
  PRESENT                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  1(1P36.23) MUTATED             1        13     1
  DEL PEAK  1(1P36.23) WILD-TYPE           4        87     1
D27V36, multiclass
             clus
vv            DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             13                             87
  OTHER                                  1                              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"
D27V37, continuous
[1] "Remove cluster labels:"       "DEL PEAK  1(1P36.23) MUTATED"
clus
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-C5-A1ML                     TCGA-C5-A1MN 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-GH-A9DA                     TCGA-HM-A3JK 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-MA-AA3W 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"DEL PEAK  1(1P36.23) WILD-TYPE" 
D27V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  1(1P36.23) MUTATED         1        0         0         0        3
  DEL PEAK  1(1P36.23) WILD-TYPE       4        1         1         1       31
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  1(1P36.23) MUTATED          11         6        1         2
  DEL PEAK  1(1P36.23) WILD-TYPE        66        31        3         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  1(1P36.23) MUTATED            1          0         6         0
  DEL PEAK  1(1P36.23) WILD-TYPE          4          7        38         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.23) MUTATED            2          3         1         2
  DEL PEAK  1(1P36.23) WILD-TYPE          1         39         6        10
D27V39, multiclass
            clus
vv           DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              3                             31
  STAGE IB1                            11                             66
  STAGE IB2                             6                             31
  STAGE II                              1                              3
  STAGE IIA                             2                              6
  STAGE IIA1                            1                              4
  STAGE IIA2                            0                              7
  STAGE IIB                             6                             38
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                            3                             39
  STAGE IVA                             1                              6
  STAGE IVB                             2                             10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    17  14
  DEL PEAK  2(1P13.2) WILD-TYPE 197  54
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           31                           251 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           14                            54 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-C5-A1BF TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A7CH TCGA-C5-A7UH 
       18.74        35.61        73.18        78.35       154.32       131.11 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-DS-A0VN TCGA-EA-A3HR 
       94.95        13.61        45.83        23.51       118.65        30.90 
TCGA-EA-A3QE TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EX-A69L TCGA-FU-A3NI TCGA-HG-A2PA 
       25.02        19.27         0.43        19.79        20.98        25.41 
TCGA-HM-A6W2 TCGA-LP-A4AW TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EB TCGA-VS-A8EC 
        9.44         0.89        17.23         9.04        10.03        46.52 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A950 
       65.49        53.59        11.51        39.78         4.73        40.14 
TCGA-VS-A9UI 
       45.11 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A 
        0.69        17.52        17.82        49.48        57.04        23.67 
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       11.44        68.84        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       30.21        35.01        57.73        53.16        38.99         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        2.43        20.91        40.93         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X8 
       20.35       147.35        17.19       155.77         9.34         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       50.99         8.35        99.91        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       14.73         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       87.75        58.88        36.76        55.63       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
       37.35        31.53        31.36        13.05        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        31.73        26.01        12.13        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       24.00        13.48         0.36        60.72        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.39         0.59         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       40.96         0.30         4.24         0.07         1.87         1.74 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.43        47.77         1.64         2.33         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A8YF 
        0.49         0.89        20.35         7.92        15.22        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       12.23        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12        17.75        16.57        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       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX 
       21.11       209.59        44.61        20.91        11.28        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         9.17         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
       19.96        54.81        35.05        20.84         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       93.99        12.16        69.50        45.57        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       19.96        32.15        36.13        59.18        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       16.64        33.37        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL 
       29.95        27.12        24.30        46.92         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       18.25        17.75        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       154.32                        210.67 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        25.41                         21.44 
[1] "0.4 - 154.3 (25.4)" "0.1 - 210.7 (21.4)"
[1] "hr=" "1.7"
D28V2, continuous
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  2(1P13.2) MUTATED    12   6   3   0
  DEL PEAK  2(1P13.2) WILD-TYPE 123  64  18   8
D28V3, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                          12                           123
  T2                           6                            64
  T3                           3                            18
  T4                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    14   3
  DEL PEAK  2(1P13.2) WILD-TYPE 115  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     14    3
  DEL PEAK  2(1P13.2) WILD-TYPE  115   53
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          14                           115
  1                           3                            53
[1] 2 2
[1] FALSE
D28V5, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   12  3
  DEL PEAK  2(1P13.2) WILD-TYPE 96  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     12    3
  DEL PEAK  2(1P13.2) WILD-TYPE   96    7
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          12                            96
  1                           3                             7
[1] 2 2
[1] FALSE
D28V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     6  16
  DEL PEAK  2(1P13.2) WILD-TYPE  47 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6   16
  DEL PEAK  2(1P13.2) WILD-TYPE   47  109
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                            6                            47
  YES                          16                           109
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.2) MUTATED               1                               31
  DEL PEAK  2(1P13.2) WILD-TYPE             5                              211
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  2(1P13.2) MUTATED                                               0
  DEL PEAK  2(1P13.2) WILD-TYPE                                             6
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  2(1P13.2) MUTATED                                     1
  DEL PEAK  2(1P13.2) WILD-TYPE                                  20
                               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                                           16
D28V7, multiclass
                                               clus
vv                                              DEL PEAK  2(1P13.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       31
  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                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        211
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, continuous
D28V9, 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    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P13.2) MUTATED                           5
  DEL PEAK  2(1P13.2) WILD-TYPE                        23
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           0    25
  DEL PEAK  2(1P13.2) WILD-TYPE                                         2   177
D28V10, multiclass
                                           clus
vv                                          DEL PEAK  2(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              25
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     2  19
  DEL PEAK  2(1P13.2) WILD-TYPE  21 144
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      2   19
  DEL PEAK  2(1P13.2) WILD-TYPE   21  144
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           144
[1] 2 2
[1] FALSE
D28V12, continuous
D28V13, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    18  13
  DEL PEAK  2(1P13.2) WILD-TYPE 175  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     18   13
  DEL PEAK  2(1P13.2) WILD-TYPE  175   63
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  TUMOR FREE                          18                           175
  WITH TUMOR                          13                            63
[1] 2 2
[1] FALSE
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK  2(1P13.2) MUTATED     2  15   9   0   4
  DEL PEAK  2(1P13.2) WILD-TYPE  16 114 106   1  20
D28V14, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  G1                           2                            16
  G2                          15                           114
  G3                           9                           106
  G4                           0                             1
  GX                           4                            20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, 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                            42 
                   TCGA-EX-A69M                    TCGA-FU-A3TX 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-VS-A9V4                    TCGA-ZJ-AAX4 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-2W-A8YY                    TCGA-BI-A0VR 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1BJ                    TCGA-C5-A1BL 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1BQ                    TCGA-C5-A1ME 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1MF                    TCGA-C5-A1MH 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A2M2                    TCGA-C5-A3HD 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A7CM                    TCGA-C5-A7CO 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A907                    TCGA-DG-A2KK 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-DS-A3LQ                    TCGA-EK-A2RA 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FU-A2QG                    TCGA-FU-A3WB 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-HM-A4S6 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-IR-A3L7                    TCGA-IR-A3LB 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-IR-A3LH                    TCGA-JX-A3Q0 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MA-AA43                    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-VS-A9V0                    TCGA-WL-A834 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-ZJ-A8QR                    TCGA-ZJ-AAXA 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-ZJ-AAXT                    TCGA-ZJ-AB0I 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
D28V16, continuous
D28V17, continuous
D28V18, continuous
D28V19, 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
D28V20, continuous
D28V21, continuous
D28V22, continuous
D28V23, continuous
D28V24, continuous
D28V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  2(1P13.2) MUTATED                                     0
  DEL PEAK  2(1P13.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  2(1P13.2) MUTATED                                     0
  DEL PEAK  2(1P13.2) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  2(1P13.2) MUTATED                         4                       0
  DEL PEAK  2(1P13.2) WILD-TYPE                      32                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  2(1P13.2) MUTATED                         0
  DEL PEAK  2(1P13.2) WILD-TYPE                      10
D28V26, multiclass
                                     clus
vv                                    DEL PEAK  2(1P13.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       4
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    DEL PEAK  2(1P13.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        32
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                        10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  2(1P13.2) MUTATED                                               0
  DEL PEAK  2(1P13.2) WILD-TYPE                                             3
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  2(1P13.2) MUTATED                                                4
  DEL PEAK  2(1P13.2) WILD-TYPE                                             21
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  2(1P13.2) MUTATED                                                                                   7
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                75
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  2(1P13.2) MUTATED                                                                                             13
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                          108
D28V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  2(1P13.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          13
                                                                                              clus
vv                                                                                             DEL PEAK  2(1P13.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       75
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V28, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6  4
  DEL PEAK  2(1P13.2) WILD-TYPE 65 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6    4
  DEL PEAK  2(1P13.2) WILD-TYPE   65   70
         clus
vv        DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ABSENT                            6                            65
  PRESENT                           4                            70
[1] 2 2
[1] FALSE
D28V29, continuous
D28V30, continuous
D28V31, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     9   9
  DEL PEAK  2(1P13.2) WILD-TYPE  40 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      9    9
  DEL PEAK  2(1P13.2) WILD-TYPE   40  108
                                          clus
vv                                         DEL PEAK  2(1P13.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           9
                                          clus
vv                                         DEL PEAK  2(1P13.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           108
[1] 2 2
[1] FALSE
D28V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  2(1P13.2) MUTATED              2           6          6
  DEL PEAK  2(1P13.2) WILD-TYPE           13          48         79
D28V33, multiclass
              clus
vv             DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CURRENT USER                           2                            13
  FORMER USER                            6                            48
  NEVER USED                             6                            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"
D28V34, continuous
D28V35, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    7  1
  DEL PEAK  2(1P13.2) WILD-TYPE 85 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7    1
  DEL PEAK  2(1P13.2) WILD-TYPE   85   17
         clus
vv        DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ABSENT                            7                            85
  PRESENT                           1                            17
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  2(1P13.2) MUTATED             1        10     1
  DEL PEAK  2(1P13.2) WILD-TYPE           4        90     1
D28V36, multiclass
             clus
vv            DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            10                            90
  OTHER                                 1                             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"
D28V37, continuous
[1] "Remove cluster labels:"      "DEL PEAK  2(1P13.2) MUTATED"
clus
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            1                            16 
                   TCGA-C5-A1BN                    TCGA-C5-A1MH 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1ML                    TCGA-C5-A1MN 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1MP                    TCGA-EK-A2RO 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-GH-A9DA                    TCGA-HM-A3JK 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-JW-A852                    TCGA-JX-A3Q8 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MA-AA3W                    TCGA-MA-AA3Z 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MA-AA42                    TCGA-MU-A51Y 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MU-A8JM                    TCGA-ZX-AA5X 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
D28V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  2(1P13.2) MUTATED         1        1         0         0        4
  DEL PEAK  2(1P13.2) WILD-TYPE       4        0         1         1       30
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED           9         2        1         2
  DEL PEAK  2(1P13.2) WILD-TYPE        68        35        3         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  2(1P13.2) MUTATED            0          0         5         0
  DEL PEAK  2(1P13.2) WILD-TYPE          5          7        39         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  2(1P13.2) MUTATED            1          5         1         2
  DEL PEAK  2(1P13.2) WILD-TYPE          2         37         6        10
D28V39, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             4                            30
  STAGE IB1                            9                            68
  STAGE IB2                            2                            35
  STAGE II                             1                             3
  STAGE IIA                            2                             6
  STAGE IIA1                           0                             5
  STAGE IIA2                           0                             7
  STAGE IIB                            5                            39
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                           5                            37
  STAGE IVA                            1                             6
  STAGE IVB                            2                            10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    49  13
  DEL PEAK  3(2Q22.1) WILD-TYPE 165  55
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           62                           220 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           13                            55 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-ZJ-AAX4 TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A2LT 
        0.69        36.56         5.46        30.21        38.99        73.18 
TCGA-C5-A2LV TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7UH TCGA-C5-A8YQ TCGA-C5-A8YR 
       73.45        18.02       210.67       131.11        23.51        27.52 
TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A3HR 
        1.12        44.94       118.65        22.98        17.52        30.90 
TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2IP 
       24.56        12.13        27.25        27.22         0.36         6.64 
TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EX-A69L TCGA-EX-A8YF 
        1.51         1.45         1.74         2.33        19.79        15.55 
TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       21.67         9.44       147.39        78.71       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 
       20.91        13.35        17.82        19.56         9.17        11.38 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-R2-A69V TCGA-UC-A7PG 
       20.84        17.23        15.58        16.41        19.59        12.16 
TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A953 
       32.42        65.49        11.51         4.73        33.37        15.68 
TCGA-VS-A9U7 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UY TCGA-VS-A9V3 
       48.39        24.30        45.11        27.25        18.25        17.75 
TCGA-VS-A9V5 TCGA-XS-A8TJ 
       16.24        29.26 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       68.84        18.74       144.16       177.04       173.29        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
        3.58        44.22        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       33.24        52.01        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
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-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
        8.35        99.91        20.81        20.91        14.73        95.11 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       82.06        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
      117.99        16.83        16.18         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       37.35        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       26.40        31.73        26.01        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       26.79        25.91        27.29        24.00        13.48        60.72 
TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27        19.27         0.39         0.43         0.59         0.89 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        40.96         0.30         4.24         0.07         1.87 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.43        47.77         1.64         0.07         0.10         0.49 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.89        20.35         7.92        15.22        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA 
       17.75        25.41        16.57        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       129.37        96.95        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AW 
       28.37         8.28        18.15        21.11        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA42 
       12.49         0.30         0.82        22.52        20.28         8.52 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA 
       28.08        34.62        19.96        54.81        35.05         2.96 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        9.34        18.64        22.62        14.60        11.67        93.99 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ 
       69.50        10.03        46.52        45.57        23.97        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        53.59        36.13        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       40.87        16.64        40.14        58.45        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        51.32        50.47        43.40        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP 
       27.12        46.92         1.71        14.53        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ 
       41.52        26.07        15.85        14.53         3.42        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ 
       18.84         5.16        18.25        15.42        26.01        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         1.41         0.16         3.91 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       210.67                        177.04 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       20.315                        23.905 
[1] "0.4 - 210.7 (20.3)" "0.1 - 177.0 (23.9)"
[1] "hr=" "1.1"
D29V2, continuous
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(2Q22.1) MUTATED    29  17   8   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 106  53  13   6
D29V3, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                          29                           106
  T2                          17                            53
  T3                           8                            13
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   31 12
  DEL PEAK  3(2Q22.1) WILD-TYPE 98 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     31   12
  DEL PEAK  3(2Q22.1) WILD-TYPE   98   44
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          31                            98
  1                          12                            44
[1] 2 2
[1] FALSE
D29V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   31  3
  DEL PEAK  3(2Q22.1) WILD-TYPE 77  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     31    3
  DEL PEAK  3(2Q22.1) WILD-TYPE   77    7
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          31                            77
  1                           3                             7
[1] 2 2
[1] FALSE
D29V6, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   10 32
  DEL PEAK  3(2Q22.1) WILD-TYPE 43 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     10   32
  DEL PEAK  3(2Q22.1) WILD-TYPE   43   93
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                           10                            43
  YES                          32                            93
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED               2                               58
  DEL PEAK  3(2Q22.1) WILD-TYPE             4                              184
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  3(2Q22.1) MUTATED                                               0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             6
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                     2
  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                                              3
  DEL PEAK  3(2Q22.1) WILD-TYPE                                           14
D29V7, multiclass
                                               clus
vv                                              DEL PEAK  3(2Q22.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       58
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              DEL PEAK  3(2Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        184
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, continuous
D29V9, 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    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(2Q22.1) MUTATED                          10
  DEL PEAK  3(2Q22.1) WILD-TYPE                        18
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(2Q22.1) MUTATED                                           0    42
  DEL PEAK  3(2Q22.1) WILD-TYPE                                         2   160
D29V10, multiclass
                                           clus
vv                                          DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              42
                                           clus
vv                                          DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               160
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     6  35
  DEL PEAK  3(2Q22.1) WILD-TYPE  17 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      6   35
  DEL PEAK  3(2Q22.1) WILD-TYPE   17  128
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          35
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           128
[1] 2 2
[1] FALSE
D29V12, continuous
D29V13, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    40  16
  DEL PEAK  3(2Q22.1) WILD-TYPE 153  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     40   16
  DEL PEAK  3(2Q22.1) WILD-TYPE  153   60
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  TUMOR FREE                          40                           153
  WITH TUMOR                          16                            60
[1] 2 2
[1] FALSE
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK  3(2Q22.1) MUTATED     3  24  30   1   5
  DEL PEAK  3(2Q22.1) WILD-TYPE  15 105  85   0  19
D29V14, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  G1                           3                            15
  G2                          24                           105
  G3                          30                            85
  G4                           1                             0
  GX                           5                            19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, continuous
D29V16, continuous
D29V17, continuous
D29V18, continuous
D29V19, 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
D29V20, continuous
D29V21, continuous
D29V22, continuous
D29V23, continuous
D29V24, continuous
D29V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  3(2Q22.1) MUTATED                                     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  3(2Q22.1) MUTATED                                     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  3(2Q22.1) MUTATED                         9                       0
  DEL PEAK  3(2Q22.1) WILD-TYPE                      27                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  3(2Q22.1) MUTATED                         3
  DEL PEAK  3(2Q22.1) WILD-TYPE                       7
D29V26, multiclass
                                     clus
vv                                    DEL PEAK  3(2Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       9
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    DEL PEAK  3(2Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        27
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  3(2Q22.1) MUTATED                                               1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  3(2Q22.1) MUTATED                                                7
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             18
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  3(2Q22.1) MUTATED                                                                                  14
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                                68
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  3(2Q22.1) MUTATED                                                                                             31
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                                           90
D29V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  3(2Q22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          31
                                                                                              clus
vv                                                                                             DEL PEAK  3(2Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            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"
D29V28, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   18 14
  DEL PEAK  3(2Q22.1) WILD-TYPE 53 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     18   14
  DEL PEAK  3(2Q22.1) WILD-TYPE   53   60
         clus
vv        DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  ABSENT                           18                            53
  PRESENT                          14                            60
[1] 2 2
[1] FALSE
D29V29, continuous
D29V30, continuous
D29V31, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   11 29
  DEL PEAK  3(2Q22.1) WILD-TYPE 38 88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     11   29
  DEL PEAK  3(2Q22.1) WILD-TYPE   38   88
                                          clus
vv                                         DEL PEAK  3(2Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          29
                                          clus
vv                                         DEL PEAK  3(2Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            88
[1] 2 2
[1] FALSE
D29V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  3(2Q22.1) MUTATED              4          19         21
  DEL PEAK  3(2Q22.1) WILD-TYPE           11          35         64
D29V33, multiclass
              clus
vv             DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           19                            35
  NEVER USED                            21                            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"
D29V34, continuous
D29V35, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   22  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 70 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     22    0
  DEL PEAK  3(2Q22.1) WILD-TYPE   70   18
         clus
vv        DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  ABSENT                           22                            70
  PRESENT                           0                            18
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  3(2Q22.1) MUTATED             1        27     0
  DEL PEAK  3(2Q22.1) WILD-TYPE           4        73     2
D29V36, multiclass
             clus
vv            DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            27                            73
  OTHER                                 0                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V37, continuous
D29V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  3(2Q22.1) MUTATED         0        0         0         0        6
  DEL PEAK  3(2Q22.1) WILD-TYPE       5        1         1         1       28
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  3(2Q22.1) MUTATED          19         7        3         2
  DEL PEAK  3(2Q22.1) WILD-TYPE        58        30        1         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  3(2Q22.1) MUTATED            1          1         7         1
  DEL PEAK  3(2Q22.1) WILD-TYPE          4          6        37         0
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  3(2Q22.1) MUTATED            1          9         2         4
  DEL PEAK  3(2Q22.1) WILD-TYPE          2         33         5         8
D29V39, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             6                            28
  STAGE IB1                           19                            58
  STAGE IB2                            7                            30
  STAGE II                             3                             1
  STAGE IIA                            2                             6
  STAGE IIA1                           1                             4
  STAGE IIA2                           1                             6
  STAGE IIB                            7                            37
  STAGE III                            1                             0
  STAGE IIIA                           1                             2
  STAGE IIIB                           9                            33
  STAGE IVA                            2                             5
  STAGE IVB                            4                             8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = DEL PEAK  4(2Q37.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.1) MUTATED    94  30
  DEL PEAK  4(2Q37.1) WILD-TYPE 120  38
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          124                           158 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                           30                            38 
$`DEL PEAK  4(2Q37.1) MUTATED`
TCGA-EK-A2GZ TCGA-ZJ-AAX4 TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       12.59         0.69        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M8 TCGA-C5-A1MH 
       18.74        36.56       177.04         5.46        30.21        38.99 
TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG 
       73.18        78.35       100.14        52.01        18.02       210.67 
TCGA-C5-A7CK TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
      134.33       155.77       131.11        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KL 
       99.91        23.51        27.52        14.73         1.12        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WH 
       63.98        87.75        55.63       117.99       118.65        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE 
        8.28        39.55        40.87        30.90        13.05        25.02 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A6QX TCGA-EA-A78R 
       24.56        26.01        12.13         7.46        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2R8 
        0.36        60.72        26.27         1.51        19.27         1.45 
TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H6 
        0.07         1.74         1.64         2.33         0.49         7.92 
TCGA-EX-A69L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A40J 
       19.79        19.04        31.36        20.98        16.14        14.01 
TCGA-FU-A770 TCGA-HM-A3JJ TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ 
        1.12        21.67        29.85        36.36        27.42        21.44 
TCGA-JW-A5VL TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 
       15.58        21.11        44.61        20.91        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-MY-A5BF 
        0.82        13.35        22.52        17.82        11.38        20.84 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-RA-A741 
       17.23        15.58        16.41         9.04        19.59        14.60 
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        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Y 
       32.42        23.97        65.49        11.51        59.18         4.73 
TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U7 
       15.68        55.50        50.14        51.32        50.47        48.39 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UU 
       27.12        24.30        45.11        27.25        47.87        14.53 
TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 
       18.25        18.84        18.25        17.75        16.24        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       29.26        67.59        19.13         3.91 

$`DEL PEAK  4(2Q37.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY 
      146.86        14.70         8.32         1.48         4.34        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       17.82        49.48       144.16       173.29        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        35.01        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF 
       44.22        73.45        83.05        38.43        33.24        17.85 
TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       20.42       154.32       101.82        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8YT 
       17.19        94.95         9.34        13.61         2.73        20.81 
TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A3LQ 
       20.91        95.11        82.06        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        37.35        31.53        31.36        36.89 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       26.40        31.73        24.82        14.89        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL 
       27.29        27.25        27.22         6.64         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         0.89         0.13        40.96         0.30         4.24 
TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
        1.87         0.43        47.77         0.07         0.10         0.89 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       20.35        15.22        15.55        12.23        23.84        16.11 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA 
       36.26        26.14        28.31        35.44        10.55        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        16.57        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       129.37        96.95        78.71        81.96 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        24.56        20.48        28.37         8.28        18.15 
TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 
      209.59        11.28         0.89        20.28        19.56         9.17 
TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.52        28.08        34.62        19.96        54.81        35.05 
TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
        2.96        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8Q8 
        9.34        18.64        22.62        69.50        19.96        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       53.59        36.13        39.78        31.27        40.87        16.64 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A9U6 TCGA-VS-A9UA 
       33.37        40.14        58.45        56.35        43.40        28.50 
TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UQ 
       29.95        46.92         1.71        14.53        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-AA62 
       26.07        15.85         3.42        67.20         5.16        15.42 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        1.41         0.16 

  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                       210.67                        209.59 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                       21.555                        23.410 
[1] "0.1 - 210.7 (21.6)" "0.1 - 209.6 (23.4)"
[1] "hr=" "1"  
D30V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  4(2Q37.1) MUTATED   65 26  9  3
  DEL PEAK  4(2Q37.1) WILD-TYPE 70 44 12  5
D30V3, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  T1                          65                            70
  T2                          26                            44
  T3                           9                            12
  T4                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   53 26
  DEL PEAK  4(2Q37.1) WILD-TYPE 76 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     53   26
  DEL PEAK  4(2Q37.1) WILD-TYPE   76   30
   clus
vv  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  0                          53                            76
  1                          26                            30
[1] 2 2
[1] FALSE
D30V5, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   51  2
  DEL PEAK  4(2Q37.1) WILD-TYPE 57  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     51    2
  DEL PEAK  4(2Q37.1) WILD-TYPE   57    8
   clus
vv  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  0                          51                            57
  1                           2                             8
[1] 2 2
[1] FALSE
D30V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   24 53
  DEL PEAK  4(2Q37.1) WILD-TYPE 29 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     24   53
  DEL PEAK  4(2Q37.1) WILD-TYPE   29   72
     clus
vv    DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  NO                           24                            29
  YES                          53                            72
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q37.1) MUTATED               1                              116
  DEL PEAK  4(2Q37.1) WILD-TYPE             5                              126
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  4(2Q37.1) MUTATED                                               2
  DEL PEAK  4(2Q37.1) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  4(2Q37.1) MUTATED                                     5
  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                                              5
  DEL PEAK  4(2Q37.1) WILD-TYPE                                           12
D30V7, multiclass
                                               clus
vv                                              DEL PEAK  4(2Q37.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      116
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
                                               clus
vv                                              DEL PEAK  4(2Q37.1) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        126
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, continuous
D30V9, 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     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(2Q37.1) MUTATED                          11
  DEL PEAK  4(2Q37.1) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(2Q37.1) MUTATED                                           1    87
  DEL PEAK  4(2Q37.1) WILD-TYPE                                         1   115
D30V10, multiclass
                                           clus
vv                                          DEL PEAK  4(2Q37.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    5
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              87
                                           clus
vv                                          DEL PEAK  4(2Q37.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 8
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               115
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED    8 72
  DEL PEAK  4(2Q37.1) WILD-TYPE 15 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED      8   72
  DEL PEAK  4(2Q37.1) WILD-TYPE   15   91
                        clus
vv                       DEL PEAK  4(2Q37.1) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          72
                        clus
vv                       DEL PEAK  4(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                            91
[1] 2 2
[1] FALSE
D30V12, continuous
D30V13, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.1) MUTATED    87  31
  DEL PEAK  4(2Q37.1) WILD-TYPE 106  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     87   31
  DEL PEAK  4(2Q37.1) WILD-TYPE  106   45
            clus
vv           DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  TUMOR FREE                          87                           106
  WITH TUMOR                          31                            45
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  4(2Q37.1) MUTATED    7 57 49  0 11
  DEL PEAK  4(2Q37.1) WILD-TYPE 11 72 66  1 13
D30V14, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  G1                           7                            11
  G2                          57                            72
  G3                          49                            66
  G4                           0                             1
  GX                          11                            13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, continuous
D30V16, continuous
D30V17, continuous
D30V18, continuous
D30V19, 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
D30V20, continuous
D30V21, continuous
D30V22, continuous
D30V23, continuous
D30V24, continuous
D30V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  4(2Q37.1) MUTATED                                     0
  DEL PEAK  4(2Q37.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  4(2Q37.1) MUTATED                                     4
  DEL PEAK  4(2Q37.1) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  4(2Q37.1) MUTATED                        15                       1
  DEL PEAK  4(2Q37.1) WILD-TYPE                      21                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  4(2Q37.1) MUTATED                         2
  DEL PEAK  4(2Q37.1) WILD-TYPE                       8
D30V26, multiclass
                                     clus
vv                                    DEL PEAK  4(2Q37.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      15
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK  4(2Q37.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        21
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  4(2Q37.1) MUTATED                                               1
  DEL PEAK  4(2Q37.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  4(2Q37.1) MUTATED                                               15
  DEL PEAK  4(2Q37.1) WILD-TYPE                                             10
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  4(2Q37.1) MUTATED                                                                                  32
  DEL PEAK  4(2Q37.1) WILD-TYPE                                                                                50
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  4(2Q37.1) MUTATED                                                                                             54
  DEL PEAK  4(2Q37.1) WILD-TYPE                                                                                           67
D30V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  4(2Q37.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     32
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          54
                                                                                              clus
vv                                                                                             DEL PEAK  4(2Q37.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          10
  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)                            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"
D30V28, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   30 31
  DEL PEAK  4(2Q37.1) WILD-TYPE 41 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     30   31
  DEL PEAK  4(2Q37.1) WILD-TYPE   41   43
         clus
vv        DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  ABSENT                           30                            41
  PRESENT                          31                            43
[1] 2 2
[1] FALSE
D30V29, continuous
D30V30, continuous
D30V31, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   24 52
  DEL PEAK  4(2Q37.1) WILD-TYPE 25 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     24   52
  DEL PEAK  4(2Q37.1) WILD-TYPE   25   65
                                          clus
vv                                         DEL PEAK  4(2Q37.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          52
                                          clus
vv                                         DEL PEAK  4(2Q37.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            65
[1] 2 2
[1] FALSE
D30V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  4(2Q37.1) MUTATED              8          24         43
  DEL PEAK  4(2Q37.1) WILD-TYPE            7          30         42
D30V33, multiclass
              clus
vv             DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  CURRENT USER                           8                             7
  FORMER USER                           24                            30
  NEVER USED                            43                            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"
D30V34, continuous
D30V35, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   39  5
  DEL PEAK  4(2Q37.1) WILD-TYPE 53 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     39    5
  DEL PEAK  4(2Q37.1) WILD-TYPE   53   13
         clus
vv        DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  ABSENT                           39                            53
  PRESENT                           5                            13
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  4(2Q37.1) MUTATED             1        48     1
  DEL PEAK  4(2Q37.1) WILD-TYPE           4        52     1
D30V36, multiclass
             clus
vv            DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            48                            52
  OTHER                                 1                             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"
D30V37, continuous
D30V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  4(2Q37.1) MUTATED         2        0         0         0       18
  DEL PEAK  4(2Q37.1) WILD-TYPE       3        1         1         1       16
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  4(2Q37.1) MUTATED          36        14        3         3
  DEL PEAK  4(2Q37.1) WILD-TYPE        41        23        1         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  4(2Q37.1) MUTATED            0          3        19         0
  DEL PEAK  4(2Q37.1) WILD-TYPE          5          4        25         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  4(2Q37.1) MUTATED            1         19         4         3
  DEL PEAK  4(2Q37.1) WILD-TYPE          2         23         3         9
D30V39, multiclass
            clus
vv           DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                            18                            16
  STAGE IB1                           36                            41
  STAGE IB2                           14                            23
  STAGE II                             3                             1
  STAGE IIA                            3                             5
  STAGE IIA1                           0                             5
  STAGE IIA2                           3                             4
  STAGE IIB                           19                            25
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          19                            23
  STAGE IVA                            4                             3
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = DEL PEAK  5(3P22.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P22.1) MUTATED    72  34
  DEL PEAK  5(3P22.1) WILD-TYPE 142  34
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                          106                           176 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           34                            34 
$`DEL PEAK  5(3P22.1) MUTATED`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-ZJ-AAX4 TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN 
      146.86        12.59         0.69        49.48        23.67        11.44 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 
       18.74        36.56       173.29        82.85         5.46        31.40 
TCGA-C5-A1M8 TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LX 
       30.21        35.61        20.91        40.93        73.45        83.05 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE 
      154.32       101.82       134.33        15.48       147.35       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8YQ 
      131.11        94.95        13.61         2.73        45.83        23.51 
TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM 
       20.91        95.11        63.98        87.75        36.76       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 
      118.65        16.83        31.53        13.05        25.02        24.56 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       31.73        12.13         7.46        27.25        27.22        24.00 
TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 
        0.36         6.64         1.51        19.27         0.43         0.89 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3HY 
        0.30         4.24         1.87        20.35        23.84        31.36 
TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3L7 
       20.98        28.31        10.55        25.41        21.67       147.39 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AX 
       24.56        21.44        18.15        21.11        44.61        12.49 
TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A73Q TCGA-Q1-A73S 
        8.52        34.62        17.23        16.41         9.34        22.62 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EI 
       14.60        93.99        12.16        10.03        46.52        23.97 
TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y 
       32.15        36.13        11.51        39.78        31.27         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A9U5 TCGA-VS-A9U6 
       33.37        40.14        15.68        55.50        50.47        43.40 
TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP 
       28.50        24.30        46.92        14.53        27.25        47.47 
TCGA-VS-A9UV TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
        3.42        29.26        19.13         0.16 

$`DEL PEAK  5(3P22.1) WILD-TYPE`
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-4J-AA1J 
       14.70         8.32         1.48         4.34        17.52        17.82 
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BQ TCGA-C5-A1M5 
       57.04        68.84       144.16       177.04        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       46.32        35.01        57.73        53.16        38.99         0.46 
TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ 
        2.43         3.58        44.22        73.18        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XI 
      210.67        20.35        17.19         9.34        50.99         8.35 
TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       99.91        27.52        20.81        14.73         1.12        82.06 
TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH 
       44.94        58.88        55.63        22.98        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT 
        8.28        39.55        40.87        37.35        30.90        31.36 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO 
       36.89        26.40        26.01        24.82        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PK 
       25.91        27.29        13.48        60.72        26.27         0.39 
TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RJ 
        0.59         1.45         0.13        40.96         0.07         1.74 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.43        47.77         1.64         2.33         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF 
        0.49         0.89         7.92        15.22        19.79        15.55 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
       12.23        19.04        16.11        36.26        26.14        16.14 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JK 
       14.01        35.44         1.12        17.75        16.57        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A5QV 
       20.48        15.58        28.37         8.28       209.59        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       11.28         0.89         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y 
       20.28        17.82        19.56         9.17        11.38        28.08 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
       19.96        54.81        35.05        20.84         2.96        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH 
       18.64        19.59        11.67        69.50        45.57        32.42 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A94W TCGA-VS-A94X 
       19.96        65.49        53.59        59.18        40.87        16.64 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U7 TCGA-VS-A9UB 
       58.45        56.35        50.14        51.32        48.39        29.95 
TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
       27.12        45.11         1.71        47.87        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       15.85        14.53        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ 
       18.25        17.75        16.24        15.42        26.01        67.59 
TCGA-ZJ-AAXA TCGA-ZX-AA5X 
        1.41         3.91 

  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                         0.16                          0.07 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                       173.29                        210.67 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                       24.560                        20.315 
[1] "0.2 - 173.3 (24.6)" "0.1 - 210.7 (20.3)"
[1] "hr=" "1.4"
D31V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  5(3P22.1) MUTATED   44 21 11  5
  DEL PEAK  5(3P22.1) WILD-TYPE 91 49 10  3
D31V3, multiclass
    clus
vv   DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  T1                          44                            91
  T2                          21                            49
  T3                          11                            10
  T4                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.1) MUTATED   33 29
  DEL PEAK  5(3P22.1) WILD-TYPE 96 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED     33   29
  DEL PEAK  5(3P22.1) WILD-TYPE   96   27
   clus
vv  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  0                          33                            96
  1                          29                            27
[1] 2 2
[1] FALSE
D31V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.1) MUTATED   38  4
  DEL PEAK  5(3P22.1) WILD-TYPE 70  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED     38    4
  DEL PEAK  5(3P22.1) WILD-TYPE   70    6
   clus
vv  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  0                          38                            70
  1                           4                             6
[1] 2 2
[1] FALSE
D31V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.1) MUTATED   16 48
  DEL PEAK  5(3P22.1) WILD-TYPE 37 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED     16   48
  DEL PEAK  5(3P22.1) WILD-TYPE   37   77
     clus
vv    DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  NO                           16                            37
  YES                          48                            77
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(3P22.1) MUTATED               1                              107
  DEL PEAK  5(3P22.1) WILD-TYPE             5                              135
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  5(3P22.1) MUTATED                                               1
  DEL PEAK  5(3P22.1) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  5(3P22.1) MUTATED                                     1
  DEL PEAK  5(3P22.1) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  5(3P22.1) MUTATED                                           0
  DEL PEAK  5(3P22.1) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  5(3P22.1) MUTATED                                              3
  DEL PEAK  5(3P22.1) WILD-TYPE                                           14
D31V7, multiclass
                                               clus
vv                                              DEL PEAK  5(3P22.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      107
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
                                               clus
vv                                              DEL PEAK  5(3P22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        135
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, continuous
D31V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P22.1) MUTATED                                  2     8
  DEL PEAK  5(3P22.1) WILD-TYPE                                6    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(3P22.1) MUTATED                          14
  DEL PEAK  5(3P22.1) WILD-TYPE                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(3P22.1) MUTATED                                           1    75
  DEL PEAK  5(3P22.1) WILD-TYPE                                         1   127
D31V10, multiclass
                                           clus
vv                                          DEL PEAK  5(3P22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              75
                                           clus
vv                                          DEL PEAK  5(3P22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D31V11, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P22.1) MUTATED     6  63
  DEL PEAK  5(3P22.1) WILD-TYPE  17 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      6   63
  DEL PEAK  5(3P22.1) WILD-TYPE   17  100
                        clus
vv                       DEL PEAK  5(3P22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK  5(3P22.1) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           100
[1] 2 2
[1] FALSE
D31V12, continuous
D31V13, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P22.1) MUTATED    65  35
  DEL PEAK  5(3P22.1) WILD-TYPE 128  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED     65   35
  DEL PEAK  5(3P22.1) WILD-TYPE  128   41
            clus
vv           DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  TUMOR FREE                          65                           128
  WITH TUMOR                          35                            41
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  5(3P22.1) MUTATED    4 47 43  0 12
  DEL PEAK  5(3P22.1) WILD-TYPE 14 82 72  1 12
D31V14, multiclass
    clus
vv   DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  G1                           4                            14
  G2                          47                            82
  G3                          43                            72
  G4                           0                             1
  GX                          12                            12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, continuous
D31V16, continuous
D31V17, continuous
D31V18, continuous
D31V19, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.1) MUTATED   13  1
  DEL PEAK  5(3P22.1) WILD-TYPE 12  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED     13    1
  DEL PEAK  5(3P22.1) WILD-TYPE   12    2
                         clus
vv                        DEL PEAK  5(3P22.1) MUTATED
  COMPLETED AS PLANNED                             13
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        DEL PEAK  5(3P22.1) WILD-TYPE
  COMPLETED AS PLANNED                               12
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
D31V20, continuous
D31V21, continuous
D31V22, continuous
D31V23, continuous
D31V24, continuous
D31V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  5(3P22.1) MUTATED                                     0
  DEL PEAK  5(3P22.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  5(3P22.1) MUTATED                                     3
  DEL PEAK  5(3P22.1) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  5(3P22.1) MUTATED                         9                       1
  DEL PEAK  5(3P22.1) WILD-TYPE                      27                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  5(3P22.1) MUTATED                         6
  DEL PEAK  5(3P22.1) WILD-TYPE                       4
D31V26, multiclass
                                     clus
vv                                    DEL PEAK  5(3P22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                       9
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       6
                                     clus
vv                                    DEL PEAK  5(3P22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                        27
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  5(3P22.1) MUTATED                                               1
  DEL PEAK  5(3P22.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  5(3P22.1) MUTATED                                               11
  DEL PEAK  5(3P22.1) WILD-TYPE                                             14
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  5(3P22.1) MUTATED                                                                                  27
  DEL PEAK  5(3P22.1) WILD-TYPE                                                                                55
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  5(3P22.1) MUTATED                                                                                             43
  DEL PEAK  5(3P22.1) WILD-TYPE                                                                                           78
D31V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  5(3P22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          43
                                                                                              clus
vv                                                                                             DEL PEAK  5(3P22.1) 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)                                       55
  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"
D31V28, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.1) MUTATED   15 34
  DEL PEAK  5(3P22.1) WILD-TYPE 56 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED     15   34
  DEL PEAK  5(3P22.1) WILD-TYPE   56   40
         clus
vv        DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  ABSENT                           15                            56
  PRESENT                          34                            40
[1] 2 2
[1] FALSE
D31V29, continuous
D31V30, continuous
D31V31, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.1) MUTATED   23 45
  DEL PEAK  5(3P22.1) WILD-TYPE 26 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED     23   45
  DEL PEAK  5(3P22.1) WILD-TYPE   26   72
                                          clus
vv                                         DEL PEAK  5(3P22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          45
                                          clus
vv                                         DEL PEAK  5(3P22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            72
[1] 2 2
[1] FALSE
D31V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  5(3P22.1) MUTATED              2          24         30
  DEL PEAK  5(3P22.1) WILD-TYPE           13          30         55
D31V33, multiclass
              clus
vv             DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  CURRENT USER                           2                            13
  FORMER USER                           24                            30
  NEVER USED                            30                            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"
D31V34, continuous
D31V35, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.1) MUTATED   27  9
  DEL PEAK  5(3P22.1) WILD-TYPE 65  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED     27    9
  DEL PEAK  5(3P22.1) WILD-TYPE   65    9
         clus
vv        DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  ABSENT                           27                            65
  PRESENT                           9                             9
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  5(3P22.1) MUTATED             1        41     1
  DEL PEAK  5(3P22.1) WILD-TYPE           4        59     1
D31V36, multiclass
             clus
vv            DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            41                            59
  OTHER                                 1                             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"
D31V37, continuous
D31V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  5(3P22.1) MUTATED         2        0         1         0       14
  DEL PEAK  5(3P22.1) WILD-TYPE       3        1         0         1       20
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  5(3P22.1) MUTATED          29         9        1         4
  DEL PEAK  5(3P22.1) WILD-TYPE        48        28        3         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  5(3P22.1) MUTATED            2          0        15         0
  DEL PEAK  5(3P22.1) WILD-TYPE          3          7        29         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  5(3P22.1) MUTATED            3         19         6         5
  DEL PEAK  5(3P22.1) WILD-TYPE          0         23         1         7
D31V39, multiclass
            clus
vv           DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IA1                            1                             0
  STAGE IA2                            0                             1
  STAGE IB                            14                            20
  STAGE IB1                           29                            48
  STAGE IB2                            9                            28
  STAGE II                             1                             3
  STAGE IIA                            4                             4
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           15                            29
  STAGE III                            0                             1
  STAGE IIIA                           3                             0
  STAGE IIIB                          19                            23
  STAGE IVA                            6                             1
  STAGE IVB                            5                             7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P14.2) MUTATED    89  35
  DEL PEAK  6(3P14.2) WILD-TYPE 125  33
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          124                           158 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           35                            33 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A 
      146.86        12.59         0.69        17.82        49.48        23.67 
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN 
       11.44        18.74        36.56       144.16       173.29         5.46 
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MN 
       31.40        30.21        53.16        35.61        20.91        40.93 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       73.18        83.05        52.01       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
       15.48       147.35       155.77       131.11        94.95        13.61 
TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM 
        2.73        45.83        23.51        20.91        95.11        63.98 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH 
       87.75        36.76       117.99       118.65        16.83        17.52 
TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 
       40.87        31.53        13.05        25.02        24.56        31.73 
TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.13         7.46        14.89        27.25        27.22        24.00 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
        0.36        60.72         6.64         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EX-A1H5 
        0.59         0.89         0.30         4.24         1.87        20.35 
TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HG-A2PA 
       23.84        31.36        20.98        28.31        10.55        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI 
       16.57        21.67       147.39        78.71        29.85        24.56 
TCGA-JW-A5VJ TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-MA-AA41 TCGA-MA-AA42 
       21.44        18.15        21.11        44.61         9.17         8.52 
TCGA-MU-A5YI TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S 
       34.62        17.23        16.41         9.04         9.34        22.62 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH 
       14.60        93.99        12.16        10.03        46.52        32.42 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       23.97        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 
       39.78        31.27         4.73        33.37        40.14        15.68 
TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UD 
       55.50        51.32        50.47        43.40        28.50        24.30 
TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UV 
       46.92        14.53        27.25        47.47        15.85         3.42 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.16 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-BI-A0VS 
       14.70         8.32         1.48         4.34        17.52        57.04 
TCGA-C5-A1BE TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
       68.84       177.04        82.85        19.86        67.46        46.32 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP 
       35.01        57.73        38.99         0.46         2.43         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        73.45        78.35       100.14        38.43        33.24 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7UC 
       18.02        17.85        20.42       210.67        20.35        17.19 
TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
        9.34        50.99         8.35        99.91        27.52        20.81 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VL 
       14.73         1.12        82.06        44.94        58.88        55.63 
TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       22.98        16.18         8.28        39.55        37.35        30.90 
TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A5FO 
       31.36        36.89        26.40        26.01        24.82        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2PK TCGA-EK-A2R8 
       25.91        27.29        13.48        26.27         0.39         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL 
        0.13        40.96         0.07         1.74         0.43        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        1.64         2.33         0.07         0.10         0.49         0.89 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
        7.92        15.22        19.79        15.55        12.23        19.04 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A57G 
       16.11        36.26        26.14        16.14        14.01        35.44 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA 
        1.12        17.75        20.78        14.93         9.44       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
       66.81       129.37        96.95        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q0 
        3.29        20.48        15.58        28.37         8.28       209.59 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA43 
       13.35        22.52        20.28        17.82        19.56        11.38 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       28.08        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EJ 
       18.64        19.59        11.67        69.50        45.57        19.96 
TCGA-VS-A8EL TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       65.49        40.87        16.64        58.45        56.35        50.14 
TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UO 
       48.39        29.95        27.12        45.11         1.71        47.87 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       41.52        26.07        14.53        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        18.25        17.75        16.24        15.42        26.01 
TCGA-ZJ-AAXA TCGA-ZX-AA5X 
        1.41         3.91 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         0.16                          0.07 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       173.29                        210.67 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       25.215                        19.960 
[1] "0.2 - 173.3 (25.2)" "0.1 - 210.7 (20.0)"
[1] "hr=" "1.1"
D32V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  6(3P14.2) MUTATED   52 24 14  5
  DEL PEAK  6(3P14.2) WILD-TYPE 83 46  7  3
D32V3, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  T1                          52                            83
  T2                          24                            46
  T3                          14                             7
  T4                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   43 31
  DEL PEAK  6(3P14.2) WILD-TYPE 86 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     43   31
  DEL PEAK  6(3P14.2) WILD-TYPE   86   25
   clus
vv  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  0                          43                            86
  1                          31                            25
[1] 2 2
[1] FALSE
D32V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   48  5
  DEL PEAK  6(3P14.2) WILD-TYPE 60  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     48    5
  DEL PEAK  6(3P14.2) WILD-TYPE   60    5
   clus
vv  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  0                          48                            60
  1                           5                             5
[1] 2 2
[1] FALSE
D32V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   18 59
  DEL PEAK  6(3P14.2) WILD-TYPE 35 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     18   59
  DEL PEAK  6(3P14.2) WILD-TYPE   35   66
     clus
vv    DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  NO                           18                            35
  YES                          59                            66
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(3P14.2) MUTATED               2                              124
  DEL PEAK  6(3P14.2) WILD-TYPE             4                              118
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  6(3P14.2) MUTATED                                               1
  DEL PEAK  6(3P14.2) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  6(3P14.2) MUTATED                                     1
  DEL PEAK  6(3P14.2) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  6(3P14.2) MUTATED                                           1
  DEL PEAK  6(3P14.2) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  6(3P14.2) MUTATED                                              5
  DEL PEAK  6(3P14.2) WILD-TYPE                                           12
D32V7, multiclass
                                               clus
vv                                              DEL PEAK  6(3P14.2) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      124
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
                                               clus
vv                                              DEL PEAK  6(3P14.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        118
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, continuous
D32V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P14.2) MUTATED                                  2     9
  DEL PEAK  6(3P14.2) WILD-TYPE                                6    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(3P14.2) MUTATED                          13
  DEL PEAK  6(3P14.2) WILD-TYPE                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(3P14.2) MUTATED                                           1    92
  DEL PEAK  6(3P14.2) WILD-TYPE                                         1   110
D32V10, multiclass
                                           clus
vv                                          DEL PEAK  6(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               9
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              92
                                           clus
vv                                          DEL PEAK  6(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               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"
D32V11, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED    7 72
  DEL PEAK  6(3P14.2) WILD-TYPE 16 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED      7   72
  DEL PEAK  6(3P14.2) WILD-TYPE   16   91
                        clus
vv                       DEL PEAK  6(3P14.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          72
                        clus
vv                       DEL PEAK  6(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                            91
[1] 2 2
[1] FALSE
D32V12, continuous
D32V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    80  39
  DEL PEAK  6(3P14.2) WILD-TYPE 113  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     80   39
  DEL PEAK  6(3P14.2) WILD-TYPE  113   37
            clus
vv           DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  TUMOR FREE                          80                           113
  WITH TUMOR                          39                            37
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  6(3P14.2) MUTATED    4 57 50  1 14
  DEL PEAK  6(3P14.2) WILD-TYPE 14 72 65  0 10
D32V14, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  G1                           4                            14
  G2                          57                            72
  G3                          50                            65
  G4                           1                             0
  GX                          14                            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, continuous
D32V16, continuous
D32V17, continuous
D32V18, continuous
D32V19, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   16  2
  DEL PEAK  6(3P14.2) WILD-TYPE  9  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     16    2
  DEL PEAK  6(3P14.2) WILD-TYPE    9    1
                         clus
vv                        DEL PEAK  6(3P14.2) MUTATED
  COMPLETED AS PLANNED                             16
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK  6(3P14.2) WILD-TYPE
  COMPLETED AS PLANNED                                9
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
D32V20, continuous
D32V21, continuous
D32V22, continuous
D32V23, continuous
D32V24, continuous
D32V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  6(3P14.2) MUTATED                                     0
  DEL PEAK  6(3P14.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  6(3P14.2) MUTATED                                     4
  DEL PEAK  6(3P14.2) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  6(3P14.2) MUTATED                        11                       1
  DEL PEAK  6(3P14.2) WILD-TYPE                      25                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  6(3P14.2) MUTATED                         6
  DEL PEAK  6(3P14.2) WILD-TYPE                       4
D32V26, multiclass
                                     clus
vv                                    DEL PEAK  6(3P14.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      11
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       6
                                     clus
vv                                    DEL PEAK  6(3P14.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        25
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  6(3P14.2) MUTATED                                               1
  DEL PEAK  6(3P14.2) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  6(3P14.2) MUTATED                                               11
  DEL PEAK  6(3P14.2) WILD-TYPE                                             14
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  6(3P14.2) MUTATED                                                                                  34
  DEL PEAK  6(3P14.2) WILD-TYPE                                                                                48
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  6(3P14.2) MUTATED                                                                                             53
  DEL PEAK  6(3P14.2) WILD-TYPE                                                                                           68
D32V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  6(3P14.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     34
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          53
                                                                                              clus
vv                                                                                             DEL PEAK  6(3P14.2) 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)                                       48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V28, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   18 36
  DEL PEAK  6(3P14.2) WILD-TYPE 53 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     18   36
  DEL PEAK  6(3P14.2) WILD-TYPE   53   38
         clus
vv        DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  ABSENT                           18                            53
  PRESENT                          36                            38
[1] 2 2
[1] FALSE
D32V29, continuous
D32V30, continuous
D32V31, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   26 52
  DEL PEAK  6(3P14.2) WILD-TYPE 23 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     26   52
  DEL PEAK  6(3P14.2) WILD-TYPE   23   65
                                          clus
vv                                         DEL PEAK  6(3P14.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          52
                                          clus
vv                                         DEL PEAK  6(3P14.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            65
[1] 2 2
[1] FALSE
D32V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  6(3P14.2) MUTATED              3          30         37
  DEL PEAK  6(3P14.2) WILD-TYPE           12          24         48
D32V33, multiclass
              clus
vv             DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           30                            24
  NEVER USED                            37                            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"
D32V34, continuous
D32V35, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   33  8
  DEL PEAK  6(3P14.2) WILD-TYPE 59 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     33    8
  DEL PEAK  6(3P14.2) WILD-TYPE   59   10
         clus
vv        DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  ABSENT                           33                            59
  PRESENT                           8                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  6(3P14.2) MUTATED             1        50     1
  DEL PEAK  6(3P14.2) WILD-TYPE           4        50     1
D32V36, multiclass
             clus
vv            DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            50                            50
  OTHER                                 1                             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"
D32V37, continuous
D32V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  6(3P14.2) MUTATED         3        0         1         0       16
  DEL PEAK  6(3P14.2) WILD-TYPE       2        1         0         1       18
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  6(3P14.2) MUTATED          31        12        1         4
  DEL PEAK  6(3P14.2) WILD-TYPE        46        25        3         4
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  6(3P14.2) MUTATED            3          0        24         0
  DEL PEAK  6(3P14.2) WILD-TYPE          2          7        20         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  6(3P14.2) MUTATED            3         22         6         5
  DEL PEAK  6(3P14.2) WILD-TYPE          0         20         1         7
D32V39, multiclass
            clus
vv           DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                             0                             1
  STAGE IA1                            1                             0
  STAGE IA2                            0                             1
  STAGE IB                            16                            18
  STAGE IB1                           31                            46
  STAGE IB2                           12                            25
  STAGE II                             1                             3
  STAGE IIA                            4                             4
  STAGE IIA1                           3                             2
  STAGE IIA2                           0                             7
  STAGE IIB                           24                            20
  STAGE III                            0                             1
  STAGE IIIA                           3                             0
  STAGE IIIB                          22                            20
  STAGE IVA                            6                             1
  STAGE IVB                            5                             7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  7(4P16.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4P16.3) MUTATED    87  33
  DEL PEAK  7(4P16.3) WILD-TYPE 127  35
  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE 
                          120                           162 
  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE 
                           33                            35 
$`DEL PEAK  7(4P16.3) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-BI-A0VR TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       12.59         4.34        49.48        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MF 
      144.16       177.04       173.29         5.46        31.40        53.16 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV 
       35.61         2.43        20.91         3.58        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL 
       83.05       100.14        18.02       154.32       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35        17.19       131.11        94.95         9.34 
TCGA-C5-A7X8 TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM 
        2.73        99.91        23.51        20.91        95.11        63.98 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-EA-A3HR 
       87.75        36.76        55.63       118.65        16.83        30.90 
TCGA-EA-A3HS TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       31.53        36.89        24.56        31.73        26.01        12.13 
TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        0.36        26.27         0.39         0.59         0.89         1.45 
TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RN 
       40.96         0.07         1.74         0.43         1.64         2.33 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI 
        0.49        20.35        15.22        23.84        31.36        20.98 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-JW-A5VI 
       10.55        17.75        16.57        21.67        78.71        24.56 
TCGA-JW-A5VK TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA3W 
       20.48        20.91        11.28         0.89         0.30        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A8JM TCGA-MY-A5BF 
       20.28        19.56         9.17        11.38        19.96        20.84 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73S 
       17.23         2.96        16.41        15.95         9.04        22.62 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       11.67        12.16        10.03        46.52        45.57        32.42 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       19.96        32.15        11.51        59.18        31.27        40.87 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       40.14        15.68        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       43.40        24.30        45.11        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UV TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       47.47         3.42        26.01        29.26        19.13         1.41 

$`DEL PEAK  7(4P16.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        14.70         8.32         1.48         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BM TCGA-C5-A1BQ 
       17.82        57.04        23.67        18.74        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH 
       67.46        46.32        30.21        35.01        57.73        38.99 
TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 
        0.46        40.93        44.22        78.35        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7UE 
       52.01        17.85        20.42       210.67       101.82       155.77 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YR TCGA-C5-A8YT 
       13.61        50.99        45.83         8.35        27.52        20.81 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VM 
       14.73         1.12        82.06        44.94        58.88       117.99 
TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       22.98        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A4BA 
       37.35        31.36        13.05        25.02        26.40        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       27.22        24.00        13.48        60.72         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
       19.27         0.43         0.13         0.30         4.24         1.87 
TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A69L 
       47.77         0.07         0.10         0.89         7.92        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ 
       15.55        12.23        19.04        16.11        36.26        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA 
       16.14        28.31        14.01        35.44         1.12        25.41 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      129.37        96.95        81.96        29.85        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        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU 
       21.11       209.59        44.61        12.49         0.82        13.35 
TCGA-MA-AA3Y TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
       17.82         8.52        28.08        34.62        54.81        35.05 
TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.58        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EI 
       18.64        19.59        14.60        93.99        69.50        23.97 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y 
       65.49        53.59        36.13        39.78        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       33.37        58.45        56.35        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.12        46.92         1.71        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
       14.53        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       17.75        16.24        15.42        67.59         0.16         3.91 

  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE 
                       177.04                        210.67 
  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE 
                       22.095                        23.325 
[1] "0.1 - 177.0 (22.1)" "0.1 - 210.7 (23.3)"
[1] "hr=" "1.2"
D33V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  7(4P16.3) MUTATED   49 30 13  4
  DEL PEAK  7(4P16.3) WILD-TYPE 86 40  8  4
D33V3, multiclass
    clus
vv   DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  T1                          49                            86
  T2                          30                            40
  T3                          13                             8
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                               cls
clus                             0  1
  DEL PEAK  7(4P16.3) MUTATED   41 32
  DEL PEAK  7(4P16.3) WILD-TYPE 88 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED     41   32
  DEL PEAK  7(4P16.3) WILD-TYPE   88   24
   clus
vv  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  0                          41                            88
  1                          32                            24
[1] 2 2
[1] FALSE
D33V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(4P16.3) MUTATED   39  6
  DEL PEAK  7(4P16.3) WILD-TYPE 69  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED     39    6
  DEL PEAK  7(4P16.3) WILD-TYPE   69    4
   clus
vv  DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  0                          39                            69
  1                           6                             4
[1] 2 2
[1] FALSE
D33V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(4P16.3) MUTATED   14 63
  DEL PEAK  7(4P16.3) WILD-TYPE 39 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED     14   63
  DEL PEAK  7(4P16.3) WILD-TYPE   39   62
     clus
vv    DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  NO                           14                            39
  YES                          63                            62
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(4P16.3) MUTATED               2                              117
  DEL PEAK  7(4P16.3) WILD-TYPE             4                              125
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  7(4P16.3) MUTATED                                               3
  DEL PEAK  7(4P16.3) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  7(4P16.3) MUTATED                                     1
  DEL PEAK  7(4P16.3) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  7(4P16.3) MUTATED                                           0
  DEL PEAK  7(4P16.3) WILD-TYPE                                         3
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  7(4P16.3) MUTATED                                              4
  DEL PEAK  7(4P16.3) WILD-TYPE                                           13
D33V7, multiclass
                                               clus
vv                                              DEL PEAK  7(4P16.3) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      117
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
                                               clus
vv                                              DEL PEAK  7(4P16.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        125
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, continuous
D33V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(4P16.3) MUTATED                                  3     5
  DEL PEAK  7(4P16.3) WILD-TYPE                                5    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(4P16.3) MUTATED                          16
  DEL PEAK  7(4P16.3) WILD-TYPE                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(4P16.3) MUTATED                                           1    86
  DEL PEAK  7(4P16.3) WILD-TYPE                                         1   116
D33V10, multiclass
                                           clus
vv                                          DEL PEAK  7(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              86
                                           clus
vv                                          DEL PEAK  7(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               116
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, binary
                               cls
clus                             0  1
  DEL PEAK  7(4P16.3) MUTATED    9 71
  DEL PEAK  7(4P16.3) WILD-TYPE 14 92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED      9   71
  DEL PEAK  7(4P16.3) WILD-TYPE   14   92
                        clus
vv                       DEL PEAK  7(4P16.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       DEL PEAK  7(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                            92
[1] 2 2
[1] FALSE
D33V12, continuous
D33V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(4P16.3) MUTATED    80  36
  DEL PEAK  7(4P16.3) WILD-TYPE 113  40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED     80   36
  DEL PEAK  7(4P16.3) WILD-TYPE  113   40
            clus
vv           DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  TUMOR FREE                          80                           113
  WITH TUMOR                          36                            40
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  7(4P16.3) MUTATED    4 54 55  1 10
  DEL PEAK  7(4P16.3) WILD-TYPE 14 75 60  0 14
D33V14, multiclass
    clus
vv   DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  G1                           4                            14
  G2                          54                            75
  G3                          55                            60
  G4                           1                             0
  GX                          10                            14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, continuous
D33V16, continuous
D33V17, continuous
D33V18, continuous
D33V19, binary
                               cls
clus                             0  1
  DEL PEAK  7(4P16.3) MUTATED   13  2
  DEL PEAK  7(4P16.3) WILD-TYPE 12  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED     13    2
  DEL PEAK  7(4P16.3) WILD-TYPE   12    1
                         clus
vv                        DEL PEAK  7(4P16.3) MUTATED
  COMPLETED AS PLANNED                             13
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK  7(4P16.3) WILD-TYPE
  COMPLETED AS PLANNED                               12
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
D33V20, continuous
D33V21, continuous
D33V22, continuous
D33V23, continuous
D33V24, continuous
D33V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  7(4P16.3) MUTATED                                     0
  DEL PEAK  7(4P16.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  7(4P16.3) MUTATED                                     4
  DEL PEAK  7(4P16.3) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  7(4P16.3) MUTATED                        15                       0
  DEL PEAK  7(4P16.3) WILD-TYPE                      21                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  7(4P16.3) MUTATED                         4
  DEL PEAK  7(4P16.3) WILD-TYPE                       6
D33V26, multiclass
                                     clus
vv                                    DEL PEAK  7(4P16.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      15
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       4
                                     clus
vv                                    DEL PEAK  7(4P16.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  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(4P16.3) MUTATED                                               1
  DEL PEAK  7(4P16.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  7(4P16.3) MUTATED                                               11
  DEL PEAK  7(4P16.3) WILD-TYPE                                             14
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  7(4P16.3) MUTATED                                                                                  35
  DEL PEAK  7(4P16.3) WILD-TYPE                                                                                47
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  7(4P16.3) MUTATED                                                                                             52
  DEL PEAK  7(4P16.3) WILD-TYPE                                                                                           69
D33V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  7(4P16.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          52
                                                                                              clus
vv                                                                                             DEL PEAK  7(4P16.3) 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)                                       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"
D33V28, binary
                               cls
clus                             0  1
  DEL PEAK  7(4P16.3) MUTATED   23 32
  DEL PEAK  7(4P16.3) WILD-TYPE 48 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED     23   32
  DEL PEAK  7(4P16.3) WILD-TYPE   48   42
         clus
vv        DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  ABSENT                           23                            48
  PRESENT                          32                            42
[1] 2 2
[1] FALSE
D33V29, continuous
D33V30, continuous
D33V31, binary
                               cls
clus                             0  1
  DEL PEAK  7(4P16.3) MUTATED   27 52
  DEL PEAK  7(4P16.3) WILD-TYPE 22 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED     27   52
  DEL PEAK  7(4P16.3) WILD-TYPE   22   65
                                          clus
vv                                         DEL PEAK  7(4P16.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          52
                                          clus
vv                                         DEL PEAK  7(4P16.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            65
[1] 2 2
[1] FALSE
D33V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  7(4P16.3) MUTATED              5          24         35
  DEL PEAK  7(4P16.3) WILD-TYPE           10          30         50
D33V33, multiclass
              clus
vv             DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  CURRENT USER                           5                            10
  FORMER USER                           24                            30
  NEVER USED                            35                            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"
D33V34, continuous
D33V35, binary
                               cls
clus                             0  1
  DEL PEAK  7(4P16.3) MUTATED   30  7
  DEL PEAK  7(4P16.3) WILD-TYPE 62 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4P16.3) MUTATED     30    7
  DEL PEAK  7(4P16.3) WILD-TYPE   62   11
         clus
vv        DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  ABSENT                           30                            62
  PRESENT                           7                            11
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  7(4P16.3) MUTATED             1        50     1
  DEL PEAK  7(4P16.3) WILD-TYPE           4        50     1
D33V36, multiclass
             clus
vv            DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            50                            50
  OTHER                                 1                             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"
D33V37, continuous
D33V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  7(4P16.3) MUTATED         2        1         0         1       15
  DEL PEAK  7(4P16.3) WILD-TYPE       3        0         1         0       19
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  7(4P16.3) MUTATED          24        17        1         2
  DEL PEAK  7(4P16.3) WILD-TYPE        53        20        3         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  7(4P16.3) MUTATED            4          2        21         0
  DEL PEAK  7(4P16.3) WILD-TYPE          1          5        23         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  7(4P16.3) MUTATED            2         23         5         3
  DEL PEAK  7(4P16.3) WILD-TYPE          1         19         2         9
D33V39, multiclass
            clus
vv           DEL PEAK  7(4P16.3) MUTATED DEL PEAK  7(4P16.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            15                            19
  STAGE IB1                           24                            53
  STAGE IB2                           17                            20
  STAGE II                             1                             3
  STAGE IIA                            2                             6
  STAGE IIA1                           4                             1
  STAGE IIA2                           2                             5
  STAGE IIB                           21                            23
  STAGE III                            0                             1
  STAGE IIIA                           2                             1
  STAGE IIIB                          23                            19
  STAGE IVA                            5                             2
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK  8(4Q21.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q21.3) MUTATED    71  27
  DEL PEAK  8(4Q21.3) WILD-TYPE 143  41
  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE 
                           98                           184 
  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE 
                           27                            41 
$`DEL PEAK  8(4Q21.3) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN 
       12.59         4.34        17.52        49.48        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LT 
       68.84         5.46        31.40        35.61        20.91        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CK TCGA-C5-A7CL 
       73.45        83.05        52.01        18.02       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
       20.35       147.35        17.19       131.11         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-DG-A2KJ 
        2.73        45.83        99.91        27.52        20.91        95.11 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 
       63.98        87.75       118.65        40.87        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EA-A97N 
       26.01         7.46        14.89        27.29        13.48         0.36 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         1.51         0.39         0.59         0.89         1.45 
TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 
       40.96         1.74         0.43         1.64         2.33        20.35 
TCGA-EX-A3L1 TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-JW-A5VK 
       15.22        20.98        10.55        17.75        21.67        20.48 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 
       20.91        11.28         0.89        20.28        17.82         9.17 
TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73S TCGA-UC-A7PD 
       11.38        17.23         2.96        16.41        22.62        11.67 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 
       12.16        10.03        32.42        23.97        19.96        32.15 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 
       31.27        40.87        16.64         4.73        40.14        15.68 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UH 
       55.50        50.14        51.32        50.47        43.40        46.92 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UT TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-WL-A834 
       14.53        47.87        15.85        18.84        18.25        26.01 
TCGA-XS-A8TJ TCGA-ZJ-AAXA 
       29.26         1.41 

$`DEL PEAK  8(4Q21.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-4J-AA1J 
      146.86        14.70         8.32         1.48         0.69        17.82 
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        33.24 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UE 
       17.85        20.42       210.67       154.32       101.82       155.77 
TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A907 
       94.95        50.99         8.35        23.51        20.81        14.73 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1.12        82.06        44.94        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A5FO 
       25.02        36.89        26.40        12.13        24.82        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP 
       25.91        27.25        27.22        24.00        60.72         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       19.27         0.43         0.13         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        1.87        47.77         0.07         0.10         0.49         0.89 
TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        7.92        19.79        15.55        12.23        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       16.11        31.36        36.26        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
       14.01        35.44         1.12        25.41        16.57        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       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        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        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-LP-A5U2 
       18.15        21.11       209.59        44.61        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MU-A51Y 
        0.82        13.35        22.52        19.56         8.52        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       34.62        19.96        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI 
        9.34        18.64        19.59        14.60        93.99        69.50 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       46.52        45.57        65.49        53.59        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A9U7 
       59.18        39.78        33.37        58.45        56.35        48.39 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UJ 
       28.50        29.95        27.12        24.30        45.11         1.71 
TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV 
       27.25        47.47        41.52        26.07        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       18.25        67.20         5.16        17.75        16.24        15.42 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         0.16         3.91 

  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE 
                       147.35                        210.67 
  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE 
                        20.35                         24.92 
[1] "0.4 - 147.3 (20.4)" "0.1 - 210.7 (24.9)"
[1] "hr=" "1.5"
D34V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  8(4Q21.3) MUTATED   44 22  9  5
  DEL PEAK  8(4Q21.3) WILD-TYPE 91 48 12  3
D34V3, multiclass
    clus
vv   DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  T1                          44                            91
  T2                          22                            48
  T3                           9                            12
  T4                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q21.3) MUTATED   34 26
  DEL PEAK  8(4Q21.3) WILD-TYPE 95 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED     34   26
  DEL PEAK  8(4Q21.3) WILD-TYPE   95   30
   clus
vv  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  0                          34                            95
  1                          26                            30
[1] 2 2
[1] FALSE
D34V5, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q21.3) MUTATED   35  6
  DEL PEAK  8(4Q21.3) WILD-TYPE 73  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED     35    6
  DEL PEAK  8(4Q21.3) WILD-TYPE   73    4
   clus
vv  DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  0                          35                            73
  1                           6                             4
[1] 2 2
[1] FALSE
D34V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q21.3) MUTATED   12 53
  DEL PEAK  8(4Q21.3) WILD-TYPE 41 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED     12   53
  DEL PEAK  8(4Q21.3) WILD-TYPE   41   72
     clus
vv    DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  NO                           12                            41
  YES                          53                            72
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(4Q21.3) MUTATED               2                               92
  DEL PEAK  8(4Q21.3) WILD-TYPE             4                              150
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  8(4Q21.3) MUTATED                                               2
  DEL PEAK  8(4Q21.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  8(4Q21.3) MUTATED                                     1
  DEL PEAK  8(4Q21.3) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  8(4Q21.3) MUTATED                                           1
  DEL PEAK  8(4Q21.3) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  8(4Q21.3) MUTATED                                              5
  DEL PEAK  8(4Q21.3) WILD-TYPE                                           12
D34V7, multiclass
                                               clus
vv                                              DEL PEAK  8(4Q21.3) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       92
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
                                               clus
vv                                              DEL PEAK  8(4Q21.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        150
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, continuous
D34V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4Q21.3) MUTATED                                  1     8
  DEL PEAK  8(4Q21.3) WILD-TYPE                                7    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(4Q21.3) MUTATED                          15
  DEL PEAK  8(4Q21.3) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(4Q21.3) MUTATED                                           0    68
  DEL PEAK  8(4Q21.3) WILD-TYPE                                         2   134
D34V10, multiclass
                                           clus
vv                                          DEL PEAK  8(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              68
                                           clus
vv                                          DEL PEAK  8(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q21.3) MUTATED     8  56
  DEL PEAK  8(4Q21.3) WILD-TYPE  15 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED      8   56
  DEL PEAK  8(4Q21.3) WILD-TYPE   15  107
                        clus
vv                       DEL PEAK  8(4Q21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          56
                        clus
vv                       DEL PEAK  8(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           107
[1] 2 2
[1] FALSE
D34V12, continuous
D34V13, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q21.3) MUTATED    61  32
  DEL PEAK  8(4Q21.3) WILD-TYPE 132  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED     61   32
  DEL PEAK  8(4Q21.3) WILD-TYPE  132   44
            clus
vv           DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  TUMOR FREE                          61                           132
  WITH TUMOR                          32                            44
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  8(4Q21.3) MUTATED    2 39 52  0  7
  DEL PEAK  8(4Q21.3) WILD-TYPE 16 90 63  1 17
D34V14, multiclass
    clus
vv   DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  G1                           2                            16
  G2                          39                            90
  G3                          52                            63
  G4                           0                             1
  GX                           7                            17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, continuous
D34V16, continuous
D34V17, continuous
D34V18, continuous
D34V19, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q21.3) MUTATED   10  1
  DEL PEAK  8(4Q21.3) WILD-TYPE 15  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED     10    1
  DEL PEAK  8(4Q21.3) WILD-TYPE   15    2
                         clus
vv                        DEL PEAK  8(4Q21.3) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        DEL PEAK  8(4Q21.3) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
D34V20, continuous
D34V21, continuous
D34V22, continuous
D34V23, continuous
D34V24, continuous
D34V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  8(4Q21.3) MUTATED                                     1
  DEL PEAK  8(4Q21.3) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  8(4Q21.3) MUTATED                                     4
  DEL PEAK  8(4Q21.3) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  8(4Q21.3) MUTATED                        12                       1
  DEL PEAK  8(4Q21.3) WILD-TYPE                      24                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  8(4Q21.3) MUTATED                         2
  DEL PEAK  8(4Q21.3) WILD-TYPE                       8
D34V26, multiclass
                                     clus
vv                                    DEL PEAK  8(4Q21.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      12
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK  8(4Q21.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        24
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  8(4Q21.3) MUTATED                                               1
  DEL PEAK  8(4Q21.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  8(4Q21.3) MUTATED                                                8
  DEL PEAK  8(4Q21.3) WILD-TYPE                                             17
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  8(4Q21.3) MUTATED                                                                                  25
  DEL PEAK  8(4Q21.3) WILD-TYPE                                                                                57
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  8(4Q21.3) MUTATED                                                                                             41
  DEL PEAK  8(4Q21.3) WILD-TYPE                                                                                           80
D34V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  8(4Q21.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          41
                                                                                              clus
vv                                                                                             DEL PEAK  8(4Q21.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V28, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q21.3) MUTATED   20 25
  DEL PEAK  8(4Q21.3) WILD-TYPE 51 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED     20   25
  DEL PEAK  8(4Q21.3) WILD-TYPE   51   49
         clus
vv        DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  ABSENT                           20                            51
  PRESENT                          25                            49
[1] 2 2
[1] FALSE
D34V29, continuous
D34V30, continuous
D34V31, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q21.3) MUTATED   20 42
  DEL PEAK  8(4Q21.3) WILD-TYPE 29 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED     20   42
  DEL PEAK  8(4Q21.3) WILD-TYPE   29   75
                                          clus
vv                                         DEL PEAK  8(4Q21.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              20
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          42
                                          clus
vv                                         DEL PEAK  8(4Q21.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            75
[1] 2 2
[1] FALSE
D34V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  8(4Q21.3) MUTATED              4          18         31
  DEL PEAK  8(4Q21.3) WILD-TYPE           11          36         54
D34V33, multiclass
              clus
vv             DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           18                            36
  NEVER USED                            31                            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"
D34V34, continuous
D34V35, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q21.3) MUTATED   23  8
  DEL PEAK  8(4Q21.3) WILD-TYPE 69 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q21.3) MUTATED     23    8
  DEL PEAK  8(4Q21.3) WILD-TYPE   69   10
         clus
vv        DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  ABSENT                           23                            69
  PRESENT                           8                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  8(4Q21.3) MUTATED             1        44     1
  DEL PEAK  8(4Q21.3) WILD-TYPE           4        56     1
D34V36, multiclass
             clus
vv            DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            44                            56
  OTHER                                 1                             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"
D34V37, continuous
D34V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  8(4Q21.3) MUTATED         0        1         0         1       13
  DEL PEAK  8(4Q21.3) WILD-TYPE       5        0         1         0       21
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  8(4Q21.3) MUTATED          23        14        0         2
  DEL PEAK  8(4Q21.3) WILD-TYPE        54        23        4         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  8(4Q21.3) MUTATED            2          1        18         0
  DEL PEAK  8(4Q21.3) WILD-TYPE          3          6        26         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  8(4Q21.3) MUTATED            1         15         5         3
  DEL PEAK  8(4Q21.3) WILD-TYPE          2         27         2         9
D34V39, multiclass
            clus
vv           DEL PEAK  8(4Q21.3) MUTATED DEL PEAK  8(4Q21.3) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            13                            21
  STAGE IB1                           23                            54
  STAGE IB2                           14                            23
  STAGE II                             0                             4
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           1                             6
  STAGE IIB                           18                            26
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          15                            27
  STAGE IVA                            5                             2
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK  9(4Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q22.1) MUTATED    72  24
  DEL PEAK  9(4Q22.1) WILD-TYPE 142  44
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                           96                           186 
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                           24                            44 
$`DEL PEAK  9(4Q22.1) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A 
       12.59         4.34        17.52        17.82        49.48        23.67 
TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LT 
       11.44         5.46        31.40        35.61        20.91        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CM 
       73.45        83.05        52.01        18.02        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       131.11         9.34        13.61         2.73 
TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM 
       45.83        99.91        27.52        20.91        95.11        63.98 
TCGA-DR-A0ZL TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 
       87.75        40.87        24.56        31.73        26.01        14.89 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK 
       13.48         0.36        60.72        26.27         1.51         0.39 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RK 
        0.59         0.89         1.45        40.96         1.74         0.43 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A3NI TCGA-FU-A5XV 
        1.64         2.33        20.35        15.22        20.98        10.55 
TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3LK TCGA-JW-A5VK TCGA-JX-A5QV TCGA-LP-A4AU 
       17.75        21.67        29.85        20.48        20.91        11.28 
TCGA-LP-A4AW TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 
        0.89        20.28        11.38        17.23         2.96        16.41 
TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH 
       22.62        11.67        12.16        10.03        46.52        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       23.97        19.96        32.15        59.18        31.27        40.87 
TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
        4.73        40.14        15.68        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UT 
       50.47        43.40        46.92        14.53        47.87        15.85 
TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       18.84        18.25        26.01        29.26        67.59         1.41 

$`DEL PEAK  9(4Q22.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-BI-A0VS 
      146.86        14.70         8.32         1.48         0.69        57.04 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        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        33.24 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YT 
      155.77        94.95        50.99         8.35        23.51        20.81 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK 
       14.73         1.12        82.06        44.94        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       55.63       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S 
       31.36        13.05        25.02        36.89        26.40        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82         7.46        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R9 
       27.22        24.00         6.64        19.27         0.43         0.13 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO 
        0.30         4.24         0.07         1.87        47.77         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF 
        0.10         0.49         0.89         7.92        19.79        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       12.23        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
       26.14        16.14        28.31        14.01        35.44         1.12 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        16.57        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       129.37        96.95        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y 
       12.49         0.30         0.82        13.35        22.52        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         9.17         8.52        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       54.81        35.05        20.84        15.58        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EL 
       19.59        14.60        93.99        69.50        45.57        65.49 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Z 
       53.59        36.13        11.51        39.78        16.64        33.37 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       58.45        56.35        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ 
       24.30        45.11         1.71        27.25        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 
       26.07        14.53         3.42        18.25        67.20         5.16 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       17.75        16.24        15.42        19.13         0.16         3.91 

  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                       147.35                        210.67 
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                       20.695                        24.430 
[1] "0.4 - 147.3 (20.7)" "0.1 - 210.7 (24.4)"
[1] "hr=" "1.3"
D35V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  9(4Q22.1) MUTATED   43 19 10  4
  DEL PEAK  9(4Q22.1) WILD-TYPE 92 51 11  4
D35V3, multiclass
    clus
vv   DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  T1                          43                            92
  T2                          19                            51
  T3                          10                            11
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q22.1) MUTATED   34 22
  DEL PEAK  9(4Q22.1) WILD-TYPE 95 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED     34   22
  DEL PEAK  9(4Q22.1) WILD-TYPE   95   34
   clus
vv  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  0                          34                            95
  1                          22                            34
[1] 2 2
[1] FALSE
D35V5, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q22.1) MUTATED   35  5
  DEL PEAK  9(4Q22.1) WILD-TYPE 73  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED     35    5
  DEL PEAK  9(4Q22.1) WILD-TYPE   73    5
   clus
vv  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  0                          35                            73
  1                           5                             5
[1] 2 2
[1] FALSE
D35V6, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q22.1) MUTATED   10 54
  DEL PEAK  9(4Q22.1) WILD-TYPE 43 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED     10   54
  DEL PEAK  9(4Q22.1) WILD-TYPE   43   71
     clus
vv    DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  NO                           10                            43
  YES                          54                            71
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED               2                               89
  DEL PEAK  9(4Q22.1) WILD-TYPE             4                              153
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  9(4Q22.1) MUTATED                                               2
  DEL PEAK  9(4Q22.1) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                                     1
  DEL PEAK  9(4Q22.1) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  9(4Q22.1) MUTATED                                           1
  DEL PEAK  9(4Q22.1) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  9(4Q22.1) MUTATED                                              5
  DEL PEAK  9(4Q22.1) WILD-TYPE                                           12
D35V7, multiclass
                                               clus
vv                                              DEL PEAK  9(4Q22.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       89
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
                                               clus
vv                                              DEL PEAK  9(4Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, continuous
D35V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4Q22.1) MUTATED                                  1     6
  DEL PEAK  9(4Q22.1) WILD-TYPE                                7    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(4Q22.1) MUTATED                          14
  DEL PEAK  9(4Q22.1) WILD-TYPE                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(4Q22.1) MUTATED                                           0    68
  DEL PEAK  9(4Q22.1) WILD-TYPE                                         2   134
D35V10, multiclass
                                           clus
vv                                          DEL PEAK  9(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               6
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              68
                                           clus
vv                                          DEL PEAK  9(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q22.1) MUTATED     6  54
  DEL PEAK  9(4Q22.1) WILD-TYPE  17 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED      6   54
  DEL PEAK  9(4Q22.1) WILD-TYPE   17  109
                        clus
vv                       DEL PEAK  9(4Q22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK  9(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           109
[1] 2 2
[1] FALSE
D35V12, continuous
D35V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q22.1) MUTATED    62  29
  DEL PEAK  9(4Q22.1) WILD-TYPE 131  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED     62   29
  DEL PEAK  9(4Q22.1) WILD-TYPE  131   47
            clus
vv           DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  TUMOR FREE                          62                           131
  WITH TUMOR                          29                            47
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  9(4Q22.1) MUTATED    2 34 54  0  8
  DEL PEAK  9(4Q22.1) WILD-TYPE 16 95 61  1 16
D35V14, multiclass
    clus
vv   DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  G1                           2                            16
  G2                          34                            95
  G3                          54                            61
  G4                           0                             1
  GX                           8                            16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, continuous
D35V16, continuous
D35V17, continuous
D35V18, continuous
D35V19, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q22.1) MUTATED    9  2
  DEL PEAK  9(4Q22.1) WILD-TYPE 16  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED      9    2
  DEL PEAK  9(4Q22.1) WILD-TYPE   16    1
                         clus
vv                        DEL PEAK  9(4Q22.1) MUTATED
  COMPLETED AS PLANNED                              9
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK  9(4Q22.1) WILD-TYPE
  COMPLETED AS PLANNED                               16
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
D35V20, continuous
D35V21, continuous
D35V22, continuous
D35V23, continuous
D35V24, continuous
D35V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  9(4Q22.1) MUTATED                                     1
  DEL PEAK  9(4Q22.1) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  9(4Q22.1) MUTATED                                     5
  DEL PEAK  9(4Q22.1) WILD-TYPE                                   2
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  9(4Q22.1) MUTATED                        10                       0
  DEL PEAK  9(4Q22.1) WILD-TYPE                      26                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  9(4Q22.1) MUTATED                         2
  DEL PEAK  9(4Q22.1) WILD-TYPE                       8
D35V26, multiclass
                                     clus
vv                                    DEL PEAK  9(4Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           5
  OTHER LOCATION, SPECIFY                                      10
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK  9(4Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        26
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  9(4Q22.1) MUTATED                                               1
  DEL PEAK  9(4Q22.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  9(4Q22.1) MUTATED                                                9
  DEL PEAK  9(4Q22.1) WILD-TYPE                                             16
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  9(4Q22.1) MUTATED                                                                                  26
  DEL PEAK  9(4Q22.1) WILD-TYPE                                                                                56
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  9(4Q22.1) MUTATED                                                                                             39
  DEL PEAK  9(4Q22.1) WILD-TYPE                                                                                           82
D35V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  9(4Q22.1) 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)                          39
                                                                                              clus
vv                                                                                             DEL PEAK  9(4Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V28, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q22.1) MUTATED   17 24
  DEL PEAK  9(4Q22.1) WILD-TYPE 54 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED     17   24
  DEL PEAK  9(4Q22.1) WILD-TYPE   54   50
         clus
vv        DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  ABSENT                           17                            54
  PRESENT                          24                            50
[1] 2 2
[1] FALSE
D35V29, continuous
D35V30, continuous
D35V31, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q22.1) MUTATED   16 41
  DEL PEAK  9(4Q22.1) WILD-TYPE 33 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED     16   41
  DEL PEAK  9(4Q22.1) WILD-TYPE   33   76
                                          clus
vv                                         DEL PEAK  9(4Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          41
                                          clus
vv                                         DEL PEAK  9(4Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            76
[1] 2 2
[1] FALSE
D35V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  9(4Q22.1) MUTATED              4          16         32
  DEL PEAK  9(4Q22.1) WILD-TYPE           11          38         53
D35V33, multiclass
              clus
vv             DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           16                            38
  NEVER USED                            32                            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"
D35V34, continuous
D35V35, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q22.1) MUTATED   22  6
  DEL PEAK  9(4Q22.1) WILD-TYPE 70 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED     22    6
  DEL PEAK  9(4Q22.1) WILD-TYPE   70   12
         clus
vv        DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  ABSENT                           22                            70
  PRESENT                           6                            12
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK  9(4Q22.1) MUTATED             1        42     1
  DEL PEAK  9(4Q22.1) WILD-TYPE           4        58     1
D35V36, multiclass
             clus
vv            DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            42                            58
  OTHER                                 1                             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"
D35V37, continuous
D35V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK  9(4Q22.1) MUTATED         0        1         0         1       12
  DEL PEAK  9(4Q22.1) WILD-TYPE       5        0         1         0       22
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK  9(4Q22.1) MUTATED          21        15        0         2
  DEL PEAK  9(4Q22.1) WILD-TYPE        56        22        4         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK  9(4Q22.1) MUTATED            2          1        18         0
  DEL PEAK  9(4Q22.1) WILD-TYPE          3          6        26         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK  9(4Q22.1) MUTATED            1         16         3         3
  DEL PEAK  9(4Q22.1) WILD-TYPE          2         26         4         9
D35V39, multiclass
            clus
vv           DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            12                            22
  STAGE IB1                           21                            56
  STAGE IB2                           15                            22
  STAGE II                             0                             4
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           1                             6
  STAGE IIB                           18                            26
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          16                            26
  STAGE IVA                            3                             4
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK 10(4Q35.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q35.2) MUTATED    83  26
  DEL PEAK 10(4Q35.2) WILD-TYPE 131  42
  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE 
                          109                           173 
  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE 
                           26                            42 
$`DEL PEAK 10(4Q35.2) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A 
       12.59         4.34        17.52        17.82        57.04        23.67 
TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI 
       11.44         5.46        67.46        31.40        57.73        35.61 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD 
       20.91        40.93        73.18        73.45        83.05        52.01 
TCGA-C5-A3HE TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
       18.02       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK 
      131.11         9.34        13.61         2.73        45.83        99.91 
TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL 
       27.52        20.91        14.73        95.11        63.98        87.75 
TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A411 
       16.83        39.55        40.87        31.36        13.05        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EA-A5ZF 
       31.73        26.01        12.13        14.89        27.25        27.22 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK 
       13.48         0.36        60.72        26.27         1.51         0.39 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RM 
        0.59         0.89         1.45         1.74         0.43         1.64 
TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3NI 
        2.33        20.35        15.22        15.55        19.04        20.98 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-JW-A5VG TCGA-JW-A5VK 
       10.55        17.75        21.67       137.16        27.42        20.48 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3W TCGA-MA-AA3X 
       21.11        20.91        11.28         0.89        22.52        20.28 
TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73R TCGA-Q1-A73S 
       11.38        17.23         2.96        16.41        18.64        22.62 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI 
       19.59        11.67        12.16        10.03        32.42        23.97 
TCGA-VS-A8Q8 TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 
       32.15        31.27        40.87         4.73        40.14        15.68 
TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UC TCGA-VS-A9UH 
       55.50        51.32        50.47        43.40        27.12        46.92 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UT TCGA-VS-A9V2 TCGA-WL-A834 TCGA-ZJ-A8QQ 
       14.53        47.87        15.85        18.25        26.01        67.59 
TCGA-ZJ-AAXA 
        1.41 

$`DEL PEAK 10(4Q35.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-BI-A0VR 
      146.86        14.70         8.32         1.48         0.69        49.48 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
       82.85        19.86        46.32        30.21        35.01        53.16 
TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY 
       38.99         0.46         2.43         3.58        44.22        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
      100.14        38.43        33.24        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XI 
      154.32       101.82       155.77        94.95        50.99         8.35 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM 
       23.51        20.81         1.12        82.06        44.94        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WF 
       36.76        55.63       117.99       118.65        22.98        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QE 
       17.52         8.28        37.35        30.90        31.53        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       36.89        26.40        24.82         7.46        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R9 
       27.29        24.00         6.64        19.27         0.43         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       40.96         0.30         4.24         0.07         1.87        47.77 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A69L 
        0.07         0.10         0.49         0.89         7.92        19.79 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
       12.23        23.84        16.11        31.36        36.26        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA 
       16.14        28.31        14.01        35.44         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
       16.57        20.78        14.93         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
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        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       18.15       209.59        44.61        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y 
       13.35        17.82        19.56         9.17         8.52        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       34.62        19.96        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
        9.34        14.60        93.99        69.50        46.52        45.57 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        65.49        53.59        36.13        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       39.78        16.64        33.37        58.45        56.35        50.14 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UJ 
       48.39        28.50        29.95        24.30        45.11         1.71 
TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV 
       27.25        47.47        41.52        26.07        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 
       18.25        67.20        18.84         5.16        17.75        16.24 
TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        29.26        19.13         0.16         3.91 

  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE 
                       147.35                        210.67 
  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE 
                        20.91                         24.82 
[1] "0.4 - 147.3 (20.9)" "0.1 - 210.7 (24.8)"
[1] "hr=" "1.1"
D36V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 10(4Q35.2) MUTATED   54 20  9  4
  DEL PEAK 10(4Q35.2) WILD-TYPE 81 50 12  4
D36V3, multiclass
    clus
vv   DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  T1                          54                            81
  T2                          20                            50
  T3                           9                            12
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q35.2) MUTATED   44 24
  DEL PEAK 10(4Q35.2) WILD-TYPE 85 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED     44   24
  DEL PEAK 10(4Q35.2) WILD-TYPE   85   32
   clus
vv  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  0                          44                            85
  1                          24                            32
[1] 2 2
[1] FALSE
D36V5, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q35.2) MUTATED   45  4
  DEL PEAK 10(4Q35.2) WILD-TYPE 63  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED     45    4
  DEL PEAK 10(4Q35.2) WILD-TYPE   63    6
   clus
vv  DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  0                          45                            63
  1                           4                             6
[1] 2 2
[1] FALSE
D36V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q35.2) MUTATED   15 56
  DEL PEAK 10(4Q35.2) WILD-TYPE 38 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED     15   56
  DEL PEAK 10(4Q35.2) WILD-TYPE   38   69
     clus
vv    DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  NO                           15                            38
  YES                          56                            69
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(4Q35.2) MUTATED               2                              101
  DEL PEAK 10(4Q35.2) WILD-TYPE             4                              141
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 10(4Q35.2) MUTATED                                               2
  DEL PEAK 10(4Q35.2) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 10(4Q35.2) MUTATED                                     3
  DEL PEAK 10(4Q35.2) WILD-TYPE                                  18
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 10(4Q35.2) MUTATED                                           2
  DEL PEAK 10(4Q35.2) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 10(4Q35.2) MUTATED                                              4
  DEL PEAK 10(4Q35.2) WILD-TYPE                                           13
D36V7, multiclass
                                               clus
vv                                              DEL PEAK 10(4Q35.2) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      101
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
                                               clus
vv                                              DEL PEAK 10(4Q35.2) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        141
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, continuous
D36V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4Q35.2) MUTATED                                  2     8
  DEL PEAK 10(4Q35.2) WILD-TYPE                                6    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(4Q35.2) MUTATED                          13
  DEL PEAK 10(4Q35.2) WILD-TYPE                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(4Q35.2) MUTATED                                           0    81
  DEL PEAK 10(4Q35.2) WILD-TYPE                                         2   121
D36V10, multiclass
                                           clus
vv                                          DEL PEAK 10(4Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              81
                                           clus
vv                                          DEL PEAK 10(4Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               121
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q35.2) MUTATED    6 68
  DEL PEAK 10(4Q35.2) WILD-TYPE 17 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED      6   68
  DEL PEAK 10(4Q35.2) WILD-TYPE   17   95
                        clus
vv                       DEL PEAK 10(4Q35.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK 10(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                            95
[1] 2 2
[1] FALSE
D36V12, continuous
D36V13, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q35.2) MUTATED    74  30
  DEL PEAK 10(4Q35.2) WILD-TYPE 119  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED     74   30
  DEL PEAK 10(4Q35.2) WILD-TYPE  119   46
            clus
vv           DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  TUMOR FREE                          74                           119
  WITH TUMOR                          30                            46
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 10(4Q35.2) MUTATED    4 41 57  0  9
  DEL PEAK 10(4Q35.2) WILD-TYPE 14 88 58  1 15
D36V14, multiclass
    clus
vv   DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  G1                           4                            14
  G2                          41                            88
  G3                          57                            58
  G4                           0                             1
  GX                           9                            15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, continuous
D36V16, continuous
D36V17, continuous
D36V18, continuous
D36V19, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q35.2) MUTATED   10  2
  DEL PEAK 10(4Q35.2) WILD-TYPE 15  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED     10    2
  DEL PEAK 10(4Q35.2) WILD-TYPE   15    1
                         clus
vv                        DEL PEAK 10(4Q35.2) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK 10(4Q35.2) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
D36V20, continuous
D36V21, continuous
D36V22, continuous
D36V23, continuous
D36V24, continuous
D36V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 10(4Q35.2) MUTATED                                     1
  DEL PEAK 10(4Q35.2) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 10(4Q35.2) MUTATED                                     4
  DEL PEAK 10(4Q35.2) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 10(4Q35.2) MUTATED                        11                       0
  DEL PEAK 10(4Q35.2) WILD-TYPE                      25                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 10(4Q35.2) MUTATED                         2
  DEL PEAK 10(4Q35.2) WILD-TYPE                       8
D36V26, multiclass
                                     clus
vv                                    DEL PEAK 10(4Q35.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                      11
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK 10(4Q35.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        25
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 10(4Q35.2) MUTATED                                               2
  DEL PEAK 10(4Q35.2) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 10(4Q35.2) MUTATED                                               13
  DEL PEAK 10(4Q35.2) WILD-TYPE                                             12
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 10(4Q35.2) MUTATED                                                                                  29
  DEL PEAK 10(4Q35.2) WILD-TYPE                                                                                53
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 10(4Q35.2) MUTATED                                                                                             43
  DEL PEAK 10(4Q35.2) WILD-TYPE                                                                                           78
D36V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 10(4Q35.2) 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)                                     29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          43
                                                                                              clus
vv                                                                                             DEL PEAK 10(4Q35.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V28, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q35.2) MUTATED   24 29
  DEL PEAK 10(4Q35.2) WILD-TYPE 47 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED     24   29
  DEL PEAK 10(4Q35.2) WILD-TYPE   47   45
         clus
vv        DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  ABSENT                           24                            47
  PRESENT                          29                            45
[1] 2 2
[1] FALSE
D36V29, continuous
D36V30, continuous
D36V31, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q35.2) MUTATED   24 48
  DEL PEAK 10(4Q35.2) WILD-TYPE 25 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED     24   48
  DEL PEAK 10(4Q35.2) WILD-TYPE   25   69
                                          clus
vv                                         DEL PEAK 10(4Q35.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          48
                                          clus
vv                                         DEL PEAK 10(4Q35.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            69
[1] 2 2
[1] FALSE
D36V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 10(4Q35.2) MUTATED              4          20         37
  DEL PEAK 10(4Q35.2) WILD-TYPE           11          34         48
D36V33, multiclass
              clus
vv             DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           20                            34
  NEVER USED                            37                            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"
D36V34, continuous
D36V35, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q35.2) MUTATED   31  5
  DEL PEAK 10(4Q35.2) WILD-TYPE 61 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q35.2) MUTATED     31    5
  DEL PEAK 10(4Q35.2) WILD-TYPE   61   13
         clus
vv        DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  ABSENT                           31                            61
  PRESENT                           5                            13
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 10(4Q35.2) MUTATED             1        46     1
  DEL PEAK 10(4Q35.2) WILD-TYPE           4        54     1
D36V36, multiclass
             clus
vv            DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            46                            54
  OTHER                                 1                             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"
D36V37, continuous
D36V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 10(4Q35.2) MUTATED         1        1         0         1       16
  DEL PEAK 10(4Q35.2) WILD-TYPE       4        0         1         0       18
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 10(4Q35.2) MUTATED          29        15        0         3
  DEL PEAK 10(4Q35.2) WILD-TYPE        48        22        4         5
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 10(4Q35.2) MUTATED            2          0        17         0
  DEL PEAK 10(4Q35.2) WILD-TYPE          3          7        27         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 10(4Q35.2) MUTATED            1         17         4         3
  DEL PEAK 10(4Q35.2) WILD-TYPE          2         25         3         9
D36V39, multiclass
            clus
vv           DEL PEAK 10(4Q35.2) MUTATED DEL PEAK 10(4Q35.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                            16                            18
  STAGE IB1                           29                            48
  STAGE IB2                           15                            22
  STAGE II                             0                             4
  STAGE IIA                            3                             5
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           17                            27
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          17                            25
  STAGE IVA                            4                             3
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK 11(5Q12.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(5Q12.1) MUTATED    49  24
  DEL PEAK 11(5Q12.1) WILD-TYPE 165  44
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                           73                           209 
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                           24                            44 
$`DEL PEAK 11(5Q12.1) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ 
       12.59         4.34        17.82        11.44        68.84       144.16 
TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MH 
      177.04         5.46        31.40        30.21        35.01        38.99 
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7X3 
       35.61        40.93        18.02       154.32        17.19         9.34 
TCGA-C5-A8XH TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       45.83        95.11        87.75        36.76        55.63       117.99 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 
       39.55        40.87        30.90        24.56        31.73        14.89 
TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2RJ 
       27.22         0.36         6.64        19.27         0.43         1.74 
TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-FU-A23L 
        0.43         1.64         0.49         0.89        20.35        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC 
       19.04        31.36        20.98        10.55        25.41        16.57 
TCGA-HM-A3JJ TCGA-JW-A5VI TCGA-LP-A4AW TCGA-MA-AA3Z TCGA-MY-A913 TCGA-Q1-A5R3 
       21.67        24.56         0.89        19.56        17.23        15.95 
TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A8QH 
        9.04        32.42        23.97        19.96        59.18        39.78 
TCGA-VS-A94Y TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL 
        4.73        50.14        50.47        24.30        45.11        14.53 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UU TCGA-WL-A834 TCGA-XS-A8TJ 
       47.87        47.47        15.85        14.53        26.01        29.26 
TCGA-ZJ-A8QR 
       19.13 

$`DEL PEAK 11(5Q12.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        14.70         8.32         1.48         0.69        17.52 
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BL 
       49.48        57.04        23.67        18.74        36.56       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MF 
       82.85        19.86        67.46        46.32        57.73        53.16 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91         3.58        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48        20.35       147.35       155.77       131.11        94.95 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
       13.61         2.73        50.99         8.35        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52        20.81        20.91        14.73         1.12        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       44.94        63.98        58.88       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       16.18        17.52         8.28        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S 
       13.05        25.02        36.89        26.40        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82         7.46        26.79        25.91        27.29        27.25 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK 
       24.00        13.48        60.72        26.27         1.51         0.39 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        4.24         0.07         1.87        47.77         2.33         0.07 
TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        0.10         7.92        15.22        19.79        15.55        12.23 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       16.11        36.26        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       35.44         1.12        17.75        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       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ 
       81.96        29.85        36.36        27.42         3.29        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 
      209.59        44.61        20.91        11.28        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 
        0.82        13.35        22.52        20.28        17.82         9.17 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV 
       35.05        20.84         2.96        15.58        16.41        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59        14.60        11.67        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       10.03        46.52        45.57        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z 
       36.13        11.51        31.27        40.87        16.64        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 
       40.14        58.45        15.68        56.35        55.50        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH 
       43.40        48.39        28.50        29.95        27.12        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY 
        1.71        27.25        41.52        26.07         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 
       67.20        18.84         5.16        18.25        17.75        16.24 
TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        67.59         1.41         0.16         3.91 

  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                       177.04                        210.67 
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                        23.97                         21.44 
[1] "0.4 - 177.0 (24.0)" "0.1 - 210.7 (21.4)"
[1] "hr=" "1.6"
D37V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 11(5Q12.1) MUTATED   36 14  7  1
  DEL PEAK 11(5Q12.1) WILD-TYPE 99 56 14  7
D37V3, multiclass
    clus
vv   DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  T1                          36                            99
  T2                          14                            56
  T3                           7                            14
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q12.1) MUTATED    28  17
  DEL PEAK 11(5Q12.1) WILD-TYPE 101  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     28   17
  DEL PEAK 11(5Q12.1) WILD-TYPE  101   39
   clus
vv  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  0                          28                           101
  1                          17                            39
[1] 2 2
[1] FALSE
D37V5, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q12.1) MUTATED   27  2
  DEL PEAK 11(5Q12.1) WILD-TYPE 81  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     27    2
  DEL PEAK 11(5Q12.1) WILD-TYPE   81    8
   clus
vv  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  0                          27                            81
  1                           2                             8
[1] 2 2
[1] FALSE
D37V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q12.1) MUTATED   11 28
  DEL PEAK 11(5Q12.1) WILD-TYPE 42 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     11   28
  DEL PEAK 11(5Q12.1) WILD-TYPE   42   97
     clus
vv    DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  NO                           11                            42
  YES                          28                            97
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED               1                               66
  DEL PEAK 11(5Q12.1) WILD-TYPE             5                              176
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 11(5Q12.1) MUTATED                                               1
  DEL PEAK 11(5Q12.1) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                                     2
  DEL PEAK 11(5Q12.1) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 11(5Q12.1) MUTATED                                           1
  DEL PEAK 11(5Q12.1) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 11(5Q12.1) MUTATED                                              5
  DEL PEAK 11(5Q12.1) WILD-TYPE                                           12
D37V7, multiclass
                                               clus
vv                                              DEL PEAK 11(5Q12.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       66
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            5
                                               clus
vv                                              DEL PEAK 11(5Q12.1) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        176
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, continuous
D37V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(5Q12.1) MUTATED                                  1     5
  DEL PEAK 11(5Q12.1) WILD-TYPE                                7    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(5Q12.1) MUTATED                           7
  DEL PEAK 11(5Q12.1) WILD-TYPE                        21
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(5Q12.1) MUTATED                                           1    56
  DEL PEAK 11(5Q12.1) WILD-TYPE                                         1   146
D37V10, multiclass
                                           clus
vv                                          DEL PEAK 11(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              56
                                           clus
vv                                          DEL PEAK 11(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               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"
D37V11, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q12.1) MUTATED     4  44
  DEL PEAK 11(5Q12.1) WILD-TYPE  19 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED      4   44
  DEL PEAK 11(5Q12.1) WILD-TYPE   19  119
                        clus
vv                       DEL PEAK 11(5Q12.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK 11(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           119
[1] 2 2
[1] FALSE
D37V12, continuous
D37V13, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q12.1) MUTATED    45  24
  DEL PEAK 11(5Q12.1) WILD-TYPE 148  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     45   24
  DEL PEAK 11(5Q12.1) WILD-TYPE  148   52
            clus
vv           DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  TUMOR FREE                          45                           148
  WITH TUMOR                          24                            52
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 11(5Q12.1) MUTATED    2 31 34  0  6
  DEL PEAK 11(5Q12.1) WILD-TYPE 16 98 81  1 18
D37V14, multiclass
    clus
vv   DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  G1                           2                            16
  G2                          31                            98
  G3                          34                            81
  G4                           0                             1
  GX                           6                            18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, continuous
D37V16, continuous
D37V17, continuous
D37V18, continuous
D37V19, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q12.1) MUTATED   11  1
  DEL PEAK 11(5Q12.1) WILD-TYPE 14  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     11    1
  DEL PEAK 11(5Q12.1) WILD-TYPE   14    2
                         clus
vv                        DEL PEAK 11(5Q12.1) MUTATED
  COMPLETED AS PLANNED                             11
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        DEL PEAK 11(5Q12.1) WILD-TYPE
  COMPLETED AS PLANNED                               14
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
D37V20, continuous
D37V21, continuous
D37V22, continuous
D37V23, continuous
D37V24, continuous
D37V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 11(5Q12.1) MUTATED                                     0
  DEL PEAK 11(5Q12.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 11(5Q12.1) MUTATED                                     3
  DEL PEAK 11(5Q12.1) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 11(5Q12.1) MUTATED                        11                       0
  DEL PEAK 11(5Q12.1) WILD-TYPE                      25                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 11(5Q12.1) MUTATED                         2
  DEL PEAK 11(5Q12.1) WILD-TYPE                       8
D37V26, multiclass
                                     clus
vv                                    DEL PEAK 11(5Q12.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                      11
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK 11(5Q12.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                        25
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 11(5Q12.1) MUTATED                                               1
  DEL PEAK 11(5Q12.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 11(5Q12.1) MUTATED                                                8
  DEL PEAK 11(5Q12.1) WILD-TYPE                                             17
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 11(5Q12.1) MUTATED                                                                                  22
  DEL PEAK 11(5Q12.1) WILD-TYPE                                                                                60
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 11(5Q12.1) MUTATED                                                                                             29
  DEL PEAK 11(5Q12.1) WILD-TYPE                                                                                           92
D37V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 11(5Q12.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          29
                                                                                              clus
vv                                                                                             DEL PEAK 11(5Q12.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       60
  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"
D37V28, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q12.1) MUTATED   14 22
  DEL PEAK 11(5Q12.1) WILD-TYPE 57 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     14   22
  DEL PEAK 11(5Q12.1) WILD-TYPE   57   52
         clus
vv        DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  ABSENT                           14                            57
  PRESENT                          22                            52
[1] 2 2
[1] FALSE
D37V29, continuous
D37V30, continuous
D37V31, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q12.1) MUTATED   12 34
  DEL PEAK 11(5Q12.1) WILD-TYPE 37 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     12   34
  DEL PEAK 11(5Q12.1) WILD-TYPE   37   83
                                          clus
vv                                         DEL PEAK 11(5Q12.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          34
                                          clus
vv                                         DEL PEAK 11(5Q12.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            83
[1] 2 2
[1] FALSE
D37V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 11(5Q12.1) MUTATED              3          15         23
  DEL PEAK 11(5Q12.1) WILD-TYPE           12          39         62
D37V33, multiclass
              clus
vv             DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           15                            39
  NEVER USED                            23                            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"
D37V34, continuous
D37V35, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q12.1) MUTATED   22  4
  DEL PEAK 11(5Q12.1) WILD-TYPE 70 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     22    4
  DEL PEAK 11(5Q12.1) WILD-TYPE   70   14
         clus
vv        DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  ABSENT                           22                            70
  PRESENT                           4                            14
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 11(5Q12.1) MUTATED             0        27     1
  DEL PEAK 11(5Q12.1) WILD-TYPE           5        73     1
D37V36, multiclass
             clus
vv            DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  CARBOPLATIN                           0                             5
  CISPLATIN                            27                            73
  OTHER                                 1                             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"
D37V37, continuous
D37V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 11(5Q12.1) MUTATED         2        1         0         1        9
  DEL PEAK 11(5Q12.1) WILD-TYPE       3        0         1         0       25
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 11(5Q12.1) MUTATED          15        11        1         2
  DEL PEAK 11(5Q12.1) WILD-TYPE        62        26        3         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 11(5Q12.1) MUTATED            2          0        15         0
  DEL PEAK 11(5Q12.1) WILD-TYPE          3          7        29         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 11(5Q12.1) MUTATED            1         13         1         0
  DEL PEAK 11(5Q12.1) WILD-TYPE          2         29         6        12
D37V39, multiclass
            clus
vv           DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             9                            25
  STAGE IB1                           15                            62
  STAGE IB2                           11                            26
  STAGE II                             1                             3
  STAGE IIA                            2                             6
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           15                            29
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          13                            29
  STAGE IVA                            1                             6
  STAGE IVB                            0                            12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK 12(5Q35.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q35.2) MUTATED    51  18
  DEL PEAK 12(5Q35.2) WILD-TYPE 163  50
  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE 
                           69                           213 
  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE 
                           18                            50 
$`DEL PEAK 12(5Q35.2) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BL 
       12.59         4.34        17.82        11.44       144.16       173.29 
TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MN 
        5.46        31.40        35.01        38.99        35.61        40.93 
TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UE TCGA-DG-A2KJ TCGA-DR-A0ZL 
       18.02       154.32        17.19       155.77        95.11        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR 
       36.76        55.63       117.99        39.55        40.87        30.90 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A97N 
       36.89        24.56        31.73        14.89        27.22         0.36 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RM 
        6.64         0.43         0.07         1.74         0.43         1.64 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A40J 
        0.49        20.35        23.84        19.04        31.36        14.01 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-JW-A5VI 
       10.55        25.41        16.57        21.67       137.16        24.56 
TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MY-A913 
        0.89         0.82        22.52        17.82        19.56        17.23 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A8QH 
       15.95         9.04        32.42        23.97        59.18        39.78 
TCGA-VS-A94Y TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9UU TCGA-WL-A834 
        4.73        50.47        24.30        14.53        14.53        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       29.26        19.13         1.41 

$`DEL PEAK 12(5Q35.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        14.70         8.32         1.48         0.69        17.52 
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        68.84        18.74        36.56 
TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      177.04        82.85        19.86        67.46        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP 
       57.73        53.16         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43        33.24        52.01        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UH 
      101.82       134.33        15.48        20.35       147.35       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       94.95         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM 
       14.73         1.12        82.06        44.94        63.98        58.88 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 
       37.35        31.53        31.36        13.05        25.02        26.40 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       26.01        12.13        24.82         7.46        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.29        27.25        24.00        13.48        60.72        26.27 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.51        19.27         0.39         0.59         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL 
        0.13        40.96         0.30         4.24         1.87        47.77 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        2.33         0.07         0.10         0.89         7.92        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI 
       19.79        15.55        12.23        16.11        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA 
       26.14        16.14        28.31        35.44         1.12        17.75 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93         9.44       147.39        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MA-AA42 
       12.49         0.30        13.35        20.28         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84         2.96        15.58        16.41        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
       14.60        11.67        93.99        12.16        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       46.52        45.57        19.96        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z 
       36.13        11.51        31.27        40.87        16.64        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       40.14        58.45        15.68        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       51.32        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       46.92        45.11         1.71        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.52        26.07        15.85         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       18.84         5.16        18.25        17.75        16.24        15.42 
TCGA-ZJ-A8QQ TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59         0.16         3.91 

  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE 
                       173.29                        210.67 
  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE 
                        22.52                         22.62 
[1] "0.1 - 173.3 (22.5)" "0.1 - 210.7 (22.6)"
[1] "hr=" "1.2"
D38V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 12(5Q35.2) MUTATED   37 10  6  1
  DEL PEAK 12(5Q35.2) WILD-TYPE 98 60 15  7
D38V3, multiclass
    clus
vv   DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  T1                          37                            98
  T2                          10                            60
  T3                           6                            15
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                               cls
clus                             0  1
  DEL PEAK 12(5Q35.2) MUTATED   30 15
  DEL PEAK 12(5Q35.2) WILD-TYPE 99 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED     30   15
  DEL PEAK 12(5Q35.2) WILD-TYPE   99   41
   clus
vv  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  0                          30                            99
  1                          15                            41
[1] 2 2
[1] FALSE
D38V5, binary
                               cls
clus                             0  1
  DEL PEAK 12(5Q35.2) MUTATED   31  1
  DEL PEAK 12(5Q35.2) WILD-TYPE 77  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED     31    1
  DEL PEAK 12(5Q35.2) WILD-TYPE   77    9
   clus
vv  DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  0                          31                            77
  1                           1                             9
[1] 2 2
[1] FALSE
D38V6, binary
                               cls
clus                             0  1
  DEL PEAK 12(5Q35.2) MUTATED   10 26
  DEL PEAK 12(5Q35.2) WILD-TYPE 43 99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED     10   26
  DEL PEAK 12(5Q35.2) WILD-TYPE   43   99
     clus
vv    DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  NO                           10                            43
  YES                          26                            99
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(5Q35.2) MUTATED               1                               62
  DEL PEAK 12(5Q35.2) WILD-TYPE             5                              180
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 12(5Q35.2) MUTATED                                               1
  DEL PEAK 12(5Q35.2) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 12(5Q35.2) MUTATED                                     3
  DEL PEAK 12(5Q35.2) WILD-TYPE                                  18
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 12(5Q35.2) MUTATED                                           2
  DEL PEAK 12(5Q35.2) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 12(5Q35.2) MUTATED                                              2
  DEL PEAK 12(5Q35.2) WILD-TYPE                                           15
D38V7, multiclass
                                               clus
vv                                              DEL PEAK 12(5Q35.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       62
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              DEL PEAK 12(5Q35.2) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        180
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, continuous
D38V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(5Q35.2) MUTATED                                  2     5
  DEL PEAK 12(5Q35.2) WILD-TYPE                                6    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(5Q35.2) MUTATED                           6
  DEL PEAK 12(5Q35.2) WILD-TYPE                        22
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(5Q35.2) MUTATED                                           1    53
  DEL PEAK 12(5Q35.2) WILD-TYPE                                         1   149
D38V10, multiclass
                                           clus
vv                                          DEL PEAK 12(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              53
                                           clus
vv                                          DEL PEAK 12(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               149
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q35.2) MUTATED     6  44
  DEL PEAK 12(5Q35.2) WILD-TYPE  17 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED      6   44
  DEL PEAK 12(5Q35.2) WILD-TYPE   17  119
                        clus
vv                       DEL PEAK 12(5Q35.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK 12(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           119
[1] 2 2
[1] FALSE
D38V12, continuous
D38V13, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q35.2) MUTATED    45  19
  DEL PEAK 12(5Q35.2) WILD-TYPE 148  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED     45   19
  DEL PEAK 12(5Q35.2) WILD-TYPE  148   57
            clus
vv           DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  TUMOR FREE                          45                           148
  WITH TUMOR                          19                            57
[1] 2 2
[1] FALSE
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK 12(5Q35.2) MUTATED     2  26  36   0   5
  DEL PEAK 12(5Q35.2) WILD-TYPE  16 103  79   1  19
D38V14, multiclass
    clus
vv   DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  G1                           2                            16
  G2                          26                           103
  G3                          36                            79
  G4                           0                             1
  GX                           5                            19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, continuous
D38V16, continuous
D38V17, continuous
D38V18, continuous
D38V19, binary
                               cls
clus                             0  1
  DEL PEAK 12(5Q35.2) MUTATED   10  1
  DEL PEAK 12(5Q35.2) WILD-TYPE 15  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED     10    1
  DEL PEAK 12(5Q35.2) WILD-TYPE   15    2
                         clus
vv                        DEL PEAK 12(5Q35.2) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           1
                         clus
vv                        DEL PEAK 12(5Q35.2) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             2
[1] 2 2
[1] FALSE
D38V20, continuous
D38V21, continuous
D38V22, continuous
D38V23, continuous
D38V24, continuous
D38V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 12(5Q35.2) MUTATED                                     0
  DEL PEAK 12(5Q35.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 12(5Q35.2) MUTATED                                     3
  DEL PEAK 12(5Q35.2) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 12(5Q35.2) MUTATED                         6                       0
  DEL PEAK 12(5Q35.2) WILD-TYPE                      30                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 12(5Q35.2) MUTATED                         2
  DEL PEAK 12(5Q35.2) WILD-TYPE                       8
D38V26, multiclass
                                     clus
vv                                    DEL PEAK 12(5Q35.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                       6
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK 12(5Q35.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                        30
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 12(5Q35.2) MUTATED                                               0
  DEL PEAK 12(5Q35.2) WILD-TYPE                                             3
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 12(5Q35.2) MUTATED                                                6
  DEL PEAK 12(5Q35.2) WILD-TYPE                                             19
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 12(5Q35.2) MUTATED                                                                                  21
  DEL PEAK 12(5Q35.2) WILD-TYPE                                                                                61
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 12(5Q35.2) MUTATED                                                                                             31
  DEL PEAK 12(5Q35.2) WILD-TYPE                                                                                           90
D38V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 12(5Q35.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          31
                                                                                              clus
vv                                                                                             DEL PEAK 12(5Q35.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          19
  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)                            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"
D38V28, binary
                               cls
clus                             0  1
  DEL PEAK 12(5Q35.2) MUTATED   14 23
  DEL PEAK 12(5Q35.2) WILD-TYPE 57 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED     14   23
  DEL PEAK 12(5Q35.2) WILD-TYPE   57   51
         clus
vv        DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  ABSENT                           14                            57
  PRESENT                          23                            51
[1] 2 2
[1] FALSE
D38V29, continuous
D38V30, continuous
D38V31, binary
                               cls
clus                             0  1
  DEL PEAK 12(5Q35.2) MUTATED   10 37
  DEL PEAK 12(5Q35.2) WILD-TYPE 39 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED     10   37
  DEL PEAK 12(5Q35.2) WILD-TYPE   39   80
                                          clus
vv                                         DEL PEAK 12(5Q35.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          37
                                          clus
vv                                         DEL PEAK 12(5Q35.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            80
[1] 2 2
[1] FALSE
D38V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 12(5Q35.2) MUTATED              3          15         20
  DEL PEAK 12(5Q35.2) WILD-TYPE           12          39         65
D38V33, multiclass
              clus
vv             DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           15                            39
  NEVER USED                            20                            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"
D38V34, continuous
D38V35, binary
                               cls
clus                             0  1
  DEL PEAK 12(5Q35.2) MUTATED   25  4
  DEL PEAK 12(5Q35.2) WILD-TYPE 67 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q35.2) MUTATED     25    4
  DEL PEAK 12(5Q35.2) WILD-TYPE   67   14
         clus
vv        DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  ABSENT                           25                            67
  PRESENT                           4                            14
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 12(5Q35.2) MUTATED             0        24     1
  DEL PEAK 12(5Q35.2) WILD-TYPE           5        76     1
D38V36, multiclass
             clus
vv            DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  CARBOPLATIN                           0                             5
  CISPLATIN                            24                            76
  OTHER                                 1                             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"
D38V37, continuous
D38V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 12(5Q35.2) MUTATED         2        1         0         1        9
  DEL PEAK 12(5Q35.2) WILD-TYPE       3        0         1         0       25
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 12(5Q35.2) MUTATED          19        10        1         1
  DEL PEAK 12(5Q35.2) WILD-TYPE        58        27        3         7
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 12(5Q35.2) MUTATED            2          0        11         0
  DEL PEAK 12(5Q35.2) WILD-TYPE          3          7        33         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 12(5Q35.2) MUTATED            1         10         1         0
  DEL PEAK 12(5Q35.2) WILD-TYPE          2         32         6        12
D38V39, multiclass
            clus
vv           DEL PEAK 12(5Q35.2) MUTATED DEL PEAK 12(5Q35.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             9                            25
  STAGE IB1                           19                            58
  STAGE IB2                           10                            27
  STAGE II                             1                             3
  STAGE IIA                            1                             7
  STAGE IIA1                           2                             3
  STAGE IIA2                           0                             7
  STAGE IIB                           11                            33
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          10                            32
  STAGE IVA                            1                             6
  STAGE IVB                            0                            12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK 13(6P24.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(6P24.2) MUTATED    32  12
  DEL PEAK 13(6P24.2) WILD-TYPE 182  56
  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE 
                           44                           238 
  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE 
                           12                            56 
$`DEL PEAK 13(6P24.2) MUTATED`
TCGA-4J-AA1J TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7CO 
       17.82        19.86        30.21        73.18       210.67       147.35 
TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KK 
        9.34        45.83        23.51        27.52         1.12        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3QE 
       44.94        63.98        36.76       117.99        22.98        25.02 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2PI TCGA-EK-A2RC 
       12.13        14.89        27.22        24.00        19.27         4.24 
TCGA-EK-A2RN TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-HG-A2PA TCGA-IR-A3L7 TCGA-JW-A5VJ 
        2.33         7.92        31.36        25.41       147.39        21.44 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-UC-A7PF 
       21.11        20.91        19.56         9.17         8.52        93.99 
TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A9UU TCGA-VS-A9UY 
       12.16        65.49         4.73        55.50        14.53        18.25 
TCGA-VS-A9V3 TCGA-ZX-AA5X 
       17.75         3.91 

$`DEL PEAK 13(6P24.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
        0.69        17.52        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 
       82.85         5.46        67.46        31.40        46.32        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       57.73        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-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-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
       20.35        17.19       155.77       131.11        94.95        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ 
        2.73        50.99         8.35        99.91        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VN 
       14.73        95.11        87.75        58.88        55.63       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 
       37.35        30.90        31.53        31.36        13.05        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        31.73        26.01        24.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N 
       26.79        25.91        27.29        27.25        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL 
       60.72        26.27         6.64         1.51         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         1.87         1.74         0.43        47.77         1.64 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 
        0.07         0.10         0.49         0.89        20.35        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79        15.55        12.23        23.84        19.04        16.11 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26        20.98        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44        10.55         1.12        17.75        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93         9.44       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       18.15       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        20.28        17.82 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       20.84        17.23         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI 
       18.64        22.62        19.59        14.60        11.67        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        46.52        45.57        32.42        23.97        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       31.27        40.87        16.64        33.37        40.14        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       15.68        56.35        50.14        51.32        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       48.39        28.50        29.95        27.12        24.30        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       45.11         1.71        14.53        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 
       41.52        26.07        15.85         3.42        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
        5.16        18.25        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       67.59        19.13         1.41         0.16 

  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE 
                         1.12                          0.07 
  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE 
                       210.67                        209.59 
  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE 
                        22.21                         22.57 
[1] "1.1 - 210.7 (22.2)" "0.1 - 209.6 (22.6)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 13(6P24.2) MUTATED    25  10   2   1
  DEL PEAK 13(6P24.2) WILD-TYPE 110  60  19   7
D39V3, multiclass
    clus
vv   DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  T1                          25                           110
  T2                          10                            60
  T3                           2                            19
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                               cls
clus                              0   1
  DEL PEAK 13(6P24.2) MUTATED    18  12
  DEL PEAK 13(6P24.2) WILD-TYPE 111  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED     18   12
  DEL PEAK 13(6P24.2) WILD-TYPE  111   44
   clus
vv  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  0                          18                           111
  1                          12                            44
[1] 2 2
[1] FALSE
D39V5, binary
                               cls
clus                             0  1
  DEL PEAK 13(6P24.2) MUTATED   24  1
  DEL PEAK 13(6P24.2) WILD-TYPE 84  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED     24    1
  DEL PEAK 13(6P24.2) WILD-TYPE   84    9
   clus
vv  DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  0                          24                            84
  1                           1                             9
[1] 2 2
[1] FALSE
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(6P24.2) MUTATED     9  19
  DEL PEAK 13(6P24.2) WILD-TYPE  44 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED      9   19
  DEL PEAK 13(6P24.2) WILD-TYPE   44  106
     clus
vv    DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  NO                            9                            44
  YES                          19                           106
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(6P24.2) MUTATED               1                               43
  DEL PEAK 13(6P24.2) WILD-TYPE             5                              199
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 13(6P24.2) MUTATED                                               0
  DEL PEAK 13(6P24.2) WILD-TYPE                                             6
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 13(6P24.2) MUTATED                                     1
  DEL PEAK 13(6P24.2) WILD-TYPE                                  20
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 13(6P24.2) MUTATED                                           1
  DEL PEAK 13(6P24.2) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 13(6P24.2) MUTATED                                              0
  DEL PEAK 13(6P24.2) WILD-TYPE                                           17
D39V7, multiclass
                                               clus
vv                                              DEL PEAK 13(6P24.2) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       43
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            0
                                               clus
vv                                              DEL PEAK 13(6P24.2) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        199
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, continuous
D39V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6P24.2) MUTATED                                  1     2
  DEL PEAK 13(6P24.2) WILD-TYPE                                7    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(6P24.2) MUTATED                           1
  DEL PEAK 13(6P24.2) WILD-TYPE                        27
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(6P24.2) MUTATED                                           0    31
  DEL PEAK 13(6P24.2) WILD-TYPE                                         2   171
D39V10, multiclass
                                           clus
vv                                          DEL PEAK 13(6P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              31
                                           clus
vv                                          DEL PEAK 13(6P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                               171
[1] 5 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 13(6P24.2) MUTATED     4  22
  DEL PEAK 13(6P24.2) WILD-TYPE  19 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED      4   22
  DEL PEAK 13(6P24.2) WILD-TYPE   19  141
                        clus
vv                       DEL PEAK 13(6P24.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       DEL PEAK 13(6P24.2) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           141
[1] 2 2
[1] FALSE
D39V12, continuous
D39V13, binary
                               cls
clus                              0   1
  DEL PEAK 13(6P24.2) MUTATED    27  14
  DEL PEAK 13(6P24.2) WILD-TYPE 166  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED     27   14
  DEL PEAK 13(6P24.2) WILD-TYPE  166   62
            clus
vv           DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  TUMOR FREE                          27                           166
  WITH TUMOR                          14                            62
[1] 2 2
[1] FALSE
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK 13(6P24.2) MUTATED     4  19  18   0   3
  DEL PEAK 13(6P24.2) WILD-TYPE  14 110  97   1  21
D39V14, multiclass
    clus
vv   DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  G1                           4                            14
  G2                          19                           110
  G3                          18                            97
  G4                           0                             1
  GX                           3                            21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, continuous
D39V16, continuous
D39V17, continuous
D39V18, continuous
D39V19, binary
                               cls
clus                             0  1
  DEL PEAK 13(6P24.2) MUTATED    3  0
  DEL PEAK 13(6P24.2) WILD-TYPE 22  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED      3    0
  DEL PEAK 13(6P24.2) WILD-TYPE   22    3
                         clus
vv                        DEL PEAK 13(6P24.2) MUTATED
  COMPLETED AS PLANNED                              3
  TREATMENT NOT COMPLETED                           0
                         clus
vv                        DEL PEAK 13(6P24.2) WILD-TYPE
  COMPLETED AS PLANNED                               22
  TREATMENT NOT COMPLETED                             3
[1] 2 2
[1] FALSE
D39V20, continuous
D39V21, continuous
D39V22, continuous
D39V23, continuous
D39V24, continuous
D39V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 13(6P24.2) MUTATED                                     0
  DEL PEAK 13(6P24.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 13(6P24.2) MUTATED                                     0
  DEL PEAK 13(6P24.2) WILD-TYPE                                   7
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 13(6P24.2) MUTATED                         8                       0
  DEL PEAK 13(6P24.2) WILD-TYPE                      28                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 13(6P24.2) MUTATED                         3
  DEL PEAK 13(6P24.2) WILD-TYPE                       7
D39V26, multiclass
                                     clus
vv                                    DEL PEAK 13(6P24.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       8
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    DEL PEAK 13(6P24.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             7
  OTHER LOCATION, SPECIFY                                        28
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 13(6P24.2) MUTATED                                               1
  DEL PEAK 13(6P24.2) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 13(6P24.2) MUTATED                                                2
  DEL PEAK 13(6P24.2) WILD-TYPE                                             23
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 13(6P24.2) MUTATED                                                                                  11
  DEL PEAK 13(6P24.2) WILD-TYPE                                                                                71
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 13(6P24.2) MUTATED                                                                                             21
  DEL PEAK 13(6P24.2) WILD-TYPE                                                                                          100
D39V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 13(6P24.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          21
                                                                                              clus
vv                                                                                             DEL PEAK 13(6P24.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       71
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V28, binary
                               cls
clus                             0  1
  DEL PEAK 13(6P24.2) MUTATED   10 15
  DEL PEAK 13(6P24.2) WILD-TYPE 61 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED     10   15
  DEL PEAK 13(6P24.2) WILD-TYPE   61   59
         clus
vv        DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  ABSENT                           10                            61
  PRESENT                          15                            59
[1] 2 2
[1] FALSE
D39V29, continuous
D39V30, continuous
D39V31, binary
                               cls
clus                             0  1
  DEL PEAK 13(6P24.2) MUTATED   10 19
  DEL PEAK 13(6P24.2) WILD-TYPE 39 98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED     10   19
  DEL PEAK 13(6P24.2) WILD-TYPE   39   98
                                          clus
vv                                         DEL PEAK 13(6P24.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          19
                                          clus
vv                                         DEL PEAK 13(6P24.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            98
[1] 2 2
[1] FALSE
D39V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 13(6P24.2) MUTATED              4          10         12
  DEL PEAK 13(6P24.2) WILD-TYPE           11          44         73
D39V33, multiclass
              clus
vv             DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  CURRENT USER                           4                            11
  FORMER USER                           10                            44
  NEVER USED                            12                            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"
D39V34, continuous
D39V35, binary
                               cls
clus                             0  1
  DEL PEAK 13(6P24.2) MUTATED   18  2
  DEL PEAK 13(6P24.2) WILD-TYPE 74 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6P24.2) MUTATED     18    2
  DEL PEAK 13(6P24.2) WILD-TYPE   74   16
         clus
vv        DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  ABSENT                           18                            74
  PRESENT                           2                            16
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 13(6P24.2) MUTATED             0        18     0
  DEL PEAK 13(6P24.2) WILD-TYPE           5        82     2
D39V36, multiclass
             clus
vv            DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  CARBOPLATIN                           0                             5
  CISPLATIN                            18                            82
  OTHER                                 0                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V37, continuous
D39V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 13(6P24.2) MUTATED         0        0         0         0        7
  DEL PEAK 13(6P24.2) WILD-TYPE       5        1         1         1       27
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 13(6P24.2) MUTATED          14         5        0         1
  DEL PEAK 13(6P24.2) WILD-TYPE        63        32        4         7
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 13(6P24.2) MUTATED            0          0         7         0
  DEL PEAK 13(6P24.2) WILD-TYPE          5          7        37         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 13(6P24.2) MUTATED            0          9         0         2
  DEL PEAK 13(6P24.2) WILD-TYPE          3         33         7        10
D39V39, multiclass
            clus
vv           DEL PEAK 13(6P24.2) MUTATED DEL PEAK 13(6P24.2) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IA1                            0                             1
  STAGE IA2                            0                             1
  STAGE IB                             7                            27
  STAGE IB1                           14                            63
  STAGE IB2                            5                            32
  STAGE II                             0                             4
  STAGE IIA                            1                             7
  STAGE IIA1                           0                             5
  STAGE IIA2                           0                             7
  STAGE IIB                            7                            37
  STAGE III                            0                             1
  STAGE IIIA                           0                             3
  STAGE IIIB                           9                            33
  STAGE IVA                            0                             7
  STAGE IVB                            2                            10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = DEL PEAK 14(6Q26) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(6Q26) MUTATED    74  18
  DEL PEAK 14(6Q26) WILD-TYPE 140  50
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                         92                         190 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                         18                          50 
$`DEL PEAK 14(6Q26) MUTATED`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BI 
       12.59        14.70        17.82        49.48        23.67        36.56 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
      173.29        82.85        67.46        30.21        35.01        57.73 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF 
       73.18        73.45       100.14        38.43        52.01        17.85 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      210.67       154.32       147.35       131.11        94.95         9.34 
TCGA-C5-A7XC TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ 
       50.99        99.91        23.51        27.52         1.12        95.11 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VM TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A439 
       44.94        63.98       117.99        40.87        25.02        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2PG 
       26.01        12.13        14.89        27.22        24.00         1.51 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RB TCGA-EK-A2RC 
       19.27         0.39         0.43         0.59         0.30         4.24 
TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A8YF 
        0.43         1.64         2.33         0.10         7.92        15.55 
TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-HM-A3JK 
       23.84        31.36        28.31        14.01        35.44        20.78 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A5QV 
      147.39       129.37        78.71        21.44        21.11        20.91 
TCGA-LP-A4AX TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       12.49         8.52        34.62        17.23        16.41         9.04 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EJ TCGA-VS-A8EL 
       19.59        11.67        12.16        10.03        19.96        65.49 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 
       11.51        59.18         4.73        40.14        55.50        51.32 
TCGA-VS-A9U5 TCGA-VS-A9UC TCGA-VS-A9UU TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 
       50.47        27.12        14.53        18.84        18.25        17.75 
TCGA-XS-A8TJ TCGA-ZJ-A8QR 
       29.26        19.13 

$`DEL PEAK 14(6Q26) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86         8.32         1.48         4.34         0.69        17.52 
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK 
       57.04        11.44        68.84        18.74       144.16       177.04 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH 
        5.46        19.86        31.40        46.32        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL 
       44.22        83.05        78.35        33.24        18.02        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48        20.35        17.19       155.77 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YT TCGA-C5-A8ZZ 
       13.61         2.73        45.83         8.35        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       14.73        82.06        87.75        58.88        36.76        55.63 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       36.89        26.40        24.56        24.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 
       25.91        27.29        27.25        13.48         0.36        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
       26.27         6.64         0.89         1.45         0.13        40.96 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK 
        0.07         1.87         1.74        47.77         0.07         0.49 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG 
        0.89        20.35        15.22        19.79        12.23        19.04 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A5XV 
       16.11        36.26        20.98        26.14        16.14        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 
        1.12        17.75        25.41        16.57        21.67        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
        9.44       137.16        66.81        96.95        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
       28.37         8.28        18.15       209.59        44.61        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89         0.30         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A8JM 
       17.82        19.56         9.17        11.38        28.08        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       54.81        35.05        20.84         2.96        15.58        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
       22.62        14.60        93.99        69.50        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH 
       32.42        23.97        32.15        53.59        36.13        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 
       31.27        40.87        16.64        33.37        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       56.35        50.14        43.40        48.39        28.50        29.95 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV 
       47.87        47.47        41.52        26.07        15.85         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
       18.25        67.20         5.16        16.24        15.42        26.01 
TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59         1.41         0.16         3.91 

  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                     210.67                      209.59 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                     23.920                      20.945 
[1] "0.1 - 210.7 (23.9)" "0.1 - 209.6 (20.9)"
[1] "hr=" "1.6"
D40V2, continuous
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK 14(6Q26) MUTATED   43 22  6  1
  DEL PEAK 14(6Q26) WILD-TYPE 92 48 15  7
D40V3, multiclass
    clus
vv   DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  T1                        43                          92
  T2                        22                          48
  T3                         6                          15
  T4                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                             cls
clus                           0  1
  DEL PEAK 14(6Q26) MUTATED   38 19
  DEL PEAK 14(6Q26) WILD-TYPE 91 37
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     38   19
  DEL PEAK 14(6Q26) WILD-TYPE   91   37
   clus
vv  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  0                        38                          91
  1                        19                          37
[1] 2 2
[1] FALSE
D40V5, binary
                             cls
clus                           0  1
  DEL PEAK 14(6Q26) MUTATED   39  4
  DEL PEAK 14(6Q26) WILD-TYPE 69  6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     39    4
  DEL PEAK 14(6Q26) WILD-TYPE   69    6
   clus
vv  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  0                        39                          69
  1                         4                           6
[1] 2 2
[1] FALSE
D40V6, binary
                             cls
clus                           0  1
  DEL PEAK 14(6Q26) MUTATED   16 38
  DEL PEAK 14(6Q26) WILD-TYPE 37 87
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     16   38
  DEL PEAK 14(6Q26) WILD-TYPE   37   87
     clus
vv    DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  NO                         16                          37
  YES                        38                          87
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(6Q26) MUTATED               1                               87
  DEL PEAK 14(6Q26) WILD-TYPE             5                              155
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 14(6Q26) MUTATED                                               1
  DEL PEAK 14(6Q26) WILD-TYPE                                             5
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                     8
  DEL PEAK 14(6Q26) WILD-TYPE                                  13
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 14(6Q26) MUTATED                                           1
  DEL PEAK 14(6Q26) WILD-TYPE                                         2
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 14(6Q26) MUTATED                                              2
  DEL PEAK 14(6Q26) WILD-TYPE                                           15
D40V7, multiclass
                                               clus
vv                                              DEL PEAK 14(6Q26) MUTATED
  ADENOSQUAMOUS                                                         1
  CERVICAL SQUAMOUS CELL CARCINOMA                                     87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          2
                                               clus
vv                                              DEL PEAK 14(6Q26) WILD-TYPE
  ADENOSQUAMOUS                                                           5
  CERVICAL SQUAMOUS CELL CARCINOMA                                      155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, continuous
D40V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(6Q26) MUTATED                                  2     4
  DEL PEAK 14(6Q26) WILD-TYPE                                6    15
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(6Q26) MUTATED                          11
  DEL PEAK 14(6Q26) WILD-TYPE                        17
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(6Q26) MUTATED                                           2    68
  DEL PEAK 14(6Q26) WILD-TYPE                                         0   134
D40V10, multiclass
                                           clus
vv                                          DEL PEAK 14(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             4
  BLACK OR AFRICAN AMERICAN                                        11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            68
                                           clus
vv                                          DEL PEAK 14(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                          17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  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"
D40V11, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED     5  56
  DEL PEAK 14(6Q26) WILD-TYPE  18 107
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED      5   56
  DEL PEAK 14(6Q26) WILD-TYPE   18  107
                        clus
vv                       DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             5                          18
  NOT HISPANIC OR LATINO                        56                         107
[1] 2 2
[1] FALSE
D40V12, continuous
D40V13, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED    60  27
  DEL PEAK 14(6Q26) WILD-TYPE 133  49
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     60   27
  DEL PEAK 14(6Q26) WILD-TYPE  133   49
            clus
vv           DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  TUMOR FREE                        60                         133
  WITH TUMOR                        27                          49
[1] 2 2
[1] FALSE
                             vv
clus                          G1 G2 G3 G4 GX
  DEL PEAK 14(6Q26) MUTATED    7 36 46  1  5
  DEL PEAK 14(6Q26) WILD-TYPE 11 93 69  0 19
D40V14, multiclass
    clus
vv   DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  G1                         7                          11
  G2                        36                          93
  G3                        46                          69
  G4                         1                           0
  GX                         5                          19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, continuous
D40V16, continuous
D40V17, continuous
D40V18, continuous
D40V19, binary
                             cls
clus                           0  1
  DEL PEAK 14(6Q26) MUTATED    8  0
  DEL PEAK 14(6Q26) WILD-TYPE 17  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED      8    0
  DEL PEAK 14(6Q26) WILD-TYPE   17    3
                         clus
vv                        DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  COMPLETED AS PLANNED                            8                          17
  TREATMENT NOT COMPLETED                         0                           3
[1] 2 2
[1] FALSE
D40V20, continuous
D40V21, continuous
D40V22, continuous
D40V23, continuous
D40V24, continuous
D40V25, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 14(6Q26) MUTATED                                     1
  DEL PEAK 14(6Q26) WILD-TYPE                                   1
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 14(6Q26) MUTATED                                     1
  DEL PEAK 14(6Q26) WILD-TYPE                                   6
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 14(6Q26) MUTATED                        14                       0
  DEL PEAK 14(6Q26) WILD-TYPE                      22                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  DEL PEAK 14(6Q26) MUTATED                         5
  DEL PEAK 14(6Q26) WILD-TYPE                       5
D40V26, multiclass
                                     clus
vv                                    DEL PEAK 14(6Q26) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  OTHER LOCATION, SPECIFY                                    14
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     5
                                     clus
vv                                    DEL PEAK 14(6Q26) 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)
  DEL PEAK 14(6Q26) MUTATED                                               3
  DEL PEAK 14(6Q26) WILD-TYPE                                             0
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 14(6Q26) MUTATED                                                8
  DEL PEAK 14(6Q26) WILD-TYPE                                             17
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 14(6Q26) MUTATED                                                                                  24
  DEL PEAK 14(6Q26) WILD-TYPE                                                                                58
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 14(6Q26) MUTATED                                                                                             39
  DEL PEAK 14(6Q26) WILD-TYPE                                                                                           82
D40V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 14(6Q26) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   24
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        39
                                                                                              clus
vv                                                                                             DEL PEAK 14(6Q26) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     58
  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"
D40V28, binary
                             cls
clus                           0  1
  DEL PEAK 14(6Q26) MUTATED   21 25
  DEL PEAK 14(6Q26) WILD-TYPE 50 49
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     21   25
  DEL PEAK 14(6Q26) WILD-TYPE   50   49
         clus
vv        DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  ABSENT                         21                          50
  PRESENT                        25                          49
[1] 2 2
[1] FALSE
D40V29, continuous
D40V30, continuous
D40V31, binary
                             cls
clus                           0  1
  DEL PEAK 14(6Q26) MUTATED   16 36
  DEL PEAK 14(6Q26) WILD-TYPE 33 81
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     16   36
  DEL PEAK 14(6Q26) WILD-TYPE   33   81
                                          clus
vv                                         DEL PEAK 14(6Q26) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        36
                                          clus
vv                                         DEL PEAK 14(6Q26) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          81
[1] 2 2
[1] FALSE
D40V32, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  DEL PEAK 14(6Q26) MUTATED              5          19         24
  DEL PEAK 14(6Q26) WILD-TYPE           10          35         61
D40V33, multiclass
              clus
vv             DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  CURRENT USER                         5                          10
  FORMER USER                         19                          35
  NEVER USED                          24                          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"
D40V34, continuous
D40V35, binary
                             cls
clus                           0  1
  DEL PEAK 14(6Q26) MUTATED   33  5
  DEL PEAK 14(6Q26) WILD-TYPE 59 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     33    5
  DEL PEAK 14(6Q26) WILD-TYPE   59   13
         clus
vv        DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  ABSENT                         33                          59
  PRESENT                         5                          13
[1] 2 2
[1] FALSE
                             vv
clus                          CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 14(6Q26) MUTATED             0        28     0
  DEL PEAK 14(6Q26) WILD-TYPE           5        72     2
D40V36, multiclass
             clus
vv            DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  CARBOPLATIN                         0                           5
  CISPLATIN                          28                          72
  OTHER                               0                           2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V37, continuous
D40V38, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 14(6Q26) MUTATED         2        0         1         1       15
  DEL PEAK 14(6Q26) WILD-TYPE       3        1         0         0       19
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  DEL PEAK 14(6Q26) MUTATED          27         7        0         3          3
  DEL PEAK 14(6Q26) WILD-TYPE        50        30        4         5          2
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  DEL PEAK 14(6Q26) MUTATED            1        15         0          1
  DEL PEAK 14(6Q26) WILD-TYPE          6        29         1          2
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 14(6Q26) MUTATED           16         1         3
  DEL PEAK 14(6Q26) WILD-TYPE         26         6         9
D40V39, multiclass
            clus
vv           DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  STAGE I                            2                           3
  STAGE IA                           0                           1
  STAGE IA1                          1                           0
  STAGE IA2                          1                           0
  STAGE IB                          15                          19
  STAGE IB1                         27                          50
  STAGE IB2                          7                          30
  STAGE II                           0                           4
  STAGE IIA                          3                           5
  STAGE IIA1                         3                           2
  STAGE IIA2                         1                           6
  STAGE IIB                         15                          29
  STAGE III                          0                           1
  STAGE IIIA                         1                           2
  STAGE IIIB                        16                          26
  STAGE IVA                          1                           6
  STAGE IVB                          3                           9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 15(7Q34) MUTATION ANALYSIS
D41V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 15(7Q34) MUTATED    40  19
  DEL PEAK 15(7Q34) WILD-TYPE 174  49
  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE 
                         59                         223 
  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE 
                         19                          49 
$`DEL PEAK 15(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 
       95.11        17.52        39.55        31.36        31.73        27.22 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2RD TCGA-EK-A2RE 
       13.48         0.36        60.72        26.27         0.07         1.87 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A40J TCGA-FU-A5XV 
        1.64         0.49        20.35        19.04        14.01        10.55 
TCGA-HM-A3JJ TCGA-JW-A5VG TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MU-A51Y 
       21.67        27.42        44.61        13.35        22.52        28.08 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-RA-A741 TCGA-UC-A7PF 
       20.84        17.23        16.41         9.04        14.60        93.99 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A957 TCGA-VS-A9U7 TCGA-VS-A9UL 
       32.42        23.97        32.15        55.50        48.39        14.53 
TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9UY TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       47.87        26.07        18.25        67.59         1.41 

$`DEL PEAK 15(7Q34) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A 
        0.69        17.52        17.82        49.48        57.04        23.67 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       19.86        46.32        30.21        57.73        53.16         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY 
        2.43        20.91         3.58        44.22        73.18        78.35 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43        33.24        18.02        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      101.82       134.33       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK 
       94.95         9.34         2.73        50.99         8.35        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       55.63       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD 
        8.28        40.87        37.35        30.90        31.53        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S 
       25.02        36.89        26.40        24.56        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       27.25        24.00         6.64         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.89         1.45         0.13        40.96 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
        0.30         4.24         1.74         0.43        47.77         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L 
        0.07         0.10         0.89         7.92        15.22        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55        12.23        23.84        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 
       20.98        26.14        16.14        28.31        35.44         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       17.75        25.41        16.57        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       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        29.85        36.36         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
      209.59        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
        0.82        20.28        17.82        19.56         9.17         8.52 
TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA 
       11.38        34.62        19.96        54.81        35.05         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG 
        9.34        18.64        22.62        19.59        11.67        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL 
       69.50        10.03        46.52        45.57        19.96        65.49 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       53.59        36.13        11.51        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       40.87        16.64         4.73        33.37        40.14        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       15.68        56.35        50.14        51.32        50.47        43.40 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       28.50        29.95        27.12        24.30        46.92        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU 
        1.71        27.25        47.47        41.52        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
        3.42        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       16.24        15.42        26.01        29.26        19.13         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE 
                     154.32                      210.67 
  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE 
                      26.27                       20.98 
[1] "0.1 - 154.3 (26.3)" "0.1 - 210.7 (21.0)"
[1] "hr=" "1.4"
D41V2, continuous
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 15(7Q34) MUTATED    28  11   4   0
  DEL PEAK 15(7Q34) WILD-TYPE 107  59  17   8
D41V3, multiclass
    clus
vv   DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  T1                        28                         107
  T2                        11                          59
  T3                         4                          17
  T4                         0                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                             cls
clus                            0   1
  DEL PEAK 15(7Q34) MUTATED    21  14
  DEL PEAK 15(7Q34) WILD-TYPE 108  42
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED     21   14
  DEL PEAK 15(7Q34) WILD-TYPE  108   42
   clus
vv  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  0                        21                         108
  1                        14                          42
[1] 2 2
[1] FALSE
D41V5, binary
                             cls
clus                           0  1
  DEL PEAK 15(7Q34) MUTATED   18  1
  DEL PEAK 15(7Q34) WILD-TYPE 90  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED     18    1
  DEL PEAK 15(7Q34) WILD-TYPE   90    9
   clus
vv  DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  0                        18                          90
  1                         1                           9
[1] 2 2
[1] FALSE
D41V6, binary
                             cls
clus                            0   1
  DEL PEAK 15(7Q34) MUTATED     9  25
  DEL PEAK 15(7Q34) WILD-TYPE  44 100
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED      9   25
  DEL PEAK 15(7Q34) WILD-TYPE   44  100
     clus
vv    DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  NO                          9                          44
  YES                        25                         100
[1] 2 2
[1] FALSE
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(7Q34) MUTATED               0                               50
  DEL PEAK 15(7Q34) WILD-TYPE             6                              192
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 15(7Q34) MUTATED                                               2
  DEL PEAK 15(7Q34) WILD-TYPE                                             4
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 15(7Q34) MUTATED                                     5
  DEL PEAK 15(7Q34) WILD-TYPE                                  16
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 15(7Q34) MUTATED                                           0
  DEL PEAK 15(7Q34) WILD-TYPE                                         3
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 15(7Q34) MUTATED                                              3
  DEL PEAK 15(7Q34) WILD-TYPE                                           14
D41V7, multiclass
                                               clus
vv                                              DEL PEAK 15(7Q34) MUTATED
  ADENOSQUAMOUS                                                         0
  CERVICAL SQUAMOUS CELL CARCINOMA                                     50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          3
                                               clus
vv                                              DEL PEAK 15(7Q34) WILD-TYPE
  ADENOSQUAMOUS                                                           6
  CERVICAL SQUAMOUS CELL CARCINOMA                                      192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, continuous
D41V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(7Q34) MUTATED                                  2     5
  DEL PEAK 15(7Q34) WILD-TYPE                                6    14
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(7Q34) MUTATED                           6
  DEL PEAK 15(7Q34) WILD-TYPE                        22
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(7Q34) MUTATED                                           0    43
  DEL PEAK 15(7Q34) WILD-TYPE                                         2   159
D41V10, multiclass
                                           clus
vv                                          DEL PEAK 15(7Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                         6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            43
                                           clus
vv                                          DEL PEAK 15(7Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    6
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                          22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                             159
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                             cls
clus                            0   1
  DEL PEAK 15(7Q34) MUTATED     4  39
  DEL PEAK 15(7Q34) WILD-TYPE  19 124
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED      4   39
  DEL PEAK 15(7Q34) WILD-TYPE   19  124
                        clus
vv                       DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             4                          19
  NOT HISPANIC OR LATINO                        39                         124
[1] 2 2
[1] FALSE
D41V12, continuous
D41V13, binary
                             cls
clus                            0   1
  DEL PEAK 15(7Q34) MUTATED    38  19
  DEL PEAK 15(7Q34) WILD-TYPE 155  57
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED     38   19
  DEL PEAK 15(7Q34) WILD-TYPE  155   57
            clus
vv           DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  TUMOR FREE                        38                         155
  WITH TUMOR                        19                          57
[1] 2 2
[1] FALSE
                             vv
clus                           G1  G2  G3  G4  GX
  DEL PEAK 15(7Q34) MUTATED     2  25  27   0   5
  DEL PEAK 15(7Q34) WILD-TYPE  16 104  88   1  19
D41V14, multiclass
    clus
vv   DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  G1                         2                          16
  G2                        25                         104
  G3                        27                          88
  G4                         0                           1
  GX                         5                          19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, continuous
D41V16, continuous
D41V17, continuous
D41V18, continuous
D41V19, binary
                             cls
clus                           0  1
  DEL PEAK 15(7Q34) MUTATED   11  2
  DEL PEAK 15(7Q34) WILD-TYPE 14  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED     11    2
  DEL PEAK 15(7Q34) WILD-TYPE   14    1
                         clus
vv                        DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  COMPLETED AS PLANNED                           11                          14
  TREATMENT NOT COMPLETED                         2                           1
[1] 2 2
[1] FALSE
D41V20, continuous
D41V21, continuous
D41V22, continuous
D41V23, continuous
D41V24, continuous
D41V25, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 15(7Q34) MUTATED                                     0
  DEL PEAK 15(7Q34) WILD-TYPE                                   2
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 15(7Q34) MUTATED                                     2
  DEL PEAK 15(7Q34) WILD-TYPE                                   5
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 15(7Q34) MUTATED                         6                       0
  DEL PEAK 15(7Q34) WILD-TYPE                      30                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  DEL PEAK 15(7Q34) MUTATED                         1
  DEL PEAK 15(7Q34) WILD-TYPE                       9
D41V26, multiclass
                                     clus
vv                                    DEL PEAK 15(7Q34) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         2
  OTHER LOCATION, SPECIFY                                     6
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     1
                                     clus
vv                                    DEL PEAK 15(7Q34) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           5
  OTHER LOCATION, SPECIFY                                      30
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 15(7Q34) MUTATED                                               1
  DEL PEAK 15(7Q34) WILD-TYPE                                             2
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 15(7Q34) MUTATED                                                6
  DEL PEAK 15(7Q34) WILD-TYPE                                             19
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 15(7Q34) MUTATED                                                                                  17
  DEL PEAK 15(7Q34) WILD-TYPE                                                                                65
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 15(7Q34) MUTATED                                                                                             23
  DEL PEAK 15(7Q34) WILD-TYPE                                                                                           98
D41V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 15(7Q34) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        23
                                                                                              clus
vv                                                                                             DEL PEAK 15(7Q34) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V28, binary
                             cls
clus                           0  1
  DEL PEAK 15(7Q34) MUTATED   11 18
  DEL PEAK 15(7Q34) WILD-TYPE 60 56
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED     11   18
  DEL PEAK 15(7Q34) WILD-TYPE   60   56
         clus
vv        DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  ABSENT                         11                          60
  PRESENT                        18                          56
[1] 2 2
[1] FALSE
D41V29, continuous
D41V30, continuous
D41V31, binary
                             cls
clus                           0  1
  DEL PEAK 15(7Q34) MUTATED   13 24
  DEL PEAK 15(7Q34) WILD-TYPE 36 93
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED     13   24
  DEL PEAK 15(7Q34) WILD-TYPE   36   93
                                          clus
vv                                         DEL PEAK 15(7Q34) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        24
                                          clus
vv                                         DEL PEAK 15(7Q34) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          93
[1] 2 2
[1] FALSE
D41V32, continuous
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  DEL PEAK 15(7Q34) MUTATED              2          12         15
  DEL PEAK 15(7Q34) WILD-TYPE           13          42         70
D41V33, multiclass
              clus
vv             DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  CURRENT USER                         2                          13
  FORMER USER                         12                          42
  NEVER USED                          15                          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"
D41V34, continuous
D41V35, binary
                             cls
clus                           0  1
  DEL PEAK 15(7Q34) MUTATED   18  4
  DEL PEAK 15(7Q34) WILD-TYPE 74 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(7Q34) MUTATED     18    4
  DEL PEAK 15(7Q34) WILD-TYPE   74   14
         clus
vv        DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  ABSENT                         18                          74
  PRESENT                         4                          14
[1] 2 2
[1] FALSE
                             vv
clus                          CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 15(7Q34) MUTATED             1        27     1
  DEL PEAK 15(7Q34) WILD-TYPE           4        73     1
D41V36, multiclass
             clus
vv            DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  CARBOPLATIN                         1                           4
  CISPLATIN                          27                          73
  OTHER                               1                           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"
D41V37, continuous
D41V38, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 15(7Q34) MUTATED         1        0         0         0        5
  DEL PEAK 15(7Q34) WILD-TYPE       4        1         1         1       29
                             vv
clus                          STAGE IB1 STAGE IB2 STAGE II STAGE IIA STAGE IIA1
  DEL PEAK 15(7Q34) MUTATED          18         7        1         4          2
  DEL PEAK 15(7Q34) WILD-TYPE        59        30        3         4          3
                             vv
clus                          STAGE IIA2 STAGE IIB STAGE III STAGE IIIA
  DEL PEAK 15(7Q34) MUTATED            1         9         0          0
  DEL PEAK 15(7Q34) WILD-TYPE          6        35         1          3
                             vv
clus                          STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 15(7Q34) MUTATED            9         0         2
  DEL PEAK 15(7Q34) WILD-TYPE         33         7        10
D41V39, multiclass
            clus
vv           DEL PEAK 15(7Q34) MUTATED DEL PEAK 15(7Q34) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                           0                           1
  STAGE IA1                          0                           1
  STAGE IA2                          0                           1
  STAGE IB                           5                          29
  STAGE IB1                         18                          59
  STAGE IB2                          7                          30
  STAGE II                           1                           3
  STAGE IIA                          4                           4
  STAGE IIA1                         2                           3
  STAGE IIA2                         1                           6
  STAGE IIB                          9                          35
  STAGE III                          0                           1
  STAGE IIIA                         0                           3
  STAGE IIIB                         9                          33
  STAGE IVA                          0                           7
  STAGE IVB                          2                          10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 16(8P23.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(8P23.3) MUTATED    66  34
  DEL PEAK 16(8P23.3) WILD-TYPE 148  34
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                          100                           182 
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                           34                            34 
$`DEL PEAK 16(8P23.3) MUTATED`
TCGA-EK-A2GZ TCGA-EX-A69M TCGA-VS-A9V4 TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BN 
       12.59         8.32         4.34        57.04        68.84         5.46 
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-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY 
        2.43        20.91        40.93        73.18        73.45        78.35 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CK TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
       33.24        52.01       134.33       131.11        94.95        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A907 
        2.73        50.99        45.83        99.91        27.52        14.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WI TCGA-EA-A1QT 
        1.12        95.11        36.76       118.65         8.28        40.87 
TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EK-A2H0 
       30.90        31.73        26.01        12.13        14.89        60.72 
TCGA-EK-A2PI TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
       19.27         0.43         1.64         0.07         0.10         0.89 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A57G 
       15.22        12.23        23.84        20.98        16.14        35.44 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LA 
        1.12        17.75        25.41        21.67        14.93       137.16 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3Q8 TCGA-LP-A4AW 
       78.71        29.85        15.58         8.28        44.61         0.89 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A5YI 
        0.82        13.35        17.82         9.17         8.52        34.62 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V 
       17.23         2.96         9.04         9.34        22.62        19.59 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA 
       11.67        10.03        46.52        19.96        65.49        36.13 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A9UD TCGA-VS-A9UI 
       59.18        39.78         4.73        33.37        24.30        45.11 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UV TCGA-VS-A9UY 
       14.53        27.25        47.87        41.52         3.42        18.25 
TCGA-VS-A9V0 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       18.84        15.42        67.59         1.41 

$`DEL PEAK 16(8P23.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J 
      146.86        14.70         1.48         0.69        17.52        17.82 
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       210.67       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       155.77 
TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KK 
        9.34         8.35        23.51        20.81        20.91        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        63.98        87.75        58.88        55.63       117.99 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ 
       22.98        16.83        16.18        17.52        39.55        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.56        24.82         7.46        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 
       27.25        27.22        24.00        13.48         0.36        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51         0.39         0.43         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H5 
        1.87         1.74        47.77         2.33         0.49        20.35 
TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        7.92        19.79        15.55        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A9SC 
       36.26        26.14        28.31        14.01        10.55        16.57 
TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       20.78         9.44       147.39        66.81       129.37        96.95 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       20.48        28.37        18.15        21.11       209.59        20.91 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z 
       11.28        12.49         0.30        22.52        20.28        19.56 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       11.38        28.08        19.96        54.81        35.05        20.84 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       15.88        18.64        14.60        93.99        12.16        69.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC 
       45.57        32.42        23.97        32.15        53.59        11.51 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       31.27        40.87        16.64        40.14        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       56.35        55.50        50.14        51.32        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ 
       48.39        28.50        29.95        27.12        46.92         1.71 
TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V1 
       47.47        26.07        15.85        14.53        67.20         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
       18.25        17.75        16.24        26.01        29.26        19.13 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                       137.16                        210.67 
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                       22.145                        22.750 
[1] "0.1 - 137.2 (22.1)" "0.1 - 210.7 (22.8)"
[1] "hr=" "1.9"
D42V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 16(8P23.3) MUTATED   48 24  6  2
  DEL PEAK 16(8P23.3) WILD-TYPE 87 46 15  6
D42V3, multiclass
    clus
vv   DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  T1                          48                            87
  T2                          24                            46
  T3                           6                            15
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                               cls
clus                             0  1
  DEL PEAK 16(8P23.3) MUTATED   47 17
  DEL PEAK 16(8P23.3) WILD-TYPE 82 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     47   17
  DEL PEAK 16(8P23.3) WILD-TYPE   82   39
   clus
vv  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  0                          47                            82
  1                          17                            39
[1] 2 2
[1] FALSE
D42V5, binary
                               cls
clus                             0  1
  DEL PEAK 16(8P23.3) MUTATED   36  4
  DEL PEAK 16(8P23.3) WILD-TYPE 72  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     36    4
  DEL PEAK 16(8P23.3) WILD-TYPE   72    6
   clus
vv  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  0                          36                            72
  1                           4                             6
[1] 2 2
[1] FALSE
D42V6, binary
                               cls
clus                             0  1
  DEL PEAK 16(8P23.3) MUTATED   16 42
  DEL PEAK 16(8P23.3) WILD-TYPE 37 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     16   42
  DEL PEAK 16(8P23.3) WILD-TYPE   37   83
     clus
vv    DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  NO                           16                            37
  YES                          42                            83
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(8P23.3) MUTATED               2                               85
  DEL PEAK 16(8P23.3) WILD-TYPE             4                              157
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 16(8P23.3) MUTATED                                               2
  DEL PEAK 16(8P23.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 16(8P23.3) MUTATED                                     7
  DEL PEAK 16(8P23.3) WILD-TYPE                                  14
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 16(8P23.3) MUTATED                                           2
  DEL PEAK 16(8P23.3) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 16(8P23.3) MUTATED                                              6
  DEL PEAK 16(8P23.3) WILD-TYPE                                           11
D42V7, multiclass
                                               clus
vv                                              DEL PEAK 16(8P23.3) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       85
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
                                               clus
vv                                              DEL PEAK 16(8P23.3) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        157
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, continuous
D42V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(8P23.3) MUTATED                                  3     5
  DEL PEAK 16(8P23.3) WILD-TYPE                                5    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(8P23.3) MUTATED                          12
  DEL PEAK 16(8P23.3) WILD-TYPE                        16
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(8P23.3) MUTATED                                           1    75
  DEL PEAK 16(8P23.3) WILD-TYPE                                         1   127
D42V10, multiclass
                                           clus
vv                                          DEL PEAK 16(8P23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              75
                                           clus
vv                                          DEL PEAK 16(8P23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D42V11, binary
                               cls
clus                              0   1
  DEL PEAK 16(8P23.3) MUTATED     8  58
  DEL PEAK 16(8P23.3) WILD-TYPE  15 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED      8   58
  DEL PEAK 16(8P23.3) WILD-TYPE   15  105
                        clus
vv                       DEL PEAK 16(8P23.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       DEL PEAK 16(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           105
[1] 2 2
[1] FALSE
D42V12, continuous
D42V13, binary
                               cls
clus                              0   1
  DEL PEAK 16(8P23.3) MUTATED    61  34
  DEL PEAK 16(8P23.3) WILD-TYPE 132  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     61   34
  DEL PEAK 16(8P23.3) WILD-TYPE  132   42
            clus
vv           DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  TUMOR FREE                          61                           132
  WITH TUMOR                          34                            42
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 16(8P23.3) MUTATED    4 43 44  1  9
  DEL PEAK 16(8P23.3) WILD-TYPE 14 86 71  0 15
D42V14, multiclass
    clus
vv   DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  G1                           4                            14
  G2                          43                            86
  G3                          44                            71
  G4                           1                             0
  GX                           9                            15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, continuous
D42V16, continuous
D42V17, continuous
D42V18, continuous
D42V19, binary
                               cls
clus                             0  1
  DEL PEAK 16(8P23.3) MUTATED   12  2
  DEL PEAK 16(8P23.3) WILD-TYPE 13  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     12    2
  DEL PEAK 16(8P23.3) WILD-TYPE   13    1
                         clus
vv                        DEL PEAK 16(8P23.3) MUTATED
  COMPLETED AS PLANNED                             12
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK 16(8P23.3) WILD-TYPE
  COMPLETED AS PLANNED                               13
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
D42V20, continuous
D42V21, continuous
D42V22, continuous
D42V23, continuous
D42V24, continuous
D42V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 16(8P23.3) MUTATED                                     0
  DEL PEAK 16(8P23.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 16(8P23.3) MUTATED                                     1
  DEL PEAK 16(8P23.3) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 16(8P23.3) MUTATED                        15                       0
  DEL PEAK 16(8P23.3) WILD-TYPE                      21                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 16(8P23.3) MUTATED                         4
  DEL PEAK 16(8P23.3) WILD-TYPE                       6
D42V26, multiclass
                                     clus
vv                                    DEL PEAK 16(8P23.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                      15
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       4
                                     clus
vv                                    DEL PEAK 16(8P23.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  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 16(8P23.3) MUTATED                                               1
  DEL PEAK 16(8P23.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 16(8P23.3) MUTATED                                                8
  DEL PEAK 16(8P23.3) WILD-TYPE                                             17
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 16(8P23.3) MUTATED                                                                                  27
  DEL PEAK 16(8P23.3) WILD-TYPE                                                                                55
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 16(8P23.3) MUTATED                                                                                             45
  DEL PEAK 16(8P23.3) WILD-TYPE                                                                                           76
D42V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 16(8P23.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          45
                                                                                              clus
vv                                                                                             DEL PEAK 16(8P23.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V28, binary
                               cls
clus                             0  1
  DEL PEAK 16(8P23.3) MUTATED   27 19
  DEL PEAK 16(8P23.3) WILD-TYPE 44 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     27   19
  DEL PEAK 16(8P23.3) WILD-TYPE   44   55
         clus
vv        DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  ABSENT                           27                            44
  PRESENT                          19                            55
[1] 2 2
[1] FALSE
D42V29, continuous
D42V30, continuous
D42V31, binary
                               cls
clus                             0  1
  DEL PEAK 16(8P23.3) MUTATED   20 36
  DEL PEAK 16(8P23.3) WILD-TYPE 29 81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     20   36
  DEL PEAK 16(8P23.3) WILD-TYPE   29   81
                                          clus
vv                                         DEL PEAK 16(8P23.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              20
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          36
                                          clus
vv                                         DEL PEAK 16(8P23.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            81
[1] 2 2
[1] FALSE
D42V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 16(8P23.3) MUTATED              5          23         28
  DEL PEAK 16(8P23.3) WILD-TYPE           10          31         57
D42V33, multiclass
              clus
vv             DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  CURRENT USER                           5                            10
  FORMER USER                           23                            31
  NEVER USED                            28                            57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V34, continuous
D42V35, binary
                               cls
clus                             0  1
  DEL PEAK 16(8P23.3) MUTATED   33  5
  DEL PEAK 16(8P23.3) WILD-TYPE 59 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     33    5
  DEL PEAK 16(8P23.3) WILD-TYPE   59   13
         clus
vv        DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  ABSENT                           33                            59
  PRESENT                           5                            13
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 16(8P23.3) MUTATED             2        39     1
  DEL PEAK 16(8P23.3) WILD-TYPE           3        61     1
D42V36, multiclass
             clus
vv            DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  CARBOPLATIN                           2                             3
  CISPLATIN                            39                            61
  OTHER                                 1                             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"
D42V37, continuous
D42V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 16(8P23.3) MUTATED         2        1         1         1       13
  DEL PEAK 16(8P23.3) WILD-TYPE       3        0         0         0       21
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 16(8P23.3) MUTATED          23        12        2         2
  DEL PEAK 16(8P23.3) WILD-TYPE        54        25        2         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 16(8P23.3) MUTATED            4          2        19         0
  DEL PEAK 16(8P23.3) WILD-TYPE          1          5        25         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 16(8P23.3) MUTATED            1         14         3         3
  DEL PEAK 16(8P23.3) WILD-TYPE          2         28         4         9
D42V39, multiclass
            clus
vv           DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            1                             0
  STAGE IA2                            1                             0
  STAGE IB                            13                            21
  STAGE IB1                           23                            54
  STAGE IB2                           12                            25
  STAGE II                             2                             2
  STAGE IIA                            2                             6
  STAGE IIA1                           4                             1
  STAGE IIA2                           2                             5
  STAGE IIB                           19                            25
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          14                            28
  STAGE IVA                            3                             4
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 17(8P23.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(8P23.1) MUTATED    63  30
  DEL PEAK 17(8P23.1) WILD-TYPE 151  38
  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE 
                           93                           189 
  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE 
                           30                            38 
$`DEL PEAK 17(8P23.1) MUTATED`
TCGA-EK-A2GZ TCGA-EX-A69M TCGA-VS-A9V4 TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1M6 
       12.59         8.32         4.34        57.04        68.84        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK 
       46.32        30.21        35.01        57.73        53.16         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A7UI 
       20.91        40.93        73.18        73.45        78.35        94.95 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A907 
       13.61         2.73        50.99        45.83        99.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WI TCGA-EA-A1QT 
        1.12        95.11        36.76       118.65         8.28        40.87 
TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EK-A2H0 
       30.90        31.73        26.01        12.13        14.89        60.72 
TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ 
       19.27         0.59         0.43         1.64         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB 
        0.89        15.22        12.23        23.84        20.98        16.14 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3LA 
       35.44         1.12        17.75        25.41        21.67       137.16 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A5U3 TCGA-LP-A7HU 
       78.71        29.85        15.58         8.28         0.82        13.35 
TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MY-A913 TCGA-PN-A8MA 
       17.82         9.17         8.52        34.62        17.23         2.96 
TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.04         9.34        22.62        19.59        14.60        11.67 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QF 
       10.03        46.52        19.96        65.49        36.13        59.18 
TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL 
       39.78         4.73        33.37        24.30        45.11        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 
       27.25        47.87        41.52         3.42        18.25        18.84 
TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       15.42        67.59         1.41 

$`DEL PEAK 17(8P23.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J 
      146.86        14.70         1.48         0.69        17.52        17.82 
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        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77       131.11         9.34 
TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KK 
        8.35        23.51        27.52        20.81        20.91        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        63.98        87.75        58.88        55.63       117.99 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ 
       22.98        16.83        16.18        17.52        39.55        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.56        24.82         7.46        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 
       27.25        27.22        24.00        13.48         0.36        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64         1.51         0.39         0.43         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        40.96         0.30         4.24         0.07         1.87 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        1.74        47.77         2.33         0.49        20.35         7.92 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       19.79        15.55        19.04        16.11        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A9SC TCGA-HM-A3JK 
       26.14        28.31        14.01        10.55        16.57        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       129.37        96.95 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       20.48        28.37        18.15        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-MA-AA3W 
       20.91        11.28         0.89        12.49         0.30        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD 
       20.28        19.56        11.38        28.08        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
       35.05        20.84        15.58        16.41        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PF TCGA-UC-A7PG 
       17.56        14.07        15.88        18.64        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       69.50        45.57        32.42        23.97        32.15        53.59 
TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A952 
       11.51        31.27        40.87        16.64        40.14        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH 
       43.40        48.39        28.50        29.95        27.12        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UZ 
        1.71        47.47        26.07        15.85        14.53        67.20 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ 
        5.16        18.25        17.75        16.24        26.01        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.16         3.91 

  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE 
                       137.16                        210.67 
  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE 
                        20.91                         23.67 
[1] "0.1 - 137.2 (20.9)" "0.1 - 210.7 (23.7)"
[1] "hr=" "1.8"
D43V2, continuous
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 17(8P23.1) MUTATED   44 24  6  2
  DEL PEAK 17(8P23.1) WILD-TYPE 91 46 15  6
D43V3, multiclass
    clus
vv   DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  T1                          44                            91
  T2                          24                            46
  T3                           6                            15
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                               cls
clus                             0  1
  DEL PEAK 17(8P23.1) MUTATED   44 16
  DEL PEAK 17(8P23.1) WILD-TYPE 85 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED     44   16
  DEL PEAK 17(8P23.1) WILD-TYPE   85   40
   clus
vv  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  0                          44                            85
  1                          16                            40
[1] 2 2
[1] FALSE
D43V5, binary
                               cls
clus                             0  1
  DEL PEAK 17(8P23.1) MUTATED   34  4
  DEL PEAK 17(8P23.1) WILD-TYPE 74  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED     34    4
  DEL PEAK 17(8P23.1) WILD-TYPE   74    6
   clus
vv  DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  0                          34                            74
  1                           4                             6
[1] 2 2
[1] FALSE
D43V6, binary
                               cls
clus                             0  1
  DEL PEAK 17(8P23.1) MUTATED   13 40
  DEL PEAK 17(8P23.1) WILD-TYPE 40 85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED     13   40
  DEL PEAK 17(8P23.1) WILD-TYPE   40   85
     clus
vv    DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  NO                           13                            40
  YES                          40                            85
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(8P23.1) MUTATED               2                               80
  DEL PEAK 17(8P23.1) WILD-TYPE             4                              162
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 17(8P23.1) MUTATED                                               2
  DEL PEAK 17(8P23.1) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 17(8P23.1) MUTATED                                     5
  DEL PEAK 17(8P23.1) WILD-TYPE                                  16
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 17(8P23.1) MUTATED                                           2
  DEL PEAK 17(8P23.1) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 17(8P23.1) MUTATED                                              6
  DEL PEAK 17(8P23.1) WILD-TYPE                                           11
D43V7, multiclass
                                               clus
vv                                              DEL PEAK 17(8P23.1) MUTATED
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       80
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            6
                                               clus
vv                                              DEL PEAK 17(8P23.1) WILD-TYPE
  ADENOSQUAMOUS                                                             4
  CERVICAL SQUAMOUS CELL CARCINOMA                                        162
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, continuous
D43V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(8P23.1) MUTATED                                  3     3
  DEL PEAK 17(8P23.1) WILD-TYPE                                5    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(8P23.1) MUTATED                          12
  DEL PEAK 17(8P23.1) WILD-TYPE                        16
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(8P23.1) MUTATED                                           1    70
  DEL PEAK 17(8P23.1) WILD-TYPE                                         1   132
D43V10, multiclass
                                           clus
vv                                          DEL PEAK 17(8P23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              70
                                           clus
vv                                          DEL PEAK 17(8P23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            16
  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"
D43V11, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.1) MUTATED     8  51
  DEL PEAK 17(8P23.1) WILD-TYPE  15 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED      8   51
  DEL PEAK 17(8P23.1) WILD-TYPE   15  112
                        clus
vv                       DEL PEAK 17(8P23.1) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       DEL PEAK 17(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           112
[1] 2 2
[1] FALSE
D43V12, continuous
D43V13, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.1) MUTATED    56  34
  DEL PEAK 17(8P23.1) WILD-TYPE 137  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED     56   34
  DEL PEAK 17(8P23.1) WILD-TYPE  137   42
            clus
vv           DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  TUMOR FREE                          56                           137
  WITH TUMOR                          34                            42
[1] 2 2
[1] FALSE
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 17(8P23.1) MUTATED    3 40 40  1 10
  DEL PEAK 17(8P23.1) WILD-TYPE 15 89 75  0 14
D43V14, multiclass
    clus
vv   DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  G1                           3                            15
  G2                          40                            89
  G3                          40                            75
  G4                           1                             0
  GX                          10                            14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, continuous
D43V16, continuous
D43V17, continuous
D43V18, continuous
D43V19, binary
                               cls
clus                             0  1
  DEL PEAK 17(8P23.1) MUTATED   10  2
  DEL PEAK 17(8P23.1) WILD-TYPE 15  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED     10    2
  DEL PEAK 17(8P23.1) WILD-TYPE   15    1
                         clus
vv                        DEL PEAK 17(8P23.1) MUTATED
  COMPLETED AS PLANNED                             10
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK 17(8P23.1) WILD-TYPE
  COMPLETED AS PLANNED                               15
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
D43V20, continuous
D43V21, continuous
D43V22, continuous
D43V23, continuous
D43V24, continuous
D43V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 17(8P23.1) MUTATED                                     0
  DEL PEAK 17(8P23.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 17(8P23.1) MUTATED                                     1
  DEL PEAK 17(8P23.1) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 17(8P23.1) MUTATED                        14                       0
  DEL PEAK 17(8P23.1) WILD-TYPE                      22                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 17(8P23.1) MUTATED                         4
  DEL PEAK 17(8P23.1) WILD-TYPE                       6
D43V26, multiclass
                                     clus
vv                                    DEL PEAK 17(8P23.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                      14
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       4
                                     clus
vv                                    DEL PEAK 17(8P23.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                        22
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 17(8P23.1) MUTATED                                               1
  DEL PEAK 17(8P23.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 17(8P23.1) MUTATED                                                7
  DEL PEAK 17(8P23.1) WILD-TYPE                                             18
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 17(8P23.1) MUTATED                                                                                  27
  DEL PEAK 17(8P23.1) WILD-TYPE                                                                                55
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 17(8P23.1) MUTATED                                                                                             43
  DEL PEAK 17(8P23.1) WILD-TYPE                                                                                           78
D43V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 17(8P23.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          43
                                                                                              clus
vv                                                                                             DEL PEAK 17(8P23.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       55
  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"
D43V28, binary
                               cls
clus                             0  1
  DEL PEAK 17(8P23.1) MUTATED   26 17
  DEL PEAK 17(8P23.1) WILD-TYPE 45 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED     26   17
  DEL PEAK 17(8P23.1) WILD-TYPE   45   57
         clus
vv        DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  ABSENT                           26                            45
  PRESENT                          17                            57
[1] 2 2
[1] FALSE
D43V29, continuous
D43V30, continuous
D43V31, binary
                               cls
clus                             0  1
  DEL PEAK 17(8P23.1) MUTATED   19 36
  DEL PEAK 17(8P23.1) WILD-TYPE 30 81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED     19   36
  DEL PEAK 17(8P23.1) WILD-TYPE   30   81
                                          clus
vv                                         DEL PEAK 17(8P23.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          36
                                          clus
vv                                         DEL PEAK 17(8P23.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            81
[1] 2 2
[1] FALSE
D43V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 17(8P23.1) MUTATED              5          18         27
  DEL PEAK 17(8P23.1) WILD-TYPE           10          36         58
D43V33, multiclass
              clus
vv             DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  CURRENT USER                           5                            10
  FORMER USER                           18                            36
  NEVER USED                            27                            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"
D43V34, continuous
D43V35, binary
                               cls
clus                             0  1
  DEL PEAK 17(8P23.1) MUTATED   31  5
  DEL PEAK 17(8P23.1) WILD-TYPE 61 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.1) MUTATED     31    5
  DEL PEAK 17(8P23.1) WILD-TYPE   61   13
         clus
vv        DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  ABSENT                           31                            61
  PRESENT                           5                            13
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 17(8P23.1) MUTATED             2        36     1
  DEL PEAK 17(8P23.1) WILD-TYPE           3        64     1
D43V36, multiclass
             clus
vv            DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  CARBOPLATIN                           2                             3
  CISPLATIN                            36                            64
  OTHER                                 1                             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"
D43V37, continuous
D43V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 17(8P23.1) MUTATED         2        0         1         1       12
  DEL PEAK 17(8P23.1) WILD-TYPE       3        1         0         0       22
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 17(8P23.1) MUTATED          22        10        2         2
  DEL PEAK 17(8P23.1) WILD-TYPE        55        27        2         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 17(8P23.1) MUTATED            4          2        20         0
  DEL PEAK 17(8P23.1) WILD-TYPE          1          5        24         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 17(8P23.1) MUTATED            1         12         2         3
  DEL PEAK 17(8P23.1) WILD-TYPE          2         30         5         9
D43V39, multiclass
            clus
vv           DEL PEAK 17(8P23.1) MUTATED DEL PEAK 17(8P23.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IA1                            1                             0
  STAGE IA2                            1                             0
  STAGE IB                            12                            22
  STAGE IB1                           22                            55
  STAGE IB2                           10                            27
  STAGE II                             2                             2
  STAGE IIA                            2                             6
  STAGE IIA1                           4                             1
  STAGE IIA2                           2                             5
  STAGE IIB                           20                            24
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                          12                            30
  STAGE IVA                            2                             5
  STAGE IVB                            3                             9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK 18(10Q23.31) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 18(10Q23.31) MUTATED    58  24
  DEL PEAK 18(10Q23.31) WILD-TYPE 156  44
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                             82                             200 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                             24                              44 
$`DEL PEAK 18(10Q23.31) MUTATED`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-BI-A0VS 
      146.86        12.59         1.48         4.34         0.69        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M6 
       23.67        11.44       173.29        82.85        19.86        31.40 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A2LT TCGA-C5-A2LV 
       38.99        35.61         0.46        20.91        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL 
       83.05        20.42       210.67       154.32       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8YR 
       20.35       147.35        17.19        13.61         2.73        27.52 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VK TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A78R 
       95.11        44.94        36.76        31.73        27.22        13.48 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RK 
       26.27         6.64        19.27         0.59         1.74         0.43 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A3TQ 
       47.77         1.64         2.33        20.35        19.04        26.14 
TCGA-FU-A40J TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3LB 
       14.01        17.75        21.67        20.78         9.44        66.81 
TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A4AX 
       78.71        36.36        20.48        28.37        44.61        12.49 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        8.52        11.38        17.23         2.96        16.41         9.04 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A94Y 
       12.16        69.50        32.42        19.96        65.49         4.73 
TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       40.14        56.35        50.47        24.30        46.92        45.11 
TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9V0 
       14.53        47.47        26.07        18.84 

$`DEL PEAK 18(10Q23.31) WILD-TYPE`
TCGA-EX-A449 TCGA-EX-A69M TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE 
       14.70         8.32        17.52        17.82        49.48        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       18.74        36.56       144.16       177.04         5.46        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK 
       46.32        30.21        35.01        57.73        53.16         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-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CJ TCGA-C5-A7UE 
       33.24        52.01        18.02        17.85       101.82       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
      131.11        94.95         9.34        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       99.91        23.51        20.81        20.91        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       82.06        63.98        87.75        58.88        55.63       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05        25.02        36.89        26.40        24.56        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.13        24.82         7.46        14.89        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG 
       27.29        27.25        24.00         0.36        60.72         1.51 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.39         0.43         0.89         1.45         0.13        40.96 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.30         4.24         0.07         1.87         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF 
        0.49         0.89         7.92        15.22        19.79        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       12.23        23.84        16.11        31.36        36.26        20.98 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
       16.14        28.31        35.44        10.55         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF 
       16.57        14.93       147.39       137.16       129.37        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        29.85        27.42         3.29        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58         8.28        18.15        21.11       209.59        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       11.28         0.89         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MU-A51Y TCGA-MU-A5YI 
       20.28        17.82        19.56         9.17        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       19.96        54.81        35.05        20.84        15.58        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB 
       22.62        19.59        14.60        11.67        93.99        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       46.52        45.57        23.97        32.15        53.59        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       33.37        58.45        15.68        55.50        50.14        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ 
       43.40        48.39        28.50        29.95        27.12         1.71 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       27.25        47.87        41.52        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 
       18.25        67.20         5.16        18.25        17.75        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       15.42        26.01        29.26        67.59        19.13         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                           0.43                            0.07 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                         210.67                          209.59 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                          21.29                           22.80 
[1] "0.4 - 210.7 (21.3)" "0.1 - 209.6 (22.8)"
[1] "hr=" "1.2"
D44V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 18(10Q23.31) MUTATED    32  23   8   2
  DEL PEAK 18(10Q23.31) WILD-TYPE 103  47  13   6
D44V3, multiclass
    clus
vv   DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  T1                            32                             103
  T2                            23                              47
  T3                             8                              13
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED    29  17
  DEL PEAK 18(10Q23.31) WILD-TYPE 100  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     29   17
  DEL PEAK 18(10Q23.31) WILD-TYPE  100   39
   clus
vv  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  0                            29                             100
  1                            17                              39
[1] 2 2
[1] FALSE
D44V5, binary
                                 cls
clus                               0  1
  DEL PEAK 18(10Q23.31) MUTATED   26  3
  DEL PEAK 18(10Q23.31) WILD-TYPE 82  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     26    3
  DEL PEAK 18(10Q23.31) WILD-TYPE   82    7
   clus
vv  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  0                            26                              82
  1                             3                               7
[1] 2 2
[1] FALSE
D44V6, binary
                                 cls
clus                               0  1
  DEL PEAK 18(10Q23.31) MUTATED   13 39
  DEL PEAK 18(10Q23.31) WILD-TYPE 40 86
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     13   39
  DEL PEAK 18(10Q23.31) WILD-TYPE   40   86
     clus
vv    DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  NO                             13                              40
  YES                            39                              86
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 18(10Q23.31) MUTATED               1
  DEL PEAK 18(10Q23.31) WILD-TYPE             5
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(10Q23.31) MUTATED                                 70
  DEL PEAK 18(10Q23.31) WILD-TYPE                              172
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 18(10Q23.31) MUTATED                                               2
  DEL PEAK 18(10Q23.31) WILD-TYPE                                             4
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 18(10Q23.31) MUTATED                                     7
  DEL PEAK 18(10Q23.31) WILD-TYPE                                  14
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 18(10Q23.31) MUTATED                                           1
  DEL PEAK 18(10Q23.31) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 18(10Q23.31) MUTATED                                              5
  DEL PEAK 18(10Q23.31) WILD-TYPE                                           12
D44V7, multiclass
                                               clus
vv                                              DEL PEAK 18(10Q23.31) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         70
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
                                               clus
vv                                              DEL PEAK 18(10Q23.31) WILD-TYPE
  ADENOSQUAMOUS                                                               5
  CERVICAL SQUAMOUS CELL CARCINOMA                                          172
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, continuous
D44V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(10Q23.31) MUTATED                                  0     5
  DEL PEAK 18(10Q23.31) WILD-TYPE                                8    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(10Q23.31) MUTATED                          15
  DEL PEAK 18(10Q23.31) WILD-TYPE                        13
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 18(10Q23.31) MUTATED                                           0
  DEL PEAK 18(10Q23.31) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  DEL PEAK 18(10Q23.31) MUTATED      57
  DEL PEAK 18(10Q23.31) WILD-TYPE   145
D44V10, multiclass
                                           clus
vv                                          DEL PEAK 18(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                57
                                           clus
vv                                          DEL PEAK 18(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  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"
D44V11, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED     6  47
  DEL PEAK 18(10Q23.31) WILD-TYPE  17 116
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED      6   47
  DEL PEAK 18(10Q23.31) WILD-TYPE   17  116
                        clus
vv                       DEL PEAK 18(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            47
                        clus
vv                       DEL PEAK 18(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  17
  NOT HISPANIC OR LATINO                             116
[1] 2 2
[1] FALSE
D44V12, continuous
D44V13, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED    49  28
  DEL PEAK 18(10Q23.31) WILD-TYPE 144  48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     49   28
  DEL PEAK 18(10Q23.31) WILD-TYPE  144   48
            clus
vv           DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  TUMOR FREE                            49                             144
  WITH TUMOR                            28                              48
[1] 2 2
[1] FALSE
                                 vv
clus                               G1  G2  G3  G4  GX
  DEL PEAK 18(10Q23.31) MUTATED     3  29  46   1   6
  DEL PEAK 18(10Q23.31) WILD-TYPE  15 100  69   0  18
D44V14, multiclass
    clus
vv   DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  G1                             3                              15
  G2                            29                             100
  G3                            46                              69
  G4                             1                               0
  GX                             6                              18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, continuous
D44V16, continuous
D44V17, continuous
D44V18, continuous
D44V19, binary
                                 cls
clus                               0  1
  DEL PEAK 18(10Q23.31) MUTATED   11  1
  DEL PEAK 18(10Q23.31) WILD-TYPE 14  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     11    1
  DEL PEAK 18(10Q23.31) WILD-TYPE   14    2
                         clus
vv                        DEL PEAK 18(10Q23.31) MUTATED
  COMPLETED AS PLANNED                               11
  TREATMENT NOT COMPLETED                             1
                         clus
vv                        DEL PEAK 18(10Q23.31) WILD-TYPE
  COMPLETED AS PLANNED                                 14
  TREATMENT NOT COMPLETED                               2
[1] 2 2
[1] FALSE
D44V20, continuous
D44V21, continuous
D44V22, continuous
D44V23, continuous
D44V24, continuous
D44V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 18(10Q23.31) MUTATED                                     0
  DEL PEAK 18(10Q23.31) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 18(10Q23.31) MUTATED                                     3
  DEL PEAK 18(10Q23.31) WILD-TYPE                                   4
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 18(10Q23.31) MUTATED                         8
  DEL PEAK 18(10Q23.31) WILD-TYPE                      28
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 18(10Q23.31) MUTATED                         0
  DEL PEAK 18(10Q23.31) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 18(10Q23.31) MUTATED                         7
  DEL PEAK 18(10Q23.31) WILD-TYPE                       3
D44V26, multiclass
                                     clus
vv                                    DEL PEAK 18(10Q23.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                         8
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         7
                                     clus
vv                                    DEL PEAK 18(10Q23.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               4
  OTHER LOCATION, SPECIFY                                          28
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 18(10Q23.31) MUTATED                                               0
  DEL PEAK 18(10Q23.31) WILD-TYPE                                             3
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 18(10Q23.31) MUTATED                                                9
  DEL PEAK 18(10Q23.31) WILD-TYPE                                             16
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 18(10Q23.31) MUTATED                                                                                  30
  DEL PEAK 18(10Q23.31) WILD-TYPE                                                                                52
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 18(10Q23.31) MUTATED                                                                                             23
  DEL PEAK 18(10Q23.31) WILD-TYPE                                                                                           98
D44V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 18(10Q23.31) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            23
                                                                                              clus
vv                                                                                             DEL PEAK 18(10Q23.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         52
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V28, binary
                                 cls
clus                               0  1
  DEL PEAK 18(10Q23.31) MUTATED   16 24
  DEL PEAK 18(10Q23.31) WILD-TYPE 55 50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     16   24
  DEL PEAK 18(10Q23.31) WILD-TYPE   55   50
         clus
vv        DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  ABSENT                             16                              55
  PRESENT                            24                              50
[1] 2 2
[1] FALSE
D44V29, continuous
D44V30, continuous
D44V31, binary
                                 cls
clus                               0  1
  DEL PEAK 18(10Q23.31) MUTATED   19 29
  DEL PEAK 18(10Q23.31) WILD-TYPE 30 88
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     19   29
  DEL PEAK 18(10Q23.31) WILD-TYPE   30   88
                                          clus
vv                                         DEL PEAK 18(10Q23.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            29
                                          clus
vv                                         DEL PEAK 18(10Q23.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              88
[1] 2 2
[1] FALSE
D44V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 18(10Q23.31) MUTATED              2          12         23
  DEL PEAK 18(10Q23.31) WILD-TYPE           13          42         62
D44V33, multiclass
              clus
vv             DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  CURRENT USER                             2                              13
  FORMER USER                             12                              42
  NEVER USED                              23                              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"
D44V34, continuous
D44V35, binary
                                 cls
clus                               0  1
  DEL PEAK 18(10Q23.31) MUTATED   22  5
  DEL PEAK 18(10Q23.31) WILD-TYPE 70 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     22    5
  DEL PEAK 18(10Q23.31) WILD-TYPE   70   13
         clus
vv        DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  ABSENT                             22                              70
  PRESENT                             5                              13
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 18(10Q23.31) MUTATED             1        33     1
  DEL PEAK 18(10Q23.31) WILD-TYPE           4        67     1
D44V36, multiclass
             clus
vv            DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  CARBOPLATIN                             1                               4
  CISPLATIN                              33                              67
  OTHER                                   1                               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"
D44V37, continuous
D44V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 18(10Q23.31) MUTATED         1        0         0         1       13
  DEL PEAK 18(10Q23.31) WILD-TYPE       4        1         1         0       21
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 18(10Q23.31) MUTATED          17        11        1         5
  DEL PEAK 18(10Q23.31) WILD-TYPE        60        26        3         3
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 18(10Q23.31) MUTATED            2          1        12         0
  DEL PEAK 18(10Q23.31) WILD-TYPE          3          6        32         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 18(10Q23.31) MUTATED            2         14         3         2
  DEL PEAK 18(10Q23.31) WILD-TYPE          1         28         4        10
D44V39, multiclass
            clus
vv           DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                              13                              21
  STAGE IB1                             17                              60
  STAGE IB2                             11                              26
  STAGE II                               1                               3
  STAGE IIA                              5                               3
  STAGE IIA1                             2                               3
  STAGE IIA2                             1                               6
  STAGE IIB                             12                              32
  STAGE III                              0                               1
  STAGE IIIA                             2                               1
  STAGE IIIB                            14                              28
  STAGE IVA                              3                               4
  STAGE IVB                              2                              10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 19(11P15.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(11P15.1) MUTATED    71  27
  DEL PEAK 19(11P15.1) WILD-TYPE 143  41
  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE 
                            98                            184 
  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE 
                            27                             41 
$`DEL PEAK 19(11P15.1) MUTATED`
TCGA-C5-A8XJ TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BK 
      146.86         8.32         0.69        49.48        18.74       177.04 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A1MI 
        5.46        19.86        46.32        30.21        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A2LV TCGA-C5-A2LZ TCGA-C5-A7CG TCGA-C5-A7CH 
        0.46        20.91        73.45       100.14       210.67       154.32 
TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XK 
       15.48       131.11        94.95         2.73        50.99        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM 
       23.51        27.52        63.98        87.75        36.76       117.99 
TCGA-DS-A0VN TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
      118.65         8.28        40.87        24.56        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N 
       12.13         7.46        27.25        27.22        13.48         0.36 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2RA TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A3GJ 
        1.51         0.43        40.96         0.43         1.64         0.10 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A770 TCGA-IR-A3LB 
       20.35        23.84        20.98        16.14         1.12        66.81 
TCGA-IR-A3LC TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-LP-A4AU 
      129.37        29.85        24.56        21.44        20.48        11.28 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA43 
       12.49         0.82        13.35        22.52        20.28        11.38 
TCGA-MY-A5BE TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-R2-A69V 
       35.05        16.41         9.04        17.56         9.34        19.59 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 
       12.16        10.03        32.42        23.97        19.96        53.59 
TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       59.18         4.73        40.14        55.50        51.32        50.47 
TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UT 
       24.30        45.11        14.53        47.87        47.47        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ 
       14.53         3.42        18.25        17.75        26.01        29.26 
TCGA-ZJ-AAXA TCGA-ZX-AA5X 
        1.41         3.91 

$`DEL PEAK 19(11P15.1) WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-4J-AA1J 
       12.59        14.70         1.48         4.34        17.52        17.82 
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        33.24        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       155.77         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 
       20.81        20.91        14.73         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       44.94        58.88        55.63        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        39.55        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A556 
       13.05        25.02        36.89        26.40        24.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2H1 
       26.79        25.91        27.29        24.00        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64        19.27         0.39         0.59         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.13         0.30         4.24         0.07         1.87         1.74 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
       47.77         2.33         0.07         0.49         0.89         7.92 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       15.22        19.79        15.55        12.23        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       31.36        36.26        26.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
       10.55        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LF TCGA-IR-A3LH 
       14.93         9.44       147.39       137.16        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VL TCGA-JW-A69B 
       81.96        36.36        27.42         3.29        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       209.59        44.61        20.91 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
        0.89         0.30        17.82        19.56         9.17         8.52 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       28.08        34.62        19.96        54.81        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P 
        2.96        15.58        15.95        16.14        14.07        15.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       18.64        22.62        14.60        11.67        93.99        69.50 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC 
       46.52        45.57        65.49        32.15        36.13        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        40.87        16.64        33.37        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       15.68        56.35        50.14        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UQ 
       29.95        27.12        46.92         1.71        27.25        41.52 
TCGA-VS-A9UR TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V5 
       26.07        18.25        67.20        18.84         5.16        16.24 
TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       15.42        67.59        19.13         0.16 

  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE 
                        210.67                         209.59 
  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE 
                        23.015                         22.145 
[1] "0.1 - 210.7 (23.0)" "0.1 - 209.6 (22.1)"
[1] "hr=" "1.2"
D45V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 19(11P15.1) MUTATED   43 23 10  3
  DEL PEAK 19(11P15.1) WILD-TYPE 92 47 11  5
D45V3, multiclass
    clus
vv   DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  T1                           43                             92
  T2                           23                             47
  T3                           10                             11
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                                cls
clus                              0  1
  DEL PEAK 19(11P15.1) MUTATED   37 20
  DEL PEAK 19(11P15.1) WILD-TYPE 92 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED     37   20
  DEL PEAK 19(11P15.1) WILD-TYPE   92   36
   clus
vv  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  0                           37                             92
  1                           20                             36
[1] 2 2
[1] FALSE
D45V5, binary
                                cls
clus                              0  1
  DEL PEAK 19(11P15.1) MUTATED   37  2
  DEL PEAK 19(11P15.1) WILD-TYPE 71  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED     37    2
  DEL PEAK 19(11P15.1) WILD-TYPE   71    8
   clus
vv  DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  0                           37                             71
  1                            2                              8
[1] 2 2
[1] FALSE
D45V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(11P15.1) MUTATED   19 46
  DEL PEAK 19(11P15.1) WILD-TYPE 34 79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED     19   46
  DEL PEAK 19(11P15.1) WILD-TYPE   34   79
     clus
vv    DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  NO                            19                             34
  YES                           46                             79
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(11P15.1) MUTATED               0                               92
  DEL PEAK 19(11P15.1) WILD-TYPE             6                              150
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 19(11P15.1) MUTATED                                               2
  DEL PEAK 19(11P15.1) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 19(11P15.1) MUTATED                                     4
  DEL PEAK 19(11P15.1) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 19(11P15.1) MUTATED                                           0
  DEL PEAK 19(11P15.1) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 19(11P15.1) MUTATED                                              4
  DEL PEAK 19(11P15.1) WILD-TYPE                                           13
D45V7, multiclass
                                               clus
vv                                              DEL PEAK 19(11P15.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        92
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
                                               clus
vv                                              DEL PEAK 19(11P15.1) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         150
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, continuous
D45V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(11P15.1) MUTATED                                  2    12
  DEL PEAK 19(11P15.1) WILD-TYPE                                6     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(11P15.1) MUTATED                          10
  DEL PEAK 19(11P15.1) WILD-TYPE                        18
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 19(11P15.1) MUTATED                                           1
  DEL PEAK 19(11P15.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 19(11P15.1) MUTATED      68
  DEL PEAK 19(11P15.1) WILD-TYPE   134
D45V10, multiclass
                                           clus
vv                                          DEL PEAK 19(11P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               68
                                           clus
vv                                          DEL PEAK 19(11P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                  7
  BLACK OR AFRICAN AMERICAN                                             18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D45V11, binary
                                cls
clus                               0   1
  DEL PEAK 19(11P15.1) MUTATED     7  59
  DEL PEAK 19(11P15.1) WILD-TYPE  16 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED      7   59
  DEL PEAK 19(11P15.1) WILD-TYPE   16  104
                        clus
vv                       DEL PEAK 19(11P15.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK 19(11P15.1) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            104
[1] 2 2
[1] FALSE
D45V12, continuous
D45V13, binary
                                cls
clus                               0   1
  DEL PEAK 19(11P15.1) MUTATED    62  31
  DEL PEAK 19(11P15.1) WILD-TYPE 131  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED     62   31
  DEL PEAK 19(11P15.1) WILD-TYPE  131   45
            clus
vv           DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  TUMOR FREE                           62                            131
  WITH TUMOR                           31                             45
[1] 2 2
[1] FALSE
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 19(11P15.1) MUTATED    3 39 49  0  8
  DEL PEAK 19(11P15.1) WILD-TYPE 15 90 66  1 16
D45V14, multiclass
    clus
vv   DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  G1                            3                             15
  G2                           39                             90
  G3                           49                             66
  G4                            0                              1
  GX                            8                             16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, continuous
D45V16, continuous
D45V17, continuous
D45V18, continuous
D45V19, binary
                                cls
clus                              0  1
  DEL PEAK 19(11P15.1) MUTATED    7  0
  DEL PEAK 19(11P15.1) WILD-TYPE 18  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED      7    0
  DEL PEAK 19(11P15.1) WILD-TYPE   18    3
                         clus
vv                        DEL PEAK 19(11P15.1) MUTATED
  COMPLETED AS PLANNED                               7
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 19(11P15.1) WILD-TYPE
  COMPLETED AS PLANNED                                18
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
D45V20, continuous
D45V21, continuous
D45V22, continuous
D45V23, continuous
D45V24, continuous
D45V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 19(11P15.1) MUTATED                                     0
  DEL PEAK 19(11P15.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 19(11P15.1) MUTATED                                     3
  DEL PEAK 19(11P15.1) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 19(11P15.1) MUTATED                        13
  DEL PEAK 19(11P15.1) WILD-TYPE                      23
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 19(11P15.1) MUTATED                         1
  DEL PEAK 19(11P15.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 19(11P15.1) MUTATED                         3
  DEL PEAK 19(11P15.1) WILD-TYPE                       7
D45V26, multiclass
                                     clus
vv                                    DEL PEAK 19(11P15.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                       13
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        3
                                     clus
vv                                    DEL PEAK 19(11P15.1) 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 19(11P15.1) MUTATED                                               1
  DEL PEAK 19(11P15.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 19(11P15.1) MUTATED                                               12
  DEL PEAK 19(11P15.1) WILD-TYPE                                             13
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 19(11P15.1) MUTATED                                                                                  36
  DEL PEAK 19(11P15.1) WILD-TYPE                                                                                46
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 19(11P15.1) MUTATED                                                                                             30
  DEL PEAK 19(11P15.1) WILD-TYPE                                                                                           91
D45V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 19(11P15.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      36
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           30
                                                                                              clus
vv                                                                                             DEL PEAK 19(11P15.1) 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)                                        46
  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"
D45V28, binary
                                cls
clus                              0  1
  DEL PEAK 19(11P15.1) MUTATED   26 21
  DEL PEAK 19(11P15.1) WILD-TYPE 45 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED     26   21
  DEL PEAK 19(11P15.1) WILD-TYPE   45   53
         clus
vv        DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  ABSENT                            26                             45
  PRESENT                           21                             53
[1] 2 2
[1] FALSE
D45V29, continuous
D45V30, continuous
D45V31, binary
                                cls
clus                              0  1
  DEL PEAK 19(11P15.1) MUTATED   15 41
  DEL PEAK 19(11P15.1) WILD-TYPE 34 76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED     15   41
  DEL PEAK 19(11P15.1) WILD-TYPE   34   76
                                          clus
vv                                         DEL PEAK 19(11P15.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           41
                                          clus
vv                                         DEL PEAK 19(11P15.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             76
[1] 2 2
[1] FALSE
D45V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 19(11P15.1) MUTATED              3          15         37
  DEL PEAK 19(11P15.1) WILD-TYPE           12          39         48
D45V33, multiclass
              clus
vv             DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                            15                             39
  NEVER USED                             37                             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"
D45V34, continuous
D45V35, binary
                                cls
clus                              0  1
  DEL PEAK 19(11P15.1) MUTATED   31  6
  DEL PEAK 19(11P15.1) WILD-TYPE 61 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.1) MUTATED     31    6
  DEL PEAK 19(11P15.1) WILD-TYPE   61   12
         clus
vv        DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  ABSENT                            31                             61
  PRESENT                            6                             12
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 19(11P15.1) MUTATED             0        37     0
  DEL PEAK 19(11P15.1) WILD-TYPE           5        63     2
D45V36, multiclass
             clus
vv            DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  CARBOPLATIN                            0                              5
  CISPLATIN                             37                             63
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V37, continuous
D45V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 19(11P15.1) MUTATED         3        0         0         1       16
  DEL PEAK 19(11P15.1) WILD-TYPE       2        1         1         0       18
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 19(11P15.1) MUTATED          26         7        2         2
  DEL PEAK 19(11P15.1) WILD-TYPE        51        30        2         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 19(11P15.1) MUTATED            2          3        13         0
  DEL PEAK 19(11P15.1) WILD-TYPE          3          4        31         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 19(11P15.1) MUTATED            2         18         2         1
  DEL PEAK 19(11P15.1) WILD-TYPE          1         24         5        11
D45V39, multiclass
            clus
vv           DEL PEAK 19(11P15.1) MUTATED DEL PEAK 19(11P15.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             16                             18
  STAGE IB1                            26                             51
  STAGE IB2                             7                             30
  STAGE II                              2                              2
  STAGE IIA                             2                              6
  STAGE IIA1                            2                              3
  STAGE IIA2                            3                              4
  STAGE IIB                            13                             31
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                           18                             24
  STAGE IVA                             2                              5
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 20(11Q23.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(11Q23.3) MUTATED   116  42
  DEL PEAK 20(11Q23.3) WILD-TYPE  98  26
  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE 
                           158                            124 
  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE 
                            42                             26 
$`DEL PEAK 20(11Q23.3) MUTATED`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-BI-A0VR 
      146.86        12.59         8.32         0.69        17.82        49.48 
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ 
       57.04        23.67        11.44        68.84        18.74       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
      177.04       173.29        82.85        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       30.21        57.73        53.16        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        2.43        20.91        73.45        83.05        78.35       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7CM 
       33.24        52.01       210.67       154.32        15.48        20.35 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       17.19       131.11        13.61         2.73        50.99        45.83 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A0VK 
       99.91        23.51        27.52        82.06        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WI 
       55.63       117.99       118.65        22.98        16.83         8.28 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 
       40.87        30.90        13.05        25.02        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R 
       26.01         7.46        25.91        27.25        27.22        13.48 
TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R9 
        0.36         6.64         1.51        19.27         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO 
       40.96         0.07         0.43        47.77         1.64         0.07 
TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.10        20.35        15.22        19.79        20.98        26.14 
TCGA-FU-A3WB TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       16.14        16.57        21.67       137.16        66.81       129.37 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ 
       78.71        81.96        36.36        20.48        28.37        21.11 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       20.91        11.28        12.49         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
       20.28        11.38        28.08        34.62        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       20.84        17.23         2.96        16.41         9.04        17.56 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       15.88         9.34        19.59        14.60        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        45.57        32.42        23.97        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94W 
       65.49        32.15        53.59        11.51        59.18        40.87 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 
       33.37        40.14        58.45        56.35        55.50        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UI 
       50.47        43.40        48.39        28.50        24.30        45.11 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU 
       14.53        47.87        47.47        41.52        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
        3.42        18.25        17.75        15.42        29.26        19.13 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

$`DEL PEAK 20(11Q23.3) WILD-TYPE`
TCGA-EX-A449 TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-C5-A1BI TCGA-C5-A1BN 
       14.70         1.48         4.34        17.52        36.56         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       19.86        35.01        40.93         3.58        44.22        73.18 
TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       38.43        18.02        17.85        20.42       101.82       134.33 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8YT 
      147.35       155.77        94.95         9.34         8.35        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91        14.73         1.12        95.11        44.94        63.98 
TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS 
       58.88        16.18        17.52        39.55        37.35        31.53 
TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 
       31.36        36.89        26.40        12.13        24.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PK 
       26.79        27.29        24.00        60.72        26.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
        0.43         0.89         1.45         0.30         4.24         1.87 
TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A8YF 
        1.74         2.33         0.49         0.89         7.92        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       12.23        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       28.31        14.01        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF 
       25.41        20.78        14.93         9.44       147.39        96.95 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       29.85        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U2 
        8.28        18.15       209.59        44.61         0.89         0.30 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A8JM TCGA-Q1-A5R1 
       17.82        19.56         9.17         8.52        19.96        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI 
       15.95        16.14        14.07        18.64        22.62        69.50 
TCGA-VS-A8EC TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       46.52        36.13        39.78        31.27        16.64         4.73 
TCGA-VS-A953 TCGA-VS-A958 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ 
       15.68        50.14        29.95        27.12        46.92         1.71 
TCGA-VS-A9UM TCGA-VS-A9UR TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       27.25        26.07        18.25        67.20        18.84         5.16 
TCGA-VS-A9V5 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       16.24        26.01        67.59         1.41 

  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE 
                          0.07                           0.30 
  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE 
                        210.67                         209.59 
  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE 
                        25.465                         19.710 
[1] "0.1 - 210.7 (25.5)" "0.3 - 209.6 (19.7)"
[1] "hr=" "1"  
D46V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 20(11Q23.3) MUTATED   74 35 13  4
  DEL PEAK 20(11Q23.3) WILD-TYPE 61 35  8  4
D46V3, multiclass
    clus
vv   DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  T1                           74                             61
  T2                           35                             35
  T3                           13                              8
  T4                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                                cls
clus                              0  1
  DEL PEAK 20(11Q23.3) MUTATED   67 31
  DEL PEAK 20(11Q23.3) WILD-TYPE 62 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED     67   31
  DEL PEAK 20(11Q23.3) WILD-TYPE   62   25
   clus
vv  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  0                           67                             62
  1                           31                             25
[1] 2 2
[1] FALSE
D46V5, binary
                                cls
clus                              0  1
  DEL PEAK 20(11Q23.3) MUTATED   63  5
  DEL PEAK 20(11Q23.3) WILD-TYPE 45  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED     63    5
  DEL PEAK 20(11Q23.3) WILD-TYPE   45    5
   clus
vv  DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  0                           63                             45
  1                            5                              5
[1] 2 2
[1] FALSE
D46V6, binary
                                cls
clus                              0  1
  DEL PEAK 20(11Q23.3) MUTATED   30 72
  DEL PEAK 20(11Q23.3) WILD-TYPE 23 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED     30   72
  DEL PEAK 20(11Q23.3) WILD-TYPE   23   53
     clus
vv    DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  NO                            30                             23
  YES                           72                             53
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(11Q23.3) MUTATED               1                              144
  DEL PEAK 20(11Q23.3) WILD-TYPE             5                               98
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 20(11Q23.3) MUTATED                                               1
  DEL PEAK 20(11Q23.3) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 20(11Q23.3) MUTATED                                     9
  DEL PEAK 20(11Q23.3) WILD-TYPE                                  12
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 20(11Q23.3) MUTATED                                           1
  DEL PEAK 20(11Q23.3) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 20(11Q23.3) MUTATED                                              6
  DEL PEAK 20(11Q23.3) WILD-TYPE                                           11
D46V7, multiclass
                                               clus
vv                                              DEL PEAK 20(11Q23.3) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       144
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             6
                                               clus
vv                                              DEL PEAK 20(11Q23.3) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                          98
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, continuous
D46V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(11Q23.3) MUTATED                                  3    12
  DEL PEAK 20(11Q23.3) WILD-TYPE                                5     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(11Q23.3) MUTATED                          20
  DEL PEAK 20(11Q23.3) WILD-TYPE                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 20(11Q23.3) MUTATED                                           2
  DEL PEAK 20(11Q23.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 20(11Q23.3) MUTATED     109
  DEL PEAK 20(11Q23.3) WILD-TYPE    93
D46V10, multiclass
                                           clus
vv                                          DEL PEAK 20(11Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                           20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                              109
                                           clus
vv                                          DEL PEAK 20(11Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                  7
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"
D46V11, binary
                                cls
clus                              0  1
  DEL PEAK 20(11Q23.3) MUTATED    9 88
  DEL PEAK 20(11Q23.3) WILD-TYPE 14 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED      9   88
  DEL PEAK 20(11Q23.3) WILD-TYPE   14   75
                        clus
vv                       DEL PEAK 20(11Q23.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       DEL PEAK 20(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                             75
[1] 2 2
[1] FALSE
D46V12, continuous
D46V13, binary
                                cls
clus                               0   1
  DEL PEAK 20(11Q23.3) MUTATED   102  46
  DEL PEAK 20(11Q23.3) WILD-TYPE  91  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED    102   46
  DEL PEAK 20(11Q23.3) WILD-TYPE   91   30
            clus
vv           DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  TUMOR FREE                          102                             91
  WITH TUMOR                           46                             30
[1] 2 2
[1] FALSE
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 20(11Q23.3) MUTATED    8 71 66  1 12
  DEL PEAK 20(11Q23.3) WILD-TYPE 10 58 49  0 12
D46V14, multiclass
    clus
vv   DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  G1                            8                             10
  G2                           71                             58
  G3                           66                             49
  G4                            1                              0
  GX                           12                             12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, continuous
D46V16, continuous
D46V17, continuous
D46V18, continuous
D46V19, binary
                                cls
clus                              0  1
  DEL PEAK 20(11Q23.3) MUTATED   17  2
  DEL PEAK 20(11Q23.3) WILD-TYPE  8  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED     17    2
  DEL PEAK 20(11Q23.3) WILD-TYPE    8    1
                         clus
vv                        DEL PEAK 20(11Q23.3) MUTATED
  COMPLETED AS PLANNED                              17
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        DEL PEAK 20(11Q23.3) WILD-TYPE
  COMPLETED AS PLANNED                                 8
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
D46V20, continuous
D46V21, continuous
D46V22, continuous
D46V23, continuous
D46V24, continuous
D46V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 20(11Q23.3) MUTATED                                     0
  DEL PEAK 20(11Q23.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 20(11Q23.3) MUTATED                                     4
  DEL PEAK 20(11Q23.3) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 20(11Q23.3) MUTATED                        23
  DEL PEAK 20(11Q23.3) WILD-TYPE                      13
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 20(11Q23.3) MUTATED                         1
  DEL PEAK 20(11Q23.3) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 20(11Q23.3) MUTATED                         6
  DEL PEAK 20(11Q23.3) WILD-TYPE                       4
D46V26, multiclass
                                     clus
vv                                    DEL PEAK 20(11Q23.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                       23
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        6
                                     clus
vv                                    DEL PEAK 20(11Q23.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              3
  OTHER LOCATION, SPECIFY                                         13
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 20(11Q23.3) MUTATED                                               2
  DEL PEAK 20(11Q23.3) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 20(11Q23.3) MUTATED                                               17
  DEL PEAK 20(11Q23.3) WILD-TYPE                                              8
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 20(11Q23.3) MUTATED                                                                                  54
  DEL PEAK 20(11Q23.3) WILD-TYPE                                                                                28
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 20(11Q23.3) MUTATED                                                                                             58
  DEL PEAK 20(11Q23.3) WILD-TYPE                                                                                           63
D46V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 20(11Q23.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           58
                                                                                              clus
vv                                                                                             DEL PEAK 20(11Q23.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        28
  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"
D46V28, binary
                                cls
clus                              0  1
  DEL PEAK 20(11Q23.3) MUTATED   35 46
  DEL PEAK 20(11Q23.3) WILD-TYPE 36 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED     35   46
  DEL PEAK 20(11Q23.3) WILD-TYPE   36   28
         clus
vv        DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  ABSENT                            35                             36
  PRESENT                           46                             28
[1] 2 2
[1] FALSE
D46V29, continuous
D46V30, continuous
D46V31, binary
                                cls
clus                              0  1
  DEL PEAK 20(11Q23.3) MUTATED   28 64
  DEL PEAK 20(11Q23.3) WILD-TYPE 21 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED     28   64
  DEL PEAK 20(11Q23.3) WILD-TYPE   21   53
                                          clus
vv                                         DEL PEAK 20(11Q23.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           64
                                          clus
vv                                         DEL PEAK 20(11Q23.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             53
[1] 2 2
[1] FALSE
D46V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 20(11Q23.3) MUTATED              7          28         51
  DEL PEAK 20(11Q23.3) WILD-TYPE            8          26         34
D46V33, multiclass
              clus
vv             DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  CURRENT USER                            7                              8
  FORMER USER                            28                             26
  NEVER USED                             51                             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"
D46V34, continuous
D46V35, binary
                                cls
clus                              0  1
  DEL PEAK 20(11Q23.3) MUTATED   49 12
  DEL PEAK 20(11Q23.3) WILD-TYPE 43  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11Q23.3) MUTATED     49   12
  DEL PEAK 20(11Q23.3) WILD-TYPE   43    6
         clus
vv        DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  ABSENT                            49                             43
  PRESENT                           12                              6
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 20(11Q23.3) MUTATED             2        56     0
  DEL PEAK 20(11Q23.3) WILD-TYPE           3        44     2
D46V36, multiclass
             clus
vv            DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  CARBOPLATIN                            2                              3
  CISPLATIN                             56                             44
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V37, continuous
D46V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 20(11Q23.3) MUTATED         4        0         1         1       27
  DEL PEAK 20(11Q23.3) WILD-TYPE       1        1         0         0        7
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 20(11Q23.3) MUTATED          42        13        3         2
  DEL PEAK 20(11Q23.3) WILD-TYPE        35        24        1         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 20(11Q23.3) MUTATED            4          4        25         0
  DEL PEAK 20(11Q23.3) WILD-TYPE          1          3        19         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 20(11Q23.3) MUTATED            3         22         3         4
  DEL PEAK 20(11Q23.3) WILD-TYPE          0         20         4         8
D46V39, multiclass
            clus
vv           DEL PEAK 20(11Q23.3) MUTATED DEL PEAK 20(11Q23.3) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                              0                              1
  STAGE IA1                             1                              0
  STAGE IA2                             1                              0
  STAGE IB                             27                              7
  STAGE IB1                            42                             35
  STAGE IB2                            13                             24
  STAGE II                              3                              1
  STAGE IIA                             2                              6
  STAGE IIA1                            4                              1
  STAGE IIA2                            4                              3
  STAGE IIB                            25                             19
  STAGE III                             0                              1
  STAGE IIIA                            3                              0
  STAGE IIIB                           22                             20
  STAGE IVA                             3                              4
  STAGE IVB                             4                              8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 21(11Q25) MUTATION ANALYSIS
D47V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 21(11Q25) MUTATED   112  44
  DEL PEAK 21(11Q25) WILD-TYPE 102  24
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                         156                          126 
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                          44                           24 
$`DEL PEAK 21(11Q25) MUTATED`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-BI-A0VR 
      146.86        12.59         8.32         0.69        17.82        49.48 
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ 
       57.04        23.67        11.44        68.84        18.74       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29        82.85         5.46        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-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        33.24        52.01       210.67       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       131.11        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KK TCGA-DR-A0ZL 
       45.83        99.91        23.51        27.52        82.06        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76        55.63       117.99       118.65        22.98        16.83 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE 
       17.52         8.28        40.87        30.90        13.05        25.02 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZE 
       24.56        31.73        26.01         7.46        25.91        27.25 
TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       27.22        13.48         0.36         6.64         1.51        19.27 
TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL 
        0.59         0.13        40.96         0.07         0.43        47.77 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L 
        1.64         0.07         0.10        20.35        15.22        19.79 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LA 
       20.98        26.14        16.14        16.57        21.67       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VK 
       66.81       129.37        78.71        81.96        36.36        20.48 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU 
       21.11        20.91        11.28        12.49         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD 
       22.52        20.28        11.38        28.08        34.62        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       35.05        20.84        17.23         2.96        16.41         9.04 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       17.56        15.88         9.34        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       93.99        12.16        10.03        45.57        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        65.49        32.15        53.59        11.51        59.18 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A9U5 TCGA-VS-A9U6 
       33.37        40.14        58.45        55.50        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP 
       48.39        24.30        45.11        14.53        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V2 
       41.52        15.85        14.53         3.42        18.25        18.25 
TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       17.75        15.42        29.26        19.13         1.41         0.16 

$`DEL PEAK 21(11Q25) WILD-TYPE`
TCGA-EX-A449 TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-C5-A1BI TCGA-C5-A1BQ 
       14.70         1.48         4.34        17.52        36.56        19.86 
TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2M1 
       35.01        40.93         3.58        44.22        73.18        38.43 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO 
       18.02        17.85        20.42       101.82       134.33       147.35 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8YT TCGA-C5-A8ZZ 
      155.77        94.95         9.34         8.35        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM 
       14.73         1.12        95.11        44.94        63.98        58.88 
TCGA-DS-A7WF TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 
       16.18        39.55        37.35        31.53        31.36        36.89 
TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       26.40        12.13        24.82        14.89        26.79        27.29 
TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 
       24.00        60.72        26.27         0.39         0.43         0.89 
TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RN 
        1.45         0.30         4.24         1.87         1.74         2.33 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        0.49         0.89         7.92        15.55        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3YQ TCGA-FU-A40J 
       19.04        16.11        31.36        36.26        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JK 
       35.44        10.55         1.12        17.75        25.41        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JW-A5VG 
       14.93         9.44       147.39        96.95        29.85        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        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA3Y 
       18.15       209.59        44.61         0.89         0.30        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A8JM TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       19.56         9.17         8.52        19.96        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        18.64        22.62        69.50        46.52 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       36.13        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9UA TCGA-VS-A9UB 
       15.68        56.35        50.14        51.32        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UR TCGA-VS-A9UZ 
       27.12        46.92         1.71        27.25        26.07        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZX-AA5X 
       18.84         5.16        16.24        26.01        67.59         3.91 

  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                        0.07                         0.30 
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                      210.67                       209.59 
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                      23.820                       20.795 
[1] "0.1 - 210.7 (23.8)" "0.3 - 209.6 (20.8)"
[1] "hr=" "1.2"
D47V2, continuous
                              vv
clus                           T1 T2 T3 T4
  DEL PEAK 21(11Q25) MUTATED   76 33 12  4
  DEL PEAK 21(11Q25) WILD-TYPE 59 37  9  4
D47V3, multiclass
    clus
vv   DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  T1                         76                           59
  T2                         33                           37
  T3                         12                            9
  T4                          4                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED   69 31
  DEL PEAK 21(11Q25) WILD-TYPE 60 25
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED     69   31
  DEL PEAK 21(11Q25) WILD-TYPE   60   25
   clus
vv  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  0                         69                           60
  1                         31                           25
[1] 2 2
[1] FALSE
D47V5, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED   64  5
  DEL PEAK 21(11Q25) WILD-TYPE 44  5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED     64    5
  DEL PEAK 21(11Q25) WILD-TYPE   44    5
   clus
vv  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  0                         64                           44
  1                          5                            5
[1] 2 2
[1] FALSE
D47V6, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED   29 70
  DEL PEAK 21(11Q25) WILD-TYPE 24 55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED     29   70
  DEL PEAK 21(11Q25) WILD-TYPE   24   55
     clus
vv    DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  NO                          29                           24
  YES                         70                           55
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(11Q25) MUTATED               1                              142
  DEL PEAK 21(11Q25) WILD-TYPE             5                              100
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 21(11Q25) MUTATED                                               1
  DEL PEAK 21(11Q25) WILD-TYPE                                             5
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 21(11Q25) MUTATED                                     8
  DEL PEAK 21(11Q25) WILD-TYPE                                  13
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 21(11Q25) MUTATED                                           1
  DEL PEAK 21(11Q25) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 21(11Q25) MUTATED                                              7
  DEL PEAK 21(11Q25) WILD-TYPE                                           10
D47V7, multiclass
                                               clus
vv                                              DEL PEAK 21(11Q25) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                     142
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           7
                                               clus
vv                                              DEL PEAK 21(11Q25) WILD-TYPE
  ADENOSQUAMOUS                                                            5
  CERVICAL SQUAMOUS CELL CARCINOMA                                       100
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, continuous
D47V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(11Q25) MUTATED                                  3    12
  DEL PEAK 21(11Q25) WILD-TYPE                                5     7
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(11Q25) MUTATED                          20
  DEL PEAK 21(11Q25) WILD-TYPE                         8
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(11Q25) MUTATED                                           2   108
  DEL PEAK 21(11Q25) WILD-TYPE                                         0    94
D47V10, multiclass
                                           clus
vv                                          DEL PEAK 21(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   3
  ASIAN                                                             12
  BLACK OR AFRICAN AMERICAN                                         20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                            108
                                           clus
vv                                          DEL PEAK 21(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               94
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED    8 90
  DEL PEAK 21(11Q25) WILD-TYPE 15 73
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED      8   90
  DEL PEAK 21(11Q25) WILD-TYPE   15   73
                        clus
vv                       DEL PEAK 21(11Q25) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         90
                        clus
vv                       DEL PEAK 21(11Q25) WILD-TYPE
  HISPANIC OR LATINO                               15
  NOT HISPANIC OR LATINO                           73
[1] 2 2
[1] FALSE
D47V12, continuous
D47V13, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED   98 47
  DEL PEAK 21(11Q25) WILD-TYPE 95 29
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED     98   47
  DEL PEAK 21(11Q25) WILD-TYPE   95   29
            clus
vv           DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  TUMOR FREE                         98                           95
  WITH TUMOR                         47                           29
[1] 2 2
[1] FALSE
                              vv
clus                           G1 G2 G3 G4 GX
  DEL PEAK 21(11Q25) MUTATED    8 71 65  1 11
  DEL PEAK 21(11Q25) WILD-TYPE 10 58 50  0 13
D47V14, multiclass
    clus
vv   DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  G1                          8                           10
  G2                         71                           58
  G3                         65                           50
  G4                          1                            0
  GX                         11                           13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, continuous
D47V16, continuous
D47V17, continuous
D47V18, continuous
D47V19, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED   18  2
  DEL PEAK 21(11Q25) WILD-TYPE  7  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED     18    2
  DEL PEAK 21(11Q25) WILD-TYPE    7    1
                         clus
vv                        DEL PEAK 21(11Q25) MUTATED
  COMPLETED AS PLANNED                            18
  TREATMENT NOT COMPLETED                          2
                         clus
vv                        DEL PEAK 21(11Q25) WILD-TYPE
  COMPLETED AS PLANNED                               7
  TREATMENT NOT COMPLETED                            1
[1] 2 2
[1] FALSE
D47V20, continuous
D47V21, continuous
D47V22, continuous
D47V23, continuous
D47V24, continuous
D47V25, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 21(11Q25) MUTATED                                     0
  DEL PEAK 21(11Q25) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 21(11Q25) MUTATED                                     4
  DEL PEAK 21(11Q25) WILD-TYPE                                   3
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 21(11Q25) MUTATED                        23                       1
  DEL PEAK 21(11Q25) WILD-TYPE                      13                       0
                              vv
clus                           POSITIVE VAGINAL MARGIN
  DEL PEAK 21(11Q25) MUTATED                         6
  DEL PEAK 21(11Q25) WILD-TYPE                       4
D47V26, multiclass
                                     clus
vv                                    DEL PEAK 21(11Q25) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          4
  OTHER LOCATION, SPECIFY                                     23
  POSITIVE BLADDER MARGIN                                      1
  POSITIVE VAGINAL MARGIN                                      6
                                     clus
vv                                    DEL PEAK 21(11Q25) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                       13
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 21(11Q25) MUTATED                                               2
  DEL PEAK 21(11Q25) WILD-TYPE                                             1
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 21(11Q25) MUTATED                                               17
  DEL PEAK 21(11Q25) WILD-TYPE                                              8
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 21(11Q25) MUTATED                                                                                  50
  DEL PEAK 21(11Q25) WILD-TYPE                                                                                32
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 21(11Q25) MUTATED                                                                                             58
  DEL PEAK 21(11Q25) WILD-TYPE                                                                                           63
D47V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 21(11Q25) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    50
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         58
                                                                                              clus
vv                                                                                             DEL PEAK 21(11Q25) 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)                                      32
  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"
D47V28, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED   34 47
  DEL PEAK 21(11Q25) WILD-TYPE 37 27
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED     34   47
  DEL PEAK 21(11Q25) WILD-TYPE   37   27
         clus
vv        DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  ABSENT                          34                           37
  PRESENT                         47                           27
[1] 2 2
[1] FALSE
D47V29, continuous
D47V30, continuous
D47V31, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED   28 66
  DEL PEAK 21(11Q25) WILD-TYPE 21 51
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED     28   66
  DEL PEAK 21(11Q25) WILD-TYPE   21   51
                                          clus
vv                                         DEL PEAK 21(11Q25) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         66
                                          clus
vv                                         DEL PEAK 21(11Q25) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           51
[1] 2 2
[1] FALSE
D47V32, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  DEL PEAK 21(11Q25) MUTATED              7          29         47
  DEL PEAK 21(11Q25) WILD-TYPE            8          25         38
D47V33, multiclass
              clus
vv             DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  CURRENT USER                          7                            8
  FORMER USER                          29                           25
  NEVER USED                           47                           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"
D47V34, continuous
D47V35, binary
                              cls
clus                            0  1
  DEL PEAK 21(11Q25) MUTATED   49 12
  DEL PEAK 21(11Q25) WILD-TYPE 43  6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED     49   12
  DEL PEAK 21(11Q25) WILD-TYPE   43    6
         clus
vv        DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  ABSENT                          49                           43
  PRESENT                         12                            6
[1] 2 2
[1] FALSE
                              vv
clus                           CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 21(11Q25) MUTATED             2        55     0
  DEL PEAK 21(11Q25) WILD-TYPE           3        45     2
D47V36, multiclass
             clus
vv            DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  CARBOPLATIN                          2                            3
  CISPLATIN                           55                           45
  OTHER                                0                            2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V37, continuous
D47V38, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 21(11Q25) MUTATED         4        0         1         1       27
  DEL PEAK 21(11Q25) WILD-TYPE       1        1         0         0        7
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 21(11Q25) MUTATED          44        13        3         2
  DEL PEAK 21(11Q25) WILD-TYPE        33        24        1         6
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 21(11Q25) MUTATED            4          4        23         0
  DEL PEAK 21(11Q25) WILD-TYPE          1          3        21         1
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 21(11Q25) MUTATED            2         21         3         5
  DEL PEAK 21(11Q25) WILD-TYPE          1         21         4         7
D47V39, multiclass
            clus
vv           DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  STAGE I                             4                            1
  STAGE IA                            0                            1
  STAGE IA1                           1                            0
  STAGE IA2                           1                            0
  STAGE IB                           27                            7
  STAGE IB1                          44                           33
  STAGE IB2                          13                           24
  STAGE II                            3                            1
  STAGE IIA                           2                            6
  STAGE IIA1                          4                            1
  STAGE IIA2                          4                            3
  STAGE IIB                          23                           21
  STAGE III                           0                            1
  STAGE IIIA                          2                            1
  STAGE IIIB                         21                           21
  STAGE IVA                           3                            4
  STAGE IVB                           5                            7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 22(13Q12.11) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 22(13Q12.11) MUTATED    72  23
  DEL PEAK 22(13Q12.11) WILD-TYPE 142  45
  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE 
                             95                             187 
  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE 
                             23                              45 
$`DEL PEAK 22(13Q12.11) MUTATED`
TCGA-EK-A2GZ TCGA-EX-A69M TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF 
       12.59         8.32        49.48        57.04        68.84        18.74 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MH 
      144.16       173.29        82.85         5.46        31.40        38.99 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG 
       73.18        73.45        83.05        38.43        18.02       210.67 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
      154.32       134.33       147.35       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A8XK TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VM 
        9.34        99.91        14.73        95.11        87.75       117.99 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A5ZD TCGA-EA-A97N 
      118.65        40.87        25.02        12.13        27.29         0.36 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       60.72        26.27        19.27         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RK 
        0.89         1.45        40.96         4.24         1.87         0.43 
TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A5XV 
        1.64        20.35        23.84        20.98        26.14        10.55 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH 
       25.41        16.57        21.67         9.44       147.39        78.71 
TCGA-JW-A5VK TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        18.15        21.11        44.61        11.28         0.89 
TCGA-LP-A4AX TCGA-MA-AA42 TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73R 
       12.49         8.52        17.23        15.95         9.04        18.64 
TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI 
       19.59        12.16        10.03        46.52        32.42        23.97 
TCGA-VS-A8Q9 TCGA-VS-A8QM TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A9U6 
       53.59        31.27        40.14        15.68        55.50        43.40 
TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UT 
       28.50        24.30        45.11        14.53        27.25        15.85 
TCGA-VS-A9UU TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       14.53        26.01        29.26        67.59        19.13 

$`DEL PEAK 22(13Q12.11) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        14.70         1.48         4.34         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BQ 
       17.82        23.67        11.44        36.56       177.04        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF 
       44.22        78.35       100.14        33.24        52.01        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X5 
       20.42       101.82        15.48        20.35        17.19        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR 
        2.73        50.99        45.83         8.35        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.81        20.91         1.12        82.06        44.94        63.98 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88        36.76        55.63        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       31.36        13.05        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       26.01        24.82         7.46        14.89        26.79        25.91 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2PG 
       27.25        27.22        24.00        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         0.30         0.07         1.74        47.77         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.10         0.49         0.89         7.92        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       19.79        15.55        12.23        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
       36.26        16.14        28.31        14.01        35.44         1.12 
TCGA-GH-A9DA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       17.75        20.78        14.93       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q0 
       24.56        21.44        15.58        28.37         8.28       209.59 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       20.91         0.30         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       17.82        19.56         9.17        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
       19.96        54.81        35.05        20.84         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       16.41        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG 
       22.62        14.60        11.67        93.99        69.50        45.57 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        65.49        32.15        36.13        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       39.78        40.87        16.64         4.73        33.37        58.45 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UB 
       56.35        50.14        51.32        50.47        48.39        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
       27.12        46.92         1.71        47.87        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       26.07         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       18.25        17.75        16.24        15.42         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE 
                           0.36                            0.07 
  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE 
                         210.67                          209.59 
  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE 
                          25.02                           20.91 
[1] "0.4 - 210.7 (25.0)" "0.1 - 209.6 (20.9)"
[1] "hr=" "1.3"
D48V2, continuous
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 22(13Q12.11) MUTATED   39 16 11  2
  DEL PEAK 22(13Q12.11) WILD-TYPE 96 54 10  6
D48V3, multiclass
    clus
vv   DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  T1                            39                              96
  T2                            16                              54
  T3                            11                              10
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                                 cls
clus                               0  1
  DEL PEAK 22(13Q12.11) MUTATED   33 22
  DEL PEAK 22(13Q12.11) WILD-TYPE 96 34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED     33   22
  DEL PEAK 22(13Q12.11) WILD-TYPE   96   34
   clus
vv  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  0                            33                              96
  1                            22                              34
[1] 2 2
[1] FALSE
D48V5, binary
                                 cls
clus                               0  1
  DEL PEAK 22(13Q12.11) MUTATED   33  5
  DEL PEAK 22(13Q12.11) WILD-TYPE 75  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED     33    5
  DEL PEAK 22(13Q12.11) WILD-TYPE   75    5
   clus
vv  DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  0                            33                              75
  1                             5                               5
[1] 2 2
[1] FALSE
D48V6, binary
                                 cls
clus                               0  1
  DEL PEAK 22(13Q12.11) MUTATED   18 42
  DEL PEAK 22(13Q12.11) WILD-TYPE 35 83
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED     18   42
  DEL PEAK 22(13Q12.11) WILD-TYPE   35   83
     clus
vv    DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  NO                             18                              35
  YES                            42                              83
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 22(13Q12.11) MUTATED               2
  DEL PEAK 22(13Q12.11) WILD-TYPE             4
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(13Q12.11) MUTATED                                 92
  DEL PEAK 22(13Q12.11) WILD-TYPE                              150
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 22(13Q12.11) MUTATED                                               0
  DEL PEAK 22(13Q12.11) WILD-TYPE                                             6
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 22(13Q12.11) MUTATED                                     3
  DEL PEAK 22(13Q12.11) WILD-TYPE                                  18
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 22(13Q12.11) MUTATED                                           0
  DEL PEAK 22(13Q12.11) WILD-TYPE                                         3
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 22(13Q12.11) MUTATED                                              1
  DEL PEAK 22(13Q12.11) WILD-TYPE                                           16
D48V7, multiclass
                                               clus
vv                                              DEL PEAK 22(13Q12.11) MUTATED
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         92
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              1
                                               clus
vv                                              DEL PEAK 22(13Q12.11) WILD-TYPE
  ADENOSQUAMOUS                                                               4
  CERVICAL SQUAMOUS CELL CARCINOMA                                          150
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, continuous
D48V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(13Q12.11) MUTATED                                  0     8
  DEL PEAK 22(13Q12.11) WILD-TYPE                                8    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(13Q12.11) MUTATED                          13
  DEL PEAK 22(13Q12.11) WILD-TYPE                        15
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 22(13Q12.11) MUTATED                                           1
  DEL PEAK 22(13Q12.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 22(13Q12.11) MUTATED      67
  DEL PEAK 22(13Q12.11) WILD-TYPE   135
D48V10, multiclass
                                           clus
vv                                          DEL PEAK 22(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 8
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                67
                                           clus
vv                                          DEL PEAK 22(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  11
  BLACK OR AFRICAN AMERICAN                                              15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 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"
D48V11, binary
                                 cls
clus                                0   1
  DEL PEAK 22(13Q12.11) MUTATED     5  53
  DEL PEAK 22(13Q12.11) WILD-TYPE  18 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED      5   53
  DEL PEAK 22(13Q12.11) WILD-TYPE   18  110
                        clus
vv                       DEL PEAK 22(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       DEL PEAK 22(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                  18
  NOT HISPANIC OR LATINO                             110
[1] 2 2
[1] FALSE
D48V12, continuous
D48V13, binary
                                 cls
clus                                0   1
  DEL PEAK 22(13Q12.11) MUTATED    70  23
  DEL PEAK 22(13Q12.11) WILD-TYPE 123  53
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED     70   23
  DEL PEAK 22(13Q12.11) WILD-TYPE  123   53
            clus
vv           DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  TUMOR FREE                            70                             123
  WITH TUMOR                            23                              53
[1] 2 2
[1] FALSE
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 22(13Q12.11) MUTATED    4 35 45  1 10
  DEL PEAK 22(13Q12.11) WILD-TYPE 14 94 70  0 14
D48V14, multiclass
    clus
vv   DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  G1                             4                              14
  G2                            35                              94
  G3                            45                              70
  G4                             1                               0
  GX                            10                              14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, continuous
D48V16, continuous
D48V17, continuous
D48V18, continuous
D48V19, binary
                                 cls
clus                               0  1
  DEL PEAK 22(13Q12.11) MUTATED   12  1
  DEL PEAK 22(13Q12.11) WILD-TYPE 13  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED     12    1
  DEL PEAK 22(13Q12.11) WILD-TYPE   13    2
                         clus
vv                        DEL PEAK 22(13Q12.11) MUTATED
  COMPLETED AS PLANNED                               12
  TREATMENT NOT COMPLETED                             1
                         clus
vv                        DEL PEAK 22(13Q12.11) WILD-TYPE
  COMPLETED AS PLANNED                                 13
  TREATMENT NOT COMPLETED                               2
[1] 2 2
[1] FALSE
D48V20, continuous
D48V21, continuous
D48V22, continuous
D48V23, continuous
D48V24, continuous
D48V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 22(13Q12.11) MUTATED                                     0
  DEL PEAK 22(13Q12.11) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 22(13Q12.11) MUTATED                                     2
  DEL PEAK 22(13Q12.11) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 22(13Q12.11) MUTATED                        11
  DEL PEAK 22(13Q12.11) WILD-TYPE                      25
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 22(13Q12.11) MUTATED                         0
  DEL PEAK 22(13Q12.11) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 22(13Q12.11) MUTATED                         5
  DEL PEAK 22(13Q12.11) WILD-TYPE                       5
D48V26, multiclass
                                     clus
vv                                    DEL PEAK 22(13Q12.11) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                        11
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         5
                                     clus
vv                                    DEL PEAK 22(13Q12.11) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                          25
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 22(13Q12.11) MUTATED                                               1
  DEL PEAK 22(13Q12.11) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 22(13Q12.11) MUTATED                                                6
  DEL PEAK 22(13Q12.11) WILD-TYPE                                             19
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 22(13Q12.11) MUTATED                                                                                  29
  DEL PEAK 22(13Q12.11) WILD-TYPE                                                                                53
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 22(13Q12.11) MUTATED                                                                                             41
  DEL PEAK 22(13Q12.11) WILD-TYPE                                                                                           80
D48V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 22(13Q12.11) 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)                                       29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            41
                                                                                              clus
vv                                                                                             DEL PEAK 22(13Q12.11) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              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"
D48V28, binary
                                 cls
clus                               0  1
  DEL PEAK 22(13Q12.11) MUTATED   19 26
  DEL PEAK 22(13Q12.11) WILD-TYPE 52 48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED     19   26
  DEL PEAK 22(13Q12.11) WILD-TYPE   52   48
         clus
vv        DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  ABSENT                             19                              52
  PRESENT                            26                              48
[1] 2 2
[1] FALSE
D48V29, continuous
D48V30, continuous
D48V31, binary
                                 cls
clus                               0  1
  DEL PEAK 22(13Q12.11) MUTATED   16 43
  DEL PEAK 22(13Q12.11) WILD-TYPE 33 74
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED     16   43
  DEL PEAK 22(13Q12.11) WILD-TYPE   33   74
                                          clus
vv                                         DEL PEAK 22(13Q12.11) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            43
                                          clus
vv                                         DEL PEAK 22(13Q12.11) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              74
[1] 2 2
[1] FALSE
D48V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 22(13Q12.11) MUTATED              3          16         28
  DEL PEAK 22(13Q12.11) WILD-TYPE           12          38         57
D48V33, multiclass
              clus
vv             DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  CURRENT USER                             3                              12
  FORMER USER                             16                              38
  NEVER USED                              28                              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V34, continuous
D48V35, binary
                                 cls
clus                               0  1
  DEL PEAK 22(13Q12.11) MUTATED   23  7
  DEL PEAK 22(13Q12.11) WILD-TYPE 69 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(13Q12.11) MUTATED     23    7
  DEL PEAK 22(13Q12.11) WILD-TYPE   69   11
         clus
vv        DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  ABSENT                             23                              69
  PRESENT                             7                              11
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 22(13Q12.11) MUTATED             0        37     1
  DEL PEAK 22(13Q12.11) WILD-TYPE           5        63     1
D48V36, multiclass
             clus
vv            DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  CARBOPLATIN                             0                               5
  CISPLATIN                              37                              63
  OTHER                                   1                               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"
D48V37, continuous
D48V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 22(13Q12.11) MUTATED         3        1         0         1       18
  DEL PEAK 22(13Q12.11) WILD-TYPE       2        0         1         0       16
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 22(13Q12.11) MUTATED          16        12        0         2
  DEL PEAK 22(13Q12.11) WILD-TYPE        61        25        4         6
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 22(13Q12.11) MUTATED            2          1        12         0
  DEL PEAK 22(13Q12.11) WILD-TYPE          3          6        32         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 22(13Q12.11) MUTATED            3         18         2         4
  DEL PEAK 22(13Q12.11) WILD-TYPE          0         24         5         8
D48V39, multiclass
            clus
vv           DEL PEAK 22(13Q12.11) MUTATED DEL PEAK 22(13Q12.11) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                               1                               0
  STAGE IA1                              0                               1
  STAGE IA2                              1                               0
  STAGE IB                              18                              16
  STAGE IB1                             16                              61
  STAGE IB2                             12                              25
  STAGE II                               0                               4
  STAGE IIA                              2                               6
  STAGE IIA1                             2                               3
  STAGE IIA2                             1                               6
  STAGE IIB                             12                              32
  STAGE III                              0                               1
  STAGE IIIA                             3                               0
  STAGE IIIB                            18                              24
  STAGE IVA                              2                               5
  STAGE IVB                              4                               8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 23(13Q14.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(13Q14.2) MUTATED    86  26
  DEL PEAK 23(13Q14.2) WILD-TYPE 128  42
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           112                            170 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                            26                             42 
$`DEL PEAK 23(13Q14.2) MUTATED`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-BI-A0VR 
      146.86        12.59         8.32         1.48         0.69        49.48 
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM 
       57.04        68.84        18.74       144.16       173.29        82.85 
TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       31.40        57.73        38.99        73.18        73.45        83.05 
TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CO 
       38.43        18.02       210.67       154.32       134.33       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XK 
      155.77       131.11        94.95         9.34         8.35        99.91 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-DS-A0VN 
       20.91        14.73        95.11        87.75       117.99       118.65 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A439 TCGA-EA-A78R 
       22.98        40.87        13.05        25.02        31.73        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
        0.36        60.72        26.27         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RE 
        0.43         0.89         1.45        40.96         0.07         1.87 
TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.43         0.10        20.35        23.84        20.98        26.14 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
       10.55        25.41        16.57        21.67        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
      147.39        78.71        20.48         8.28        18.15        21.11 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MA-AA3W TCGA-MA-AA42 
       44.61        11.28         0.89        12.49        22.52         8.52 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
       35.05        17.23         9.04         9.34        18.64        19.59 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       12.16        10.03        46.52        32.42        23.97        19.96 
TCGA-VS-A8EL TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 
       65.49        59.18        31.27         4.73        40.14        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UI 
       56.35        55.50        50.47        28.50        24.30        45.11 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9V1 
       14.53        27.25        47.47        15.85        14.53         5.16 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       26.01        29.26        67.59        19.13 

$`DEL PEAK 23(13Q14.2) WILD-TYPE`
TCGA-EX-A449 TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN 
       14.70         4.34        17.52        17.82        23.67        11.44 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
       36.56       177.04         5.46        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       30.21        35.01        53.16        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ 
       20.91        40.93         3.58        44.22        78.35       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL 
       33.24        52.01        17.85        20.42       101.82        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       20.35        17.19        13.61         2.73        50.99        45.83 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       23.51        27.52        20.81         1.12        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A5RQ TCGA-DS-A7WF 
       63.98        58.88        36.76        55.63        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S 
       31.36        36.89        26.40        24.56        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PM TCGA-EK-A2R9 
       27.25        27.22        24.00         6.64         0.59         0.13 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.30         4.24         1.74        47.77         1.64         2.33 
TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L 
        0.07         0.49         0.89         7.92        15.22        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55        12.23        19.04        16.11        31.36        36.26 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA 
       16.14        28.31        14.01        35.44         1.12        17.75 
TCGA-HM-A3JK TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
       20.78       137.16        66.81       129.37        96.95        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 
       15.58        28.37       209.59        20.91         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 
       13.35        20.28        17.82        19.56         9.17        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA 
       28.08        34.62        19.96        54.81        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       15.88        22.62        14.60        11.67        93.99        69.50 
TCGA-VS-A8EG TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH 
       45.57        32.15        53.59        36.13        11.51        39.78 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A958 TCGA-VS-A959 
       40.87        16.64        33.37        58.45        50.14        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ 
       43.40        48.39        29.95        27.12        46.92         1.71 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       47.87        41.52        26.07         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-AAXA 
       18.84        18.25        17.75        16.24        15.42         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                        210.67                         209.59 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                        23.905                         20.910 
[1] "0.1 - 210.7 (23.9)" "0.1 - 209.6 (20.9)"
[1] "hr=" "1.4"
D49V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 23(13Q14.2) MUTATED   49 23 15  1
  DEL PEAK 23(13Q14.2) WILD-TYPE 86 47  6  7
D49V3, multiclass
    clus
vv   DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  T1                           49                             86
  T2                           23                             47
  T3                           15                              6
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                                cls
clus                              0  1
  DEL PEAK 23(13Q14.2) MUTATED   41 27
  DEL PEAK 23(13Q14.2) WILD-TYPE 88 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     41   27
  DEL PEAK 23(13Q14.2) WILD-TYPE   88   29
   clus
vv  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  0                           41                             88
  1                           27                             29
[1] 2 2
[1] FALSE
D49V5, binary
                                cls
clus                              0  1
  DEL PEAK 23(13Q14.2) MUTATED   42  5
  DEL PEAK 23(13Q14.2) WILD-TYPE 66  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     42    5
  DEL PEAK 23(13Q14.2) WILD-TYPE   66    5
   clus
vv  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  0                           42                             66
  1                            5                              5
[1] 2 2
[1] FALSE
D49V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(13Q14.2) MUTATED   19 55
  DEL PEAK 23(13Q14.2) WILD-TYPE 34 70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     19   55
  DEL PEAK 23(13Q14.2) WILD-TYPE   34   70
     clus
vv    DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  NO                            19                             34
  YES                           55                             70
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(13Q14.2) MUTATED               2                              108
  DEL PEAK 23(13Q14.2) WILD-TYPE             4                              134
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 23(13Q14.2) MUTATED                                               1
  DEL PEAK 23(13Q14.2) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 23(13Q14.2) MUTATED                                     4
  DEL PEAK 23(13Q14.2) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 23(13Q14.2) MUTATED                                           0
  DEL PEAK 23(13Q14.2) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 23(13Q14.2) MUTATED                                              3
  DEL PEAK 23(13Q14.2) WILD-TYPE                                           14
D49V7, multiclass
                                               clus
vv                                              DEL PEAK 23(13Q14.2) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       108
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             3
                                               clus
vv                                              DEL PEAK 23(13Q14.2) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         134
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, continuous
D49V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(13Q14.2) MUTATED                                  1     9
  DEL PEAK 23(13Q14.2) WILD-TYPE                                7    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(13Q14.2) MUTATED                          17
  DEL PEAK 23(13Q14.2) WILD-TYPE                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 23(13Q14.2) MUTATED                                           2
  DEL PEAK 23(13Q14.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 23(13Q14.2) MUTATED      76
  DEL PEAK 23(13Q14.2) WILD-TYPE   126
D49V10, multiclass
                                           clus
vv                                          DEL PEAK 23(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               76
                                           clus
vv                                          DEL PEAK 23(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 10
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D49V11, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED     7  61
  DEL PEAK 23(13Q14.2) WILD-TYPE  16 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED      7   61
  DEL PEAK 23(13Q14.2) WILD-TYPE   16  102
                        clus
vv                       DEL PEAK 23(13Q14.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 23(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            102
[1] 2 2
[1] FALSE
D49V12, continuous
D49V13, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED    82  25
  DEL PEAK 23(13Q14.2) WILD-TYPE 111  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     82   25
  DEL PEAK 23(13Q14.2) WILD-TYPE  111   51
            clus
vv           DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  TUMOR FREE                           82                            111
  WITH TUMOR                           25                             51
[1] 2 2
[1] FALSE
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 23(13Q14.2) MUTATED    5 39 57  1 11
  DEL PEAK 23(13Q14.2) WILD-TYPE 13 90 58  0 13
D49V14, multiclass
    clus
vv   DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  G1                            5                             13
  G2                           39                             90
  G3                           57                             58
  G4                            1                              0
  GX                           11                             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, continuous
D49V16, continuous
D49V17, continuous
D49V18, continuous
D49V19, binary
                                cls
clus                              0  1
  DEL PEAK 23(13Q14.2) MUTATED   12  1
  DEL PEAK 23(13Q14.2) WILD-TYPE 13  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     12    1
  DEL PEAK 23(13Q14.2) WILD-TYPE   13    2
                         clus
vv                        DEL PEAK 23(13Q14.2) MUTATED
  COMPLETED AS PLANNED                              12
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 23(13Q14.2) WILD-TYPE
  COMPLETED AS PLANNED                                13
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D49V20, continuous
D49V21, continuous
D49V22, continuous
D49V23, continuous
D49V24, continuous
D49V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 23(13Q14.2) MUTATED                                     0
  DEL PEAK 23(13Q14.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 23(13Q14.2) MUTATED                                     2
  DEL PEAK 23(13Q14.2) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 23(13Q14.2) MUTATED                        15
  DEL PEAK 23(13Q14.2) WILD-TYPE                      21
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 23(13Q14.2) MUTATED                         0
  DEL PEAK 23(13Q14.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 23(13Q14.2) MUTATED                         5
  DEL PEAK 23(13Q14.2) WILD-TYPE                       5
D49V26, multiclass
                                     clus
vv                                    DEL PEAK 23(13Q14.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       15
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        5
                                     clus
vv                                    DEL PEAK 23(13Q14.2) 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 23(13Q14.2) MUTATED                                               1
  DEL PEAK 23(13Q14.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 23(13Q14.2) MUTATED                                                9
  DEL PEAK 23(13Q14.2) WILD-TYPE                                             16
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 23(13Q14.2) MUTATED                                                                                  35
  DEL PEAK 23(13Q14.2) WILD-TYPE                                                                                47
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 23(13Q14.2) MUTATED                                                                                             48
  DEL PEAK 23(13Q14.2) WILD-TYPE                                                                                           73
D49V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 23(13Q14.2) 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)                                      35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           48
                                                                                              clus
vv                                                                                             DEL PEAK 23(13Q14.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        47
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D49V28, binary
                                cls
clus                              0  1
  DEL PEAK 23(13Q14.2) MUTATED   22 29
  DEL PEAK 23(13Q14.2) WILD-TYPE 49 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     22   29
  DEL PEAK 23(13Q14.2) WILD-TYPE   49   45
         clus
vv        DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  ABSENT                            22                             49
  PRESENT                           29                             45
[1] 2 2
[1] FALSE
D49V29, continuous
D49V30, continuous
D49V31, binary
                                cls
clus                              0  1
  DEL PEAK 23(13Q14.2) MUTATED   19 50
  DEL PEAK 23(13Q14.2) WILD-TYPE 30 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     19   50
  DEL PEAK 23(13Q14.2) WILD-TYPE   30   67
                                          clus
vv                                         DEL PEAK 23(13Q14.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           50
                                          clus
vv                                         DEL PEAK 23(13Q14.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             67
[1] 2 2
[1] FALSE
D49V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 23(13Q14.2) MUTATED              4          20         30
  DEL PEAK 23(13Q14.2) WILD-TYPE           11          34         55
D49V33, multiclass
              clus
vv             DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  CURRENT USER                            4                             11
  FORMER USER                            20                             34
  NEVER USED                             30                             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"
D49V34, continuous
D49V35, binary
                                cls
clus                              0  1
  DEL PEAK 23(13Q14.2) MUTATED   25  9
  DEL PEAK 23(13Q14.2) WILD-TYPE 67  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     25    9
  DEL PEAK 23(13Q14.2) WILD-TYPE   67    9
         clus
vv        DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  ABSENT                            25                             67
  PRESENT                            9                              9
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 23(13Q14.2) MUTATED             0        45     1
  DEL PEAK 23(13Q14.2) WILD-TYPE           5        55     1
D49V36, multiclass
             clus
vv            DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  CARBOPLATIN                            0                              5
  CISPLATIN                             45                             55
  OTHER                                  1                              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"
D49V37, continuous
D49V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 23(13Q14.2) MUTATED         4        1         0         1       18
  DEL PEAK 23(13Q14.2) WILD-TYPE       1        0         1         0       16
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 23(13Q14.2) MUTATED          19        14        1         3
  DEL PEAK 23(13Q14.2) WILD-TYPE        58        23        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 23(13Q14.2) MUTATED            3          1        18         0
  DEL PEAK 23(13Q14.2) WILD-TYPE          2          6        26         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 23(13Q14.2) MUTATED            3         22         2         4
  DEL PEAK 23(13Q14.2) WILD-TYPE          0         20         5         8
D49V39, multiclass
            clus
vv           DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                             18                             16
  STAGE IB1                            19                             58
  STAGE IB2                            14                             23
  STAGE II                              1                              3
  STAGE IIA                             3                              5
  STAGE IIA1                            3                              2
  STAGE IIA2                            1                              6
  STAGE IIB                            18                             26
  STAGE III                             0                              1
  STAGE IIIA                            3                              0
  STAGE IIIB                           22                             20
  STAGE IVA                             2                              5
  STAGE IVB                             4                              8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 24(14Q32.31) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(14Q32.31) MUTATED    36   8
  DEL PEAK 24(14Q32.31) WILD-TYPE 178  60
  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE 
                             44                             238 
  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE 
                              8                              60 
$`DEL PEAK 24(14Q32.31) MUTATED`
TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-BI-A20A TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
        1.48         4.34        23.67        57.73        53.16         0.46 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CM TCGA-C5-A8XH TCGA-C5-A8YR 
       83.05        38.43        18.02        20.35        45.83        27.52 
TCGA-DG-A2KJ TCGA-EA-A3HQ TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A78R 
       95.11        37.35        36.89        24.56        26.01        13.48 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM 
        1.51         0.39         0.59         0.89         1.74         1.64 
TCGA-EX-A8YF TCGA-FU-A23L TCGA-IR-A3LA TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-LP-A4AU 
       15.55        23.84       137.16        78.71        21.11        11.28 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA42 TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A73R 
        0.30        13.35         8.52        54.81        16.41        18.64 
TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A959 TCGA-VS-A9U7 
       12.16        65.49        39.78         4.73        51.32        48.39 
TCGA-VS-A9UA TCGA-VS-A9V3 
       28.50        17.75 

$`DEL PEAK 24(14Q32.31) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        12.59        14.70         8.32         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       17.82        49.48        57.04        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       38.99        35.61         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 
       44.22        73.18        73.45        78.35       100.14        33.24 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       52.01        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI 
       94.95         9.34        13.61         2.73        50.99         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       99.91        23.51        20.81        20.91        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       55.63       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        39.55        40.87        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A44S 
       31.36        13.05        25.02        26.40        31.73        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.25        27.22        24.00         0.36        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        6.64        19.27         0.43         1.45         0.13        40.96 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RL 
        0.30         4.24         0.07         1.87         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.33         0.07         0.10         0.49         0.89        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92        15.22        19.79        12.23        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        20.98        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       14.01        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        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       129.37        96.95        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       28.37         8.28        18.15       209.59        44.61        20.91 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.89        12.49         0.82        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         9.17        11.38        28.08        34.62        19.96 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       35.05        20.84        17.23         2.96        15.58        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       22.62        19.59        14.60        11.67        93.99        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        46.52        45.57        32.42        23.97        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       32.15        53.59        36.13        11.51        59.18        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       40.87        16.64        33.37        40.14        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB 
       56.35        55.50        50.14        50.47        43.40        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       27.12        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       18.25        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         1.41         0.16         3.91 

  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE 
                           0.30                            0.07 
  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE 
                         137.16                          210.67 
  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE 
                          20.73                           22.80 
[1] "0.3 - 137.2 (20.7)" "0.1 - 210.7 (22.8)"
[1] "hr=" "1.2"
D50V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 24(14Q32.31) MUTATED    21  14   3   2
  DEL PEAK 24(14Q32.31) WILD-TYPE 114  56  18   6
D50V3, multiclass
    clus
vv   DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  T1                            21                             114
  T2                            14                              56
  T3                             3                              18
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.31) MUTATED    23  10
  DEL PEAK 24(14Q32.31) WILD-TYPE 106  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED     23   10
  DEL PEAK 24(14Q32.31) WILD-TYPE  106   46
   clus
vv  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  0                            23                             106
  1                            10                              46
[1] 2 2
[1] FALSE
D50V5, binary
                                 cls
clus                               0  1
  DEL PEAK 24(14Q32.31) MUTATED   25  0
  DEL PEAK 24(14Q32.31) WILD-TYPE 83 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED     25    0
  DEL PEAK 24(14Q32.31) WILD-TYPE   83   10
   clus
vv  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  0                            25                              83
  1                             0                              10
[1] 2 2
[1] FALSE
D50V6, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.31) MUTATED     7  20
  DEL PEAK 24(14Q32.31) WILD-TYPE  46 105
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED      7   20
  DEL PEAK 24(14Q32.31) WILD-TYPE   46  105
     clus
vv    DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  NO                              7                              46
  YES                            20                             105
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 24(14Q32.31) MUTATED               0
  DEL PEAK 24(14Q32.31) WILD-TYPE             6
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(14Q32.31) MUTATED                                 38
  DEL PEAK 24(14Q32.31) WILD-TYPE                              204
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 24(14Q32.31) MUTATED                                               3
  DEL PEAK 24(14Q32.31) WILD-TYPE                                             3
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 24(14Q32.31) MUTATED                                     6
  DEL PEAK 24(14Q32.31) WILD-TYPE                                  15
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 24(14Q32.31) MUTATED                                           1
  DEL PEAK 24(14Q32.31) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 24(14Q32.31) MUTATED                                              2
  DEL PEAK 24(14Q32.31) WILD-TYPE                                           15
D50V7, multiclass
                                               clus
vv                                              DEL PEAK 24(14Q32.31) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              2
                                               clus
vv                                              DEL PEAK 24(14Q32.31) WILD-TYPE
  ADENOSQUAMOUS                                                               6
  CERVICAL SQUAMOUS CELL CARCINOMA                                          204
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, continuous
D50V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(14Q32.31) MUTATED                                  0     4
  DEL PEAK 24(14Q32.31) WILD-TYPE                                8    15
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(14Q32.31) MUTATED                           3
  DEL PEAK 24(14Q32.31) WILD-TYPE                        25
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 24(14Q32.31) MUTATED                                           0
  DEL PEAK 24(14Q32.31) WILD-TYPE                                         2
                                 vv
clus                              WHITE
  DEL PEAK 24(14Q32.31) MUTATED      38
  DEL PEAK 24(14Q32.31) WILD-TYPE   164
D50V10, multiclass
                                           clus
vv                                          DEL PEAK 24(14Q32.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 4
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                38
                                           clus
vv                                          DEL PEAK 24(14Q32.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        8
  ASIAN                                                                  15
  BLACK OR AFRICAN AMERICAN                                              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               2
  WHITE                                                                 164
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.31) MUTATED     4  24
  DEL PEAK 24(14Q32.31) WILD-TYPE  19 139
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED      4   24
  DEL PEAK 24(14Q32.31) WILD-TYPE   19  139
                        clus
vv                       DEL PEAK 24(14Q32.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            24
                        clus
vv                       DEL PEAK 24(14Q32.31) WILD-TYPE
  HISPANIC OR LATINO                                  19
  NOT HISPANIC OR LATINO                             139
[1] 2 2
[1] FALSE
D50V12, continuous
D50V13, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.31) MUTATED    31   9
  DEL PEAK 24(14Q32.31) WILD-TYPE 162  67
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED     31    9
  DEL PEAK 24(14Q32.31) WILD-TYPE  162   67
            clus
vv           DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  TUMOR FREE                            31                             162
  WITH TUMOR                             9                              67
[1] 2 2
[1] FALSE
                                 vv
clus                               G1  G2  G3  G4  GX
  DEL PEAK 24(14Q32.31) MUTATED     3  13  26   1   2
  DEL PEAK 24(14Q32.31) WILD-TYPE  15 116  89   0  22
D50V14, multiclass
    clus
vv   DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  G1                             3                              15
  G2                            13                             116
  G3                            26                              89
  G4                             1                               0
  GX                             2                              22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, continuous
D50V16, continuous
D50V17, continuous
D50V18, continuous
D50V19, binary
                                 cls
clus                               0  1
  DEL PEAK 24(14Q32.31) MUTATED    2  0
  DEL PEAK 24(14Q32.31) WILD-TYPE 23  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED      2    0
  DEL PEAK 24(14Q32.31) WILD-TYPE   23    3
                         clus
vv                        DEL PEAK 24(14Q32.31) MUTATED
  COMPLETED AS PLANNED                                2
  TREATMENT NOT COMPLETED                             0
                         clus
vv                        DEL PEAK 24(14Q32.31) WILD-TYPE
  COMPLETED AS PLANNED                                 23
  TREATMENT NOT COMPLETED                               3
[1] 2 2
[1] FALSE
D50V20, continuous
D50V21, continuous
D50V22, continuous
D50V23, continuous
D50V24, continuous
D50V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 24(14Q32.31) MUTATED                                     0
  DEL PEAK 24(14Q32.31) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 24(14Q32.31) MUTATED                                     1
  DEL PEAK 24(14Q32.31) WILD-TYPE                                   6
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 24(14Q32.31) MUTATED                         6
  DEL PEAK 24(14Q32.31) WILD-TYPE                      30
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 24(14Q32.31) MUTATED                         0
  DEL PEAK 24(14Q32.31) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 24(14Q32.31) MUTATED                         2
  DEL PEAK 24(14Q32.31) WILD-TYPE                       8
D50V26, multiclass
                                     clus
vv                                    DEL PEAK 24(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 24(14Q32.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               6
  OTHER LOCATION, SPECIFY                                          30
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 24(14Q32.31) MUTATED                                               1
  DEL PEAK 24(14Q32.31) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 24(14Q32.31) MUTATED                                                1
  DEL PEAK 24(14Q32.31) WILD-TYPE                                             24
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 24(14Q32.31) MUTATED                                                                                  18
  DEL PEAK 24(14Q32.31) WILD-TYPE                                                                                64
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 24(14Q32.31) MUTATED                                                                                             16
  DEL PEAK 24(14Q32.31) WILD-TYPE                                                                                          105
D50V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 24(14Q32.31) 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(14Q32.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V28, binary
                                 cls
clus                               0  1
  DEL PEAK 24(14Q32.31) MUTATED   10 14
  DEL PEAK 24(14Q32.31) WILD-TYPE 61 60
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED     10   14
  DEL PEAK 24(14Q32.31) WILD-TYPE   61   60
         clus
vv        DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  ABSENT                             10                              61
  PRESENT                            14                              60
[1] 2 2
[1] FALSE
D50V29, continuous
D50V30, continuous
D50V31, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.31) MUTATED     8  17
  DEL PEAK 24(14Q32.31) WILD-TYPE  41 100
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED      8   17
  DEL PEAK 24(14Q32.31) WILD-TYPE   41  100
                                          clus
vv                                         DEL PEAK 24(14Q32.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            17
                                          clus
vv                                         DEL PEAK 24(14Q32.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             100
[1] 2 2
[1] FALSE
D50V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 24(14Q32.31) MUTATED              3           9          9
  DEL PEAK 24(14Q32.31) WILD-TYPE           12          45         76
D50V33, multiclass
              clus
vv             DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  CURRENT USER                             3                              12
  FORMER USER                              9                              45
  NEVER USED                               9                              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"
D50V34, continuous
D50V35, binary
                                 cls
clus                               0  1
  DEL PEAK 24(14Q32.31) MUTATED   16  3
  DEL PEAK 24(14Q32.31) WILD-TYPE 76 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.31) MUTATED     16    3
  DEL PEAK 24(14Q32.31) WILD-TYPE   76   15
         clus
vv        DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  ABSENT                             16                              76
  PRESENT                             3                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 24(14Q32.31) MUTATED             0        13     1
  DEL PEAK 24(14Q32.31) WILD-TYPE           5        87     1
D50V36, multiclass
             clus
vv            DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  CARBOPLATIN                             0                               5
  CISPLATIN                              13                              87
  OTHER                                   1                               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"
D50V37, continuous
[1] "Remove cluster labels:"        "DEL PEAK 24(14Q32.31) MUTATED"
clus
  DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE 
                              1                              16 
                     TCGA-C5-A1BN                      TCGA-C5-A1MH 
"DEL PEAK 24(14Q32.31) WILD-TYPE" "DEL PEAK 24(14Q32.31) WILD-TYPE" 
                     TCGA-C5-A1ML                      TCGA-C5-A1MN 
"DEL PEAK 24(14Q32.31) WILD-TYPE" "DEL PEAK 24(14Q32.31) WILD-TYPE" 
                     TCGA-C5-A1MP                      TCGA-EK-A2RO 
"DEL PEAK 24(14Q32.31) WILD-TYPE" "DEL PEAK 24(14Q32.31) WILD-TYPE" 
                     TCGA-GH-A9DA                      TCGA-HM-A3JK 
"DEL PEAK 24(14Q32.31) WILD-TYPE" "DEL PEAK 24(14Q32.31) WILD-TYPE" 
                     TCGA-JW-A852                      TCGA-JX-A3Q8 
"DEL PEAK 24(14Q32.31) WILD-TYPE" "DEL PEAK 24(14Q32.31) WILD-TYPE" 
                     TCGA-MA-AA3W                      TCGA-MA-AA3Z 
"DEL PEAK 24(14Q32.31) WILD-TYPE" "DEL PEAK 24(14Q32.31) WILD-TYPE" 
                     TCGA-MU-A51Y                      TCGA-MU-A8JM 
"DEL PEAK 24(14Q32.31) WILD-TYPE" "DEL PEAK 24(14Q32.31) WILD-TYPE" 
                     TCGA-MY-A913                      TCGA-ZX-AA5X 
"DEL PEAK 24(14Q32.31) WILD-TYPE" "DEL PEAK 24(14Q32.31) WILD-TYPE" 
D50V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 24(14Q32.31) MUTATED         1        0         0         0        5
  DEL PEAK 24(14Q32.31) WILD-TYPE       4        1         1         1       29
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 24(14Q32.31) MUTATED          14         7        2         1
  DEL PEAK 24(14Q32.31) WILD-TYPE        63        30        2         7
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 24(14Q32.31) MUTATED            2          0         7         0
  DEL PEAK 24(14Q32.31) WILD-TYPE          3          7        37         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 24(14Q32.31) MUTATED            1          5         1         1
  DEL PEAK 24(14Q32.31) WILD-TYPE          2         37         6        11
D50V39, multiclass
            clus
vv           DEL PEAK 24(14Q32.31) MUTATED DEL PEAK 24(14Q32.31) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               5                              29
  STAGE IB1                             14                              63
  STAGE IB2                              7                              30
  STAGE II                               2                               2
  STAGE IIA                              1                               7
  STAGE IIA1                             2                               3
  STAGE IIA2                             0                               7
  STAGE IIB                              7                              37
  STAGE III                              0                               1
  STAGE IIIA                             1                               2
  STAGE IIIB                             5                              37
  STAGE IVA                              1                               6
  STAGE IVB                              1                              11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 25(15Q21.1) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(15Q21.1) MUTATED    50  16
  DEL PEAK 25(15Q21.1) WILD-TYPE 164  52
  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE 
                            66                            216 
  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE 
                            16                             52 
$`DEL PEAK 25(15Q21.1) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-BI-A0VS TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1ML 
       12.59         4.34        57.04        35.01        38.99        20.91 
TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UC 
       40.93        73.45        52.01       210.67       154.32        17.19 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A7WH TCGA-EA-A439 
       99.91        23.51        82.06        87.75        17.52        31.73 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RM 
       26.01        14.89         0.59         1.74         0.43         1.64 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-FU-A23L TCGA-FU-A40J TCGA-HM-A3JJ TCGA-HM-A6W2 
        2.33         0.10        23.84        14.01        21.67         9.44 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A69B TCGA-JX-A3Q8 
      137.16        66.81        78.71        29.85        28.37        44.61 
TCGA-LP-A4AX TCGA-MA-AA3X TCGA-MA-AA42 TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A913 
       12.49        20.28         8.52        19.96        54.81        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-VS-A8EI TCGA-VS-A8EJ 
        2.96        15.58        16.41        15.95        23.97        19.96 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Z TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       59.18        39.78        33.37        15.68        56.35        55.50 
TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UO TCGA-VS-A9UQ 
       50.47        24.30        46.92        45.11        47.87        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-ZJ-A8QR 
       26.07        15.85         3.42        67.20        18.84        19.13 

$`DEL PEAK 25(15Q21.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        14.70         8.32         1.48         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       17.82        49.48        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       53.16        35.61         0.46         2.43         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.18        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       18.02        17.85        20.42       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35       155.77       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YR 
       13.61         2.73        50.99        45.83         8.35        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL 
       20.81        20.91        14.73         1.12        95.11        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       63.98        58.88        36.76        55.63       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        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       36.89        26.40        24.56        12.13        24.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48         0.36        60.72        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.39         0.43         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       40.96         0.30         4.24         0.07         1.87        47.77 
TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.49         0.89        20.35         7.92        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       19.79        15.55        12.23        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
       36.26        20.98        26.14        16.14        28.31        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
       10.55         1.12        17.75        25.41        16.57        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL 
       14.93       147.39       129.37        96.95        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU 
        8.28        18.15        21.11       209.59        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y 
        0.89         0.30         0.82        13.35        22.52        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE 
       19.56         9.17        11.38        28.08        34.62        35.05 
TCGA-MY-A5BF TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       20.84         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        69.50        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       32.42        65.49        32.15        53.59        36.13        11.51 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A952 
       31.27        40.87        16.64         4.73        40.14        58.45 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        51.32        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UU 
       27.12         1.71        14.53        27.25        47.47        14.53 
TCGA-VS-A9UY TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 
       18.25         5.16        18.25        17.75        16.24        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       26.01        29.26        67.59         1.41         0.16         3.91 

  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE 
                        210.67                         209.59 
  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE 
                        24.135                         21.045 
[1] "0.1 - 210.7 (24.1)" "0.1 - 209.6 (21.0)"
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 25(15Q21.1) MUTATED    27  16   6   4
  DEL PEAK 25(15Q21.1) WILD-TYPE 108  54  15   4
D51V3, multiclass
    clus
vv   DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  T1                           27                            108
  T2                           16                             54
  T3                            6                             15
  T4                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                                cls
clus                              0  1
  DEL PEAK 25(15Q21.1) MUTATED   30  8
  DEL PEAK 25(15Q21.1) WILD-TYPE 99 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED     30    8
  DEL PEAK 25(15Q21.1) WILD-TYPE   99   48
   clus
vv  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  0                           30                             99
  1                            8                             48
[1] 2 2
[1] FALSE
D51V5, binary
                                cls
clus                              0  1
  DEL PEAK 25(15Q21.1) MUTATED   19  3
  DEL PEAK 25(15Q21.1) WILD-TYPE 89  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED     19    3
  DEL PEAK 25(15Q21.1) WILD-TYPE   89    7
   clus
vv  DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  0                           19                             89
  1                            3                              7
[1] 2 2
[1] FALSE
D51V6, binary
                                cls
clus                              0  1
  DEL PEAK 25(15Q21.1) MUTATED    9 34
  DEL PEAK 25(15Q21.1) WILD-TYPE 44 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED      9   34
  DEL PEAK 25(15Q21.1) WILD-TYPE   44   91
     clus
vv    DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  NO                             9                             44
  YES                           34                             91
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(15Q21.1) MUTATED               1                               52
  DEL PEAK 25(15Q21.1) WILD-TYPE             5                              190
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 25(15Q21.1) MUTATED                                               0
  DEL PEAK 25(15Q21.1) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 25(15Q21.1) MUTATED                                     5
  DEL PEAK 25(15Q21.1) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 25(15Q21.1) MUTATED                                           2
  DEL PEAK 25(15Q21.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 25(15Q21.1) MUTATED                                             10
  DEL PEAK 25(15Q21.1) WILD-TYPE                                            7
D51V7, multiclass
                                               clus
vv                                              DEL PEAK 25(15Q21.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        52
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            10
                                               clus
vv                                              DEL PEAK 25(15Q21.1) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         190
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, continuous
D51V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(15Q21.1) MUTATED                                  0     5
  DEL PEAK 25(15Q21.1) WILD-TYPE                                8    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(15Q21.1) MUTATED                          10
  DEL PEAK 25(15Q21.1) WILD-TYPE                        18
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 25(15Q21.1) MUTATED                                           2
  DEL PEAK 25(15Q21.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 25(15Q21.1) MUTATED      44
  DEL PEAK 25(15Q21.1) WILD-TYPE   158
D51V10, multiclass
                                           clus
vv                                          DEL PEAK 25(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               44
                                           clus
vv                                          DEL PEAK 25(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q21.1) MUTATED     4  33
  DEL PEAK 25(15Q21.1) WILD-TYPE  19 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED      4   33
  DEL PEAK 25(15Q21.1) WILD-TYPE   19  130
                        clus
vv                       DEL PEAK 25(15Q21.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           33
                        clus
vv                       DEL PEAK 25(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            130
[1] 2 2
[1] FALSE
D51V12, continuous
D51V13, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q21.1) MUTATED    45  19
  DEL PEAK 25(15Q21.1) WILD-TYPE 148  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED     45   19
  DEL PEAK 25(15Q21.1) WILD-TYPE  148   57
            clus
vv           DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  TUMOR FREE                           45                            148
  WITH TUMOR                           19                             57
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 25(15Q21.1) MUTATED     1  23  34   1   8
  DEL PEAK 25(15Q21.1) WILD-TYPE  17 106  81   0  16
D51V14, multiclass
    clus
vv   DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  G1                            1                             17
  G2                           23                            106
  G3                           34                             81
  G4                            1                              0
  GX                            8                             16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, continuous
D51V16, continuous
D51V17, continuous
D51V18, continuous
D51V19, binary
                                cls
clus                              0  1
  DEL PEAK 25(15Q21.1) MUTATED    6  0
  DEL PEAK 25(15Q21.1) WILD-TYPE 19  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED      6    0
  DEL PEAK 25(15Q21.1) WILD-TYPE   19    3
                         clus
vv                        DEL PEAK 25(15Q21.1) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 25(15Q21.1) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
D51V20, continuous
D51V21, continuous
D51V22, continuous
D51V23, continuous
D51V24, continuous
D51V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 25(15Q21.1) MUTATED                                     0
  DEL PEAK 25(15Q21.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 25(15Q21.1) MUTATED                                     2
  DEL PEAK 25(15Q21.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 25(15Q21.1) MUTATED                         7
  DEL PEAK 25(15Q21.1) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 25(15Q21.1) MUTATED                         0
  DEL PEAK 25(15Q21.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 25(15Q21.1) MUTATED                         2
  DEL PEAK 25(15Q21.1) WILD-TYPE                       8
D51V26, multiclass
                                     clus
vv                                    DEL PEAK 25(15Q21.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        7
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 25(15Q21.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 25(15Q21.1) MUTATED                                               0
  DEL PEAK 25(15Q21.1) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 25(15Q21.1) MUTATED                                                5
  DEL PEAK 25(15Q21.1) WILD-TYPE                                             20
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 25(15Q21.1) MUTATED                                                                                  28
  DEL PEAK 25(15Q21.1) WILD-TYPE                                                                                54
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 25(15Q21.1) MUTATED                                                                                             22
  DEL PEAK 25(15Q21.1) WILD-TYPE                                                                                           99
D51V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 25(15Q21.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           22
                                                                                              clus
vv                                                                                             DEL PEAK 25(15Q21.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V28, binary
                                cls
clus                              0  1
  DEL PEAK 25(15Q21.1) MUTATED   10 12
  DEL PEAK 25(15Q21.1) WILD-TYPE 61 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED     10   12
  DEL PEAK 25(15Q21.1) WILD-TYPE   61   62
         clus
vv        DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  ABSENT                            10                             61
  PRESENT                           12                             62
[1] 2 2
[1] FALSE
D51V29, continuous
D51V30, continuous
D51V31, binary
                                cls
clus                              0  1
  DEL PEAK 25(15Q21.1) MUTATED   11 20
  DEL PEAK 25(15Q21.1) WILD-TYPE 38 97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED     11   20
  DEL PEAK 25(15Q21.1) WILD-TYPE   38   97
                                          clus
vv                                         DEL PEAK 25(15Q21.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           20
                                          clus
vv                                         DEL PEAK 25(15Q21.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             97
[1] 2 2
[1] FALSE
D51V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 25(15Q21.1) MUTATED              2          11         24
  DEL PEAK 25(15Q21.1) WILD-TYPE           13          43         61
D51V33, multiclass
              clus
vv             DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                            11                             43
  NEVER USED                             24                             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"
D51V34, continuous
D51V35, binary
                                cls
clus                              0  1
  DEL PEAK 25(15Q21.1) MUTATED   13  3
  DEL PEAK 25(15Q21.1) WILD-TYPE 79 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.1) MUTATED     13    3
  DEL PEAK 25(15Q21.1) WILD-TYPE   79   15
         clus
vv        DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  ABSENT                            13                             79
  PRESENT                            3                             15
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 25(15Q21.1) MUTATED             0        30     1
  DEL PEAK 25(15Q21.1) WILD-TYPE           5        70     1
D51V36, multiclass
             clus
vv            DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  CARBOPLATIN                            0                              5
  CISPLATIN                             30                             70
  OTHER                                  1                              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"
D51V37, continuous
D51V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 25(15Q21.1) MUTATED         1        0         0         1        9
  DEL PEAK 25(15Q21.1) WILD-TYPE       4        1         1         0       25
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 25(15Q21.1) MUTATED          17         5        0         2
  DEL PEAK 25(15Q21.1) WILD-TYPE        60        32        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 25(15Q21.1) MUTATED            3          0        14         0
  DEL PEAK 25(15Q21.1) WILD-TYPE          2          7        30         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 25(15Q21.1) MUTATED            1          8         4         1
  DEL PEAK 25(15Q21.1) WILD-TYPE          2         34         3        11
D51V39, multiclass
            clus
vv           DEL PEAK 25(15Q21.1) MUTATED DEL PEAK 25(15Q21.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              9                             25
  STAGE IB1                            17                             60
  STAGE IB2                             5                             32
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            3                              2
  STAGE IIA2                            0                              7
  STAGE IIB                            14                             30
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                            8                             34
  STAGE IVA                             4                              3
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 26(16Q11.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(16Q11.2) MUTATED    37  12
  DEL PEAK 26(16Q11.2) WILD-TYPE 177  56
  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE 
                            49                            233 
  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE 
                            12                             56 
$`DEL PEAK 26(16Q11.2) MUTATED`
TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M8 TCGA-C5-A1M9 
        1.48         4.34        23.67       173.29        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 
       57.73        20.91        44.22        73.18        83.05        38.43 
TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CO TCGA-C5-A8XH TCGA-DS-A5RQ TCGA-DS-A7WH 
       18.02       210.67       147.35        45.83        16.83        17.52 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2RJ 
       40.87        30.90        26.01         1.51        19.27         1.74 
TCGA-EX-A1H6 TCGA-FU-A40J TCGA-FU-A770 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
        7.92        14.01         1.12       137.16        66.81        96.95 
TCGA-IR-A3LK TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA43 TCGA-MY-A5BF 
       29.85        20.91         0.30        13.35        11.38        20.84 
TCGA-MY-A913 TCGA-Q1-A6DT TCGA-Q1-A73P TCGA-UC-A7PD TCGA-VS-A8EC TCGA-VS-A8EJ 
       17.23         9.04        15.88        11.67        46.52        19.96 
TCGA-VS-A8Q8 TCGA-VS-A952 TCGA-VS-A9UD TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9UY 
       32.15        58.45        24.30        47.87        26.07        18.25 
TCGA-VS-A9V5 
       16.24 

$`DEL PEAK 26(16Q11.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        12.59        14.70         8.32         0.69        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       17.82        49.48        57.04        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       67.46        31.40        46.32        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LY 
        0.46         2.43        40.93         3.58        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
      100.14        33.24        52.01        17.85        20.42       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48        20.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       14.73         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76        55.63       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        39.55        37.35        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       31.73        12.13        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL 
        0.36        60.72        26.27         6.64         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM 
        4.24         0.07         1.87         0.43        47.77         1.64 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.33         0.07         0.10         0.49         0.89        20.35 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       15.22        19.79        15.55        12.23        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       28.31        35.44        10.55        17.75        25.41        16.57 
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       129.37 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        22.52        20.28        17.82        19.56         9.17 
TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.52        28.08        34.62        19.96        54.81        35.05 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        15.58        16.41        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        12.16        69.50        10.03        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       23.97        65.49        53.59        36.13        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        40.87        16.64         4.73        33.37 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       40.14        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP 
       46.92        45.11         1.71        14.53        27.25        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 
       41.52        15.85        14.53         3.42        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
        5.16        18.25        17.75        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE 
                          0.30                           0.07 
  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE 
                        210.67                         209.59 
  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE 
                         23.67                          22.52 
[1] "0.3 - 210.7 (23.7)" "0.1 - 209.6 (22.5)"
[1] "hr=" "1.1"
D52V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 26(16Q11.2) MUTATED    28  11   4   1
  DEL PEAK 26(16Q11.2) WILD-TYPE 107  59  17   7
D52V3, multiclass
    clus
vv   DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  T1                           28                            107
  T2                           11                             59
  T3                            4                             17
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q11.2) MUTATED   32  5
  DEL PEAK 26(16Q11.2) WILD-TYPE 97 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED     32    5
  DEL PEAK 26(16Q11.2) WILD-TYPE   97   51
   clus
vv  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  0                           32                             97
  1                            5                             51
[1] 2 2
[1] FALSE
D52V5, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q11.2) MUTATED   20  2
  DEL PEAK 26(16Q11.2) WILD-TYPE 88  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED     20    2
  DEL PEAK 26(16Q11.2) WILD-TYPE   88    8
   clus
vv  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  0                           20                             88
  1                            2                              8
[1] 2 2
[1] FALSE
D52V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q11.2) MUTATED    13  21
  DEL PEAK 26(16Q11.2) WILD-TYPE  40 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED     13   21
  DEL PEAK 26(16Q11.2) WILD-TYPE   40  104
     clus
vv    DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  NO                            13                             40
  YES                           21                            104
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(16Q11.2) MUTATED               0                               32
  DEL PEAK 26(16Q11.2) WILD-TYPE             6                              210
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 26(16Q11.2) MUTATED                                               5
  DEL PEAK 26(16Q11.2) WILD-TYPE                                             1
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 26(16Q11.2) MUTATED                                     9
  DEL PEAK 26(16Q11.2) WILD-TYPE                                  12
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 26(16Q11.2) MUTATED                                           1
  DEL PEAK 26(16Q11.2) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 26(16Q11.2) MUTATED                                              6
  DEL PEAK 26(16Q11.2) WILD-TYPE                                           11
D52V7, multiclass
                                               clus
vv                                              DEL PEAK 26(16Q11.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        32
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             6
                                               clus
vv                                              DEL PEAK 26(16Q11.2) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         210
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, continuous
D52V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(16Q11.2) MUTATED                                  1     3
  DEL PEAK 26(16Q11.2) WILD-TYPE                                7    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(16Q11.2) MUTATED                           2
  DEL PEAK 26(16Q11.2) WILD-TYPE                        26
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 26(16Q11.2) MUTATED                                           0
  DEL PEAK 26(16Q11.2) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 26(16Q11.2) MUTATED      44
  DEL PEAK 26(16Q11.2) WILD-TYPE   158
D52V10, multiclass
                                           clus
vv                                          DEL PEAK 26(16Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               44
                                           clus
vv                                          DEL PEAK 26(16Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q11.2) MUTATED     3  30
  DEL PEAK 26(16Q11.2) WILD-TYPE  20 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED      3   30
  DEL PEAK 26(16Q11.2) WILD-TYPE   20  133
                        clus
vv                       DEL PEAK 26(16Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK 26(16Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            133
[1] 2 2
[1] FALSE
D52V12, continuous
D52V13, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q11.2) MUTATED    34  13
  DEL PEAK 26(16Q11.2) WILD-TYPE 159  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED     34   13
  DEL PEAK 26(16Q11.2) WILD-TYPE  159   63
            clus
vv           DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  TUMOR FREE                           34                            159
  WITH TUMOR                           13                             63
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 26(16Q11.2) MUTATED     5  25  19   0   2
  DEL PEAK 26(16Q11.2) WILD-TYPE  13 104  96   1  22
D52V14, multiclass
    clus
vv   DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  G1                            5                             13
  G2                           25                            104
  G3                           19                             96
  G4                            0                              1
  GX                            2                             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, continuous
D52V16, continuous
D52V17, continuous
D52V18, continuous
D52V19, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q11.2) MUTATED    6  0
  DEL PEAK 26(16Q11.2) WILD-TYPE 19  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED      6    0
  DEL PEAK 26(16Q11.2) WILD-TYPE   19    3
                         clus
vv                        DEL PEAK 26(16Q11.2) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 26(16Q11.2) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
D52V20, continuous
D52V21, continuous
D52V22, continuous
D52V23, continuous
D52V24, continuous
D52V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 26(16Q11.2) MUTATED                                     0
  DEL PEAK 26(16Q11.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 26(16Q11.2) MUTATED                                     2
  DEL PEAK 26(16Q11.2) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 26(16Q11.2) MUTATED                        10
  DEL PEAK 26(16Q11.2) WILD-TYPE                      26
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 26(16Q11.2) MUTATED                         0
  DEL PEAK 26(16Q11.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 26(16Q11.2) MUTATED                         1
  DEL PEAK 26(16Q11.2) WILD-TYPE                       9
D52V26, multiclass
                                     clus
vv                                    DEL PEAK 26(16Q11.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       10
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 26(16Q11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         26
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 26(16Q11.2) MUTATED                                               1
  DEL PEAK 26(16Q11.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 26(16Q11.2) MUTATED                                                3
  DEL PEAK 26(16Q11.2) WILD-TYPE                                             22
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 26(16Q11.2) MUTATED                                                                                  20
  DEL PEAK 26(16Q11.2) WILD-TYPE                                                                                62
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 26(16Q11.2) MUTATED                                                                                             17
  DEL PEAK 26(16Q11.2) WILD-TYPE                                                                                          104
D52V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 26(16Q11.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           17
                                                                                              clus
vv                                                                                             DEL PEAK 26(16Q11.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V28, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q11.2) MUTATED   16 12
  DEL PEAK 26(16Q11.2) WILD-TYPE 55 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED     16   12
  DEL PEAK 26(16Q11.2) WILD-TYPE   55   62
         clus
vv        DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  ABSENT                            16                             55
  PRESENT                           12                             62
[1] 2 2
[1] FALSE
D52V29, continuous
D52V30, continuous
D52V31, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q11.2) MUTATED    10  11
  DEL PEAK 26(16Q11.2) WILD-TYPE  39 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED     10   11
  DEL PEAK 26(16Q11.2) WILD-TYPE   39  106
                                          clus
vv                                         DEL PEAK 26(16Q11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           11
                                          clus
vv                                         DEL PEAK 26(16Q11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            106
[1] 2 2
[1] FALSE
D52V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 26(16Q11.2) MUTATED              2          10         19
  DEL PEAK 26(16Q11.2) WILD-TYPE           13          44         66
D52V33, multiclass
              clus
vv             DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                            10                             44
  NEVER USED                             19                             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"
D52V34, continuous
D52V35, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q11.2) MUTATED   22  1
  DEL PEAK 26(16Q11.2) WILD-TYPE 70 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q11.2) MUTATED     22    1
  DEL PEAK 26(16Q11.2) WILD-TYPE   70   17
         clus
vv        DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  ABSENT                            22                             70
  PRESENT                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 26(16Q11.2) MUTATED             1        16     0
  DEL PEAK 26(16Q11.2) WILD-TYPE           4        84     2
D52V36, multiclass
             clus
vv            DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             16                             84
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V37, continuous
[1] "Remove cluster labels:"       "DEL PEAK 26(16Q11.2) MUTATED"
clus
  DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 26(16Q11.2) WILD-TYPE" "DEL PEAK 26(16Q11.2) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-C5-A1MP 
"DEL PEAK 26(16Q11.2) WILD-TYPE" "DEL PEAK 26(16Q11.2) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-GH-A9DA 
"DEL PEAK 26(16Q11.2) WILD-TYPE" "DEL PEAK 26(16Q11.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 26(16Q11.2) WILD-TYPE" "DEL PEAK 26(16Q11.2) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MA-AA3W 
"DEL PEAK 26(16Q11.2) WILD-TYPE" "DEL PEAK 26(16Q11.2) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK 26(16Q11.2) WILD-TYPE" "DEL PEAK 26(16Q11.2) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 26(16Q11.2) WILD-TYPE" "DEL PEAK 26(16Q11.2) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"DEL PEAK 26(16Q11.2) WILD-TYPE" 
D52V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 26(16Q11.2) MUTATED         1        0         0         0        7
  DEL PEAK 26(16Q11.2) WILD-TYPE       4        1         1         1       27
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 26(16Q11.2) MUTATED          17         8        2         3
  DEL PEAK 26(16Q11.2) WILD-TYPE        60        29        2         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 26(16Q11.2) MUTATED            0          1         3         0
  DEL PEAK 26(16Q11.2) WILD-TYPE          5          6        41         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 26(16Q11.2) MUTATED            1          6         1         1
  DEL PEAK 26(16Q11.2) WILD-TYPE          2         36         6        11
D52V39, multiclass
            clus
vv           DEL PEAK 26(16Q11.2) MUTATED DEL PEAK 26(16Q11.2) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              7                             27
  STAGE IB1                            17                             60
  STAGE IB2                             8                             29
  STAGE II                              2                              2
  STAGE IIA                             3                              5
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             3                             41
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                            6                             36
  STAGE IVA                             1                              6
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 27(16Q23.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(16Q23.1) MUTATED    40  11
  DEL PEAK 27(16Q23.1) WILD-TYPE 174  57
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            51                            231 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            11                             57 
$`DEL PEAK 27(16Q23.1) MUTATED`
TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 
        8.32         1.48         4.34        23.67       173.29        35.01 
TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 
       57.73        20.91        44.22        73.18        83.05        38.43 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A8XH 
       52.01        18.02       210.67       147.35       131.11        45.83 
TCGA-DG-A2KJ TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2PI 
       95.11        22.98        17.52        26.01        14.89        19.27 
TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A8YF 
        0.59         1.45         1.74         0.89         7.92        15.55 
TCGA-FU-A3EO TCGA-FU-A3TQ TCGA-FU-A40J TCGA-FU-A770 TCGA-IR-A3LA TCGA-IR-A3LB 
       16.11        26.14        14.01         1.12       137.16        66.81 
TCGA-IR-A3LF TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MA-AA43 TCGA-MY-A5BF TCGA-VS-A8EC 
       96.95        20.91        13.35        11.38        20.84        46.52 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A94Y TCGA-VS-A9UD TCGA-VS-A9UO TCGA-VS-A9UP 
       19.96        32.15         4.73        24.30        47.87        47.47 
TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V5 
       18.25        18.84        16.24 

$`DEL PEAK 27(16Q23.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J 
      146.86        12.59        14.70         0.69        17.52        17.82 
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        33.24        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       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK 
        9.34        13.61         2.73        50.99         8.35        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI 
       55.63       117.99       118.65        16.83        16.18         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.13        24.82         7.46        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 
       27.25        27.22        24.00        13.48         0.36        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 
       26.27         6.64         1.51         0.39         0.43         0.89 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        40.96         0.30         4.24         0.07         1.87 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.43        47.77         1.64         2.33         0.07         0.10 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L 
        0.49        20.35        15.22        19.79        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ 
       19.04        31.36        36.26        20.98        16.14        28.31 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44        10.55        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH 
       20.78        14.93         9.44       147.39       129.37        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30         0.82        22.52        20.28        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        9.17         8.52        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       35.05        17.23         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       12.16        69.50        10.03        45.57        32.42        23.97 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       65.49        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       31.27        40.87        16.64        33.37        40.14        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH 
       43.40        48.39        28.50        29.95        27.12        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UQ TCGA-VS-A9UR 
       45.11         1.71        14.53        27.25        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 
       15.85        14.53         3.42        67.20         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       17.75        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                          0.59                           0.07 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                        210.67                         209.59 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                         20.91                          22.62 
[1] "0.6 - 210.7 (20.9)" "0.1 - 209.6 (22.6)"
[1] "hr=" "1.3"
D53V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(16Q23.1) MUTATED    26  13   5   1
  DEL PEAK 27(16Q23.1) WILD-TYPE 109  57  16   7
D53V3, multiclass
    clus
vv   DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  T1                           26                            109
  T2                           13                             57
  T3                            5                             16
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(16Q23.1) MUTATED    27   8
  DEL PEAK 27(16Q23.1) WILD-TYPE 102  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     27    8
  DEL PEAK 27(16Q23.1) WILD-TYPE  102   48
   clus
vv  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  0                           27                            102
  1                            8                             48
[1] 2 2
[1] FALSE
D53V5, binary
                                cls
clus                              0  1
  DEL PEAK 27(16Q23.1) MUTATED   21  1
  DEL PEAK 27(16Q23.1) WILD-TYPE 87  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     21    1
  DEL PEAK 27(16Q23.1) WILD-TYPE   87    9
   clus
vv  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  0                           21                             87
  1                            1                              9
[1] 2 2
[1] FALSE
D53V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(16Q23.1) MUTATED     9  24
  DEL PEAK 27(16Q23.1) WILD-TYPE  44 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED      9   24
  DEL PEAK 27(16Q23.1) WILD-TYPE   44  101
     clus
vv    DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  NO                             9                             44
  YES                           24                            101
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(16Q23.1) MUTATED               0                               34
  DEL PEAK 27(16Q23.1) WILD-TYPE             6                              208
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 27(16Q23.1) MUTATED                                               4
  DEL PEAK 27(16Q23.1) WILD-TYPE                                             2
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 27(16Q23.1) MUTATED                                     9
  DEL PEAK 27(16Q23.1) WILD-TYPE                                  12
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 27(16Q23.1) MUTATED                                           2
  DEL PEAK 27(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 27(16Q23.1) MUTATED                                              6
  DEL PEAK 27(16Q23.1) WILD-TYPE                                           11
D53V7, multiclass
                                               clus
vv                                              DEL PEAK 27(16Q23.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        34
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             6
                                               clus
vv                                              DEL PEAK 27(16Q23.1) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         208
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, continuous
D53V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(16Q23.1) MUTATED                                  0     2
  DEL PEAK 27(16Q23.1) WILD-TYPE                                8    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(16Q23.1) MUTATED                           0
  DEL PEAK 27(16Q23.1) WILD-TYPE                        28
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(16Q23.1) MUTATED                                           0
  DEL PEAK 27(16Q23.1) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 27(16Q23.1) MUTATED      46
  DEL PEAK 27(16Q23.1) WILD-TYPE   156
D53V10, multiclass
                                           clus
vv                                          DEL PEAK 27(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               46
                                           clus
vv                                          DEL PEAK 27(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       8
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                156
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                                cls
clus                               0   1
  DEL PEAK 27(16Q23.1) MUTATED     2  30
  DEL PEAK 27(16Q23.1) WILD-TYPE  21 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED      2   30
  DEL PEAK 27(16Q23.1) WILD-TYPE   21  133
                        clus
vv                       DEL PEAK 27(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK 27(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            133
[1] 2 2
[1] FALSE
D53V12, continuous
D53V13, binary
                                cls
clus                               0   1
  DEL PEAK 27(16Q23.1) MUTATED    34  16
  DEL PEAK 27(16Q23.1) WILD-TYPE 159  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     34   16
  DEL PEAK 27(16Q23.1) WILD-TYPE  159   60
            clus
vv           DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  TUMOR FREE                           34                            159
  WITH TUMOR                           16                             60
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 27(16Q23.1) MUTATED     4  22  26   0   1
  DEL PEAK 27(16Q23.1) WILD-TYPE  14 107  89   1  23
D53V14, multiclass
    clus
vv   DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  G1                            4                             14
  G2                           22                            107
  G3                           26                             89
  G4                            0                              1
  GX                            1                             23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, continuous
D53V16, continuous
D53V17, continuous
D53V18, continuous
D53V19, binary
                                cls
clus                              0  1
  DEL PEAK 27(16Q23.1) MUTATED    7  0
  DEL PEAK 27(16Q23.1) WILD-TYPE 18  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED      7    0
  DEL PEAK 27(16Q23.1) WILD-TYPE   18    3
                         clus
vv                        DEL PEAK 27(16Q23.1) MUTATED
  COMPLETED AS PLANNED                               7
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 27(16Q23.1) WILD-TYPE
  COMPLETED AS PLANNED                                18
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
D53V20, continuous
D53V21, continuous
D53V22, continuous
D53V23, continuous
D53V24, continuous
D53V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 27(16Q23.1) MUTATED                                     0
  DEL PEAK 27(16Q23.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 27(16Q23.1) MUTATED                                     1
  DEL PEAK 27(16Q23.1) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 27(16Q23.1) MUTATED                         9
  DEL PEAK 27(16Q23.1) WILD-TYPE                      27
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 27(16Q23.1) MUTATED                         0
  DEL PEAK 27(16Q23.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 27(16Q23.1) MUTATED                         2
  DEL PEAK 27(16Q23.1) WILD-TYPE                       8
D53V26, multiclass
                                     clus
vv                                    DEL PEAK 27(16Q23.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        9
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 27(16Q23.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         27
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 27(16Q23.1) MUTATED                                               0
  DEL PEAK 27(16Q23.1) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 27(16Q23.1) MUTATED                                                4
  DEL PEAK 27(16Q23.1) WILD-TYPE                                             21
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 27(16Q23.1) MUTATED                                                                                  17
  DEL PEAK 27(16Q23.1) WILD-TYPE                                                                                65
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 27(16Q23.1) MUTATED                                                                                             19
  DEL PEAK 27(16Q23.1) WILD-TYPE                                                                                          102
D53V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 27(16Q23.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           19
                                                                                              clus
vv                                                                                             DEL PEAK 27(16Q23.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V28, binary
                                cls
clus                              0  1
  DEL PEAK 27(16Q23.1) MUTATED   14 12
  DEL PEAK 27(16Q23.1) WILD-TYPE 57 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     14   12
  DEL PEAK 27(16Q23.1) WILD-TYPE   57   62
         clus
vv        DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  ABSENT                            14                             57
  PRESENT                           12                             62
[1] 2 2
[1] FALSE
D53V29, continuous
D53V30, continuous
D53V31, binary
                                cls
clus                               0   1
  DEL PEAK 27(16Q23.1) MUTATED    10  13
  DEL PEAK 27(16Q23.1) WILD-TYPE  39 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     10   13
  DEL PEAK 27(16Q23.1) WILD-TYPE   39  104
                                          clus
vv                                         DEL PEAK 27(16Q23.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           13
                                          clus
vv                                         DEL PEAK 27(16Q23.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            104
[1] 2 2
[1] FALSE
D53V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 27(16Q23.1) MUTATED              3          12         16
  DEL PEAK 27(16Q23.1) WILD-TYPE           12          42         69
D53V33, multiclass
              clus
vv             DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                            12                             42
  NEVER USED                             16                             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"
D53V34, continuous
D53V35, binary
                                cls
clus                              0  1
  DEL PEAK 27(16Q23.1) MUTATED   20  2
  DEL PEAK 27(16Q23.1) WILD-TYPE 72 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     20    2
  DEL PEAK 27(16Q23.1) WILD-TYPE   72   16
         clus
vv        DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  ABSENT                            20                             72
  PRESENT                            2                             16
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 27(16Q23.1) MUTATED             1        19     0
  DEL PEAK 27(16Q23.1) WILD-TYPE           4        81     2
D53V36, multiclass
             clus
vv            DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             19                             81
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V37, continuous
[1] "Remove cluster labels:"       "DEL PEAK 27(16Q23.1) MUTATED"
clus
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                             1                             16 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 27(16Q23.1) WILD-TYPE" "DEL PEAK 27(16Q23.1) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-C5-A1MP 
"DEL PEAK 27(16Q23.1) WILD-TYPE" "DEL PEAK 27(16Q23.1) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-GH-A9DA 
"DEL PEAK 27(16Q23.1) WILD-TYPE" "DEL PEAK 27(16Q23.1) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 27(16Q23.1) WILD-TYPE" "DEL PEAK 27(16Q23.1) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MA-AA3W 
"DEL PEAK 27(16Q23.1) WILD-TYPE" "DEL PEAK 27(16Q23.1) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK 27(16Q23.1) WILD-TYPE" "DEL PEAK 27(16Q23.1) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 27(16Q23.1) WILD-TYPE" "DEL PEAK 27(16Q23.1) WILD-TYPE" 
                    TCGA-MY-A913                     TCGA-ZX-AA5X 
"DEL PEAK 27(16Q23.1) WILD-TYPE" "DEL PEAK 27(16Q23.1) WILD-TYPE" 
D53V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 27(16Q23.1) MUTATED         0        0         0         0        6
  DEL PEAK 27(16Q23.1) WILD-TYPE       5        1         1         1       28
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 27(16Q23.1) MUTATED          15         9        1         2
  DEL PEAK 27(16Q23.1) WILD-TYPE        62        28        3         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 27(16Q23.1) MUTATED            0          1         7         0
  DEL PEAK 27(16Q23.1) WILD-TYPE          5          6        37         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 27(16Q23.1) MUTATED            1         10         1         1
  DEL PEAK 27(16Q23.1) WILD-TYPE          2         32         6        11
D53V39, multiclass
            clus
vv           DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              6                             28
  STAGE IB1                            15                             62
  STAGE IB2                             9                             28
  STAGE II                              1                              3
  STAGE IIA                             2                              6
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             7                             37
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                           10                             32
  STAGE IVA                             1                              6
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 28(17P12) MUTATION ANALYSIS
D54V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 28(17P12) MUTATED    78  29
  DEL PEAK 28(17P12) WILD-TYPE 136  39
  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE 
                         107                          175 
  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE 
                          29                           39 
$`DEL PEAK 28(17P12) MUTATED`
TCGA-C5-A8XJ TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1BE 
      146.86         8.32         0.69        17.82        23.67        68.84 
TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
       18.74       144.16       173.29         5.46        19.86        67.46 
TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HD 
       38.99        40.93        73.18        83.05        38.43        52.01 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       15.48       147.35        17.19         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DR-A0ZL 
       50.99        45.83        23.51        20.91        95.11        87.75 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A439 TCGA-EA-A44S 
       55.63       118.65        22.98        40.87        31.73        12.13 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 
       27.25        27.22        24.00        13.48         0.36        60.72 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD 
        1.51         0.59         1.45         0.13        40.96         0.07 
TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H5 
        1.74         0.43         1.64         2.33         0.10        20.35 
TCGA-EX-A3L1 TCGA-FU-A3EO TCGA-FU-A3NI TCGA-GH-A9DA TCGA-IR-A3LB TCGA-IR-A3LH 
       15.22        16.11        20.98        17.75        66.81        78.71 
TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3X 
       29.85        24.56        28.37        11.28         0.89        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA43 TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A5R2 
       17.82        19.56        11.38        34.62         2.96        16.41 
TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI 
        9.04         9.34        22.62        14.60        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QF 
       10.03        46.52        23.97        19.96        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 
       39.78         4.73        33.37        40.14        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9UI TCGA-VS-A9UO TCGA-VS-A9UP 
       50.14        51.32        43.40        45.11        47.87        47.47 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V2 
       26.07        15.85         3.42        18.25        18.84        18.25 
TCGA-VS-A9V3 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       17.75        67.59        19.13         1.41         3.91 

$`DEL PEAK 28(17P12) WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-BI-A0VR 
       12.59        14.70         1.48         4.34        17.52        49.48 
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1M6 
       57.04        11.44        36.56       177.04        82.85        31.40 
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-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        0.46         2.43        20.91         3.58        44.22        73.45 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14        33.24        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7UE 
      210.67       154.32       101.82       134.33        20.35       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
      131.11        94.95         8.35        99.91        27.52        20.81 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM 
       14.73         1.12        82.06        44.94        63.98        58.88 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       36.76       117.99        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A4BA 
       25.02        36.89        26.40        24.56        26.01        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EK-A2H1 
        7.46        14.89        26.79        25.91        27.29        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2RB 
        6.64        19.27         0.39         0.43         0.89         0.30 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
        4.24         1.87        47.77         0.07         0.49         0.89 
TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        7.92        19.79        15.55        12.23        23.84        19.04 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       31.36        36.26        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44        10.55         1.12        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC 
       20.78        14.93         9.44       147.39       137.16       129.37 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ 
       96.95        81.96        36.36        27.42         3.29        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       20.48        15.58         8.28        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       44.61        20.91        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD 
       22.52         9.17         8.52        28.08        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
       35.05        20.84        17.23        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        18.64        19.59        11.67 
TCGA-UC-A7PF TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       93.99        45.57        32.42        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A953 
       36.13        31.27        40.87        16.64        58.45        15.68 
TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       50.47        48.39        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UQ TCGA-VS-A9UU 
       46.92         1.71        14.53        27.25        41.52        14.53 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       67.20         5.16        16.24        15.42        26.01        29.26 
TCGA-ZJ-AAXU 
        0.16 

  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE 
                      173.29                       210.67 
  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE 
                       20.91                        24.30 
[1] "0.1 - 173.3 (20.9)" "0.1 - 210.7 (24.3)"
[1] "hr=" "1.3"
D54V2, continuous
                              vv
clus                           T1 T2 T3 T4
  DEL PEAK 28(17P12) MUTATED   45 23  9  3
  DEL PEAK 28(17P12) WILD-TYPE 90 47 12  5
D54V3, multiclass
    clus
vv   DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  T1                         45                           90
  T2                         23                           47
  T3                          9                           12
  T4                          3                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                              cls
clus                            0  1
  DEL PEAK 28(17P12) MUTATED   40 15
  DEL PEAK 28(17P12) WILD-TYPE 89 41
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED     40   15
  DEL PEAK 28(17P12) WILD-TYPE   89   41
   clus
vv  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  0                         40                           89
  1                         15                           41
[1] 2 2
[1] FALSE
D54V5, binary
                              cls
clus                            0  1
  DEL PEAK 28(17P12) MUTATED   35  3
  DEL PEAK 28(17P12) WILD-TYPE 73  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED     35    3
  DEL PEAK 28(17P12) WILD-TYPE   73    7
   clus
vv  DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  0                         35                           73
  1                          3                            7
[1] 2 2
[1] FALSE
D54V6, binary
                              cls
clus                            0  1
  DEL PEAK 28(17P12) MUTATED   21 53
  DEL PEAK 28(17P12) WILD-TYPE 32 72
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED     21   53
  DEL PEAK 28(17P12) WILD-TYPE   32   72
     clus
vv    DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  NO                          21                           32
  YES                         53                           72
[1] 2 2
[1] FALSE
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(17P12) MUTATED               1                               94
  DEL PEAK 28(17P12) WILD-TYPE             5                              148
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 28(17P12) MUTATED                                               1
  DEL PEAK 28(17P12) WILD-TYPE                                             5
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 28(17P12) MUTATED                                     5
  DEL PEAK 28(17P12) WILD-TYPE                                  16
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 28(17P12) MUTATED                                           1
  DEL PEAK 28(17P12) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 28(17P12) MUTATED                                              7
  DEL PEAK 28(17P12) WILD-TYPE                                           10
D54V7, multiclass
                                               clus
vv                                              DEL PEAK 28(17P12) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      94
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           7
                                               clus
vv                                              DEL PEAK 28(17P12) WILD-TYPE
  ADENOSQUAMOUS                                                            5
  CERVICAL SQUAMOUS CELL CARCINOMA                                       148
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, continuous
D54V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(17P12) MUTATED                                  2     9
  DEL PEAK 28(17P12) WILD-TYPE                                6    10
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(17P12) MUTATED                           7
  DEL PEAK 28(17P12) WILD-TYPE                        21
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 28(17P12) MUTATED                                           2    79
  DEL PEAK 28(17P12) WILD-TYPE                                         0   123
D54V10, multiclass
                                           clus
vv                                          DEL PEAK 28(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              9
  BLACK OR AFRICAN AMERICAN                                          7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             79
                                           clus
vv                                          DEL PEAK 28(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                           21
  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"
D54V11, binary
                              cls
clus                             0   1
  DEL PEAK 28(17P12) MUTATED     7  61
  DEL PEAK 28(17P12) WILD-TYPE  16 102
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED      7   61
  DEL PEAK 28(17P12) WILD-TYPE   16  102
                        clus
vv                       DEL PEAK 28(17P12) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         61
                        clus
vv                       DEL PEAK 28(17P12) WILD-TYPE
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          102
[1] 2 2
[1] FALSE
D54V12, continuous
D54V13, binary
                              cls
clus                             0   1
  DEL PEAK 28(17P12) MUTATED    65  37
  DEL PEAK 28(17P12) WILD-TYPE 128  39
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED     65   37
  DEL PEAK 28(17P12) WILD-TYPE  128   39
            clus
vv           DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  TUMOR FREE                         65                          128
  WITH TUMOR                         37                           39
[1] 2 2
[1] FALSE
                              vv
clus                           G1 G2 G3 G4 GX
  DEL PEAK 28(17P12) MUTATED    4 43 45  1 14
  DEL PEAK 28(17P12) WILD-TYPE 14 86 70  0 10
D54V14, multiclass
    clus
vv   DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  G1                          4                           14
  G2                         43                           86
  G3                         45                           70
  G4                          1                            0
  GX                         14                           10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, continuous
D54V16, continuous
D54V17, continuous
D54V18, continuous
D54V19, binary
                              cls
clus                            0  1
  DEL PEAK 28(17P12) MUTATED   12  1
  DEL PEAK 28(17P12) WILD-TYPE 13  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED     12    1
  DEL PEAK 28(17P12) WILD-TYPE   13    2
                         clus
vv                        DEL PEAK 28(17P12) MUTATED
  COMPLETED AS PLANNED                            12
  TREATMENT NOT COMPLETED                          1
                         clus
vv                        DEL PEAK 28(17P12) WILD-TYPE
  COMPLETED AS PLANNED                              13
  TREATMENT NOT COMPLETED                            2
[1] 2 2
[1] FALSE
D54V20, continuous
D54V21, continuous
D54V22, continuous
D54V23, continuous
D54V24, continuous
D54V25, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 28(17P12) MUTATED                                     0
  DEL PEAK 28(17P12) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 28(17P12) MUTATED                                     3
  DEL PEAK 28(17P12) WILD-TYPE                                   4
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 28(17P12) MUTATED                        13                       0
  DEL PEAK 28(17P12) WILD-TYPE                      23                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  DEL PEAK 28(17P12) MUTATED                         5
  DEL PEAK 28(17P12) WILD-TYPE                       5
D54V26, multiclass
                                     clus
vv                                    DEL PEAK 28(17P12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          3
  OTHER LOCATION, SPECIFY                                     13
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      5
                                     clus
vv                                    DEL PEAK 28(17P12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  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 28(17P12) MUTATED                                               1
  DEL PEAK 28(17P12) WILD-TYPE                                             2
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 28(17P12) MUTATED                                               11
  DEL PEAK 28(17P12) WILD-TYPE                                             14
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 28(17P12) MUTATED                                                                                  33
  DEL PEAK 28(17P12) WILD-TYPE                                                                                49
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 28(17P12) MUTATED                                                                                             40
  DEL PEAK 28(17P12) WILD-TYPE                                                                                           81
D54V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 28(17P12) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         40
                                                                                              clus
vv                                                                                             DEL PEAK 28(17P12) 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)                                      49
  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"
D54V28, binary
                              cls
clus                            0  1
  DEL PEAK 28(17P12) MUTATED   23 24
  DEL PEAK 28(17P12) WILD-TYPE 48 50
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED     23   24
  DEL PEAK 28(17P12) WILD-TYPE   48   50
         clus
vv        DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  ABSENT                          23                           48
  PRESENT                         24                           50
[1] 2 2
[1] FALSE
D54V29, continuous
D54V30, continuous
D54V31, binary
                              cls
clus                            0  1
  DEL PEAK 28(17P12) MUTATED   21 44
  DEL PEAK 28(17P12) WILD-TYPE 28 73
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED     21   44
  DEL PEAK 28(17P12) WILD-TYPE   28   73
                                          clus
vv                                         DEL PEAK 28(17P12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         44
                                          clus
vv                                         DEL PEAK 28(17P12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           73
[1] 2 2
[1] FALSE
D54V32, continuous
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  DEL PEAK 28(17P12) MUTATED              3          18         35
  DEL PEAK 28(17P12) WILD-TYPE           12          36         50
D54V33, multiclass
              clus
vv             DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  CURRENT USER                          3                           12
  FORMER USER                          18                           36
  NEVER USED                           35                           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"
D54V34, continuous
D54V35, binary
                              cls
clus                            0  1
  DEL PEAK 28(17P12) MUTATED   30  5
  DEL PEAK 28(17P12) WILD-TYPE 62 13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 28(17P12) MUTATED     30    5
  DEL PEAK 28(17P12) WILD-TYPE   62   13
         clus
vv        DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  ABSENT                          30                           62
  PRESENT                          5                           13
[1] 2 2
[1] FALSE
                              vv
clus                           CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 28(17P12) MUTATED             1        46     1
  DEL PEAK 28(17P12) WILD-TYPE           4        54     1
D54V36, multiclass
             clus
vv            DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  CARBOPLATIN                          1                            4
  CISPLATIN                           46                           54
  OTHER                                1                            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"
D54V37, continuous
D54V38, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 28(17P12) MUTATED         3        1         1         1       13
  DEL PEAK 28(17P12) WILD-TYPE       2        0         0         0       21
                              vv
clus                           STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 28(17P12) MUTATED          24        12        1         3
  DEL PEAK 28(17P12) WILD-TYPE        53        25        3         5
                              vv
clus                           STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 28(17P12) MUTATED            3          1        20         0
  DEL PEAK 28(17P12) WILD-TYPE          2          6        24         1
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 28(17P12) MUTATED            1         17         2         4
  DEL PEAK 28(17P12) WILD-TYPE          2         25         5         8
D54V39, multiclass
            clus
vv           DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                            1                            0
  STAGE IA1                           1                            0
  STAGE IA2                           1                            0
  STAGE IB                           13                           21
  STAGE IB1                          24                           53
  STAGE IB2                          12                           25
  STAGE II                            1                            3
  STAGE IIA                           3                            5
  STAGE IIA1                          3                            2
  STAGE IIA2                          1                            6
  STAGE IIB                          20                           24
  STAGE III                           0                            1
  STAGE IIIA                          1                            2
  STAGE IIIB                         17                           25
  STAGE IVA                           2                            5
  STAGE IVB                           4                            8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK 29(17Q25.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(17Q25.3) MUTATED    38  11
  DEL PEAK 29(17Q25.3) WILD-TYPE 176  57
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                            49                            233 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                            11                             57 
$`DEL PEAK 29(17Q25.3) MUTATED`
TCGA-C5-A8XJ TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-C5-A1BN TCGA-C5-A1MH TCGA-C5-A1MN 
      146.86         0.69        17.82         5.46        38.99        40.93 
TCGA-C5-A2LT TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VK 
       73.18        17.19       131.11        13.61         2.73        36.76 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PG 
      118.65        40.87        30.90         0.36         6.64         1.51 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RN 
        0.89         1.45         0.07         1.74         0.43         2.33 
TCGA-EK-A3GJ TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-GH-A9DA TCGA-HM-A4S6 
        0.10        31.36        20.98        26.14        17.75        14.93 
TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VL TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3X 
       29.85        24.56        15.58        12.49         0.82        20.28 
TCGA-MA-AA41 TCGA-MU-A51Y TCGA-Q1-A73O TCGA-VS-A8EB TCGA-VS-A8QC TCGA-VS-A950 
        9.17        28.08        14.07        10.03        11.51        40.14 
TCGA-VS-A954 TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9V3 TCGA-WL-A834 TCGA-ZJ-AAXA 
       56.35        45.11        47.47        17.75        26.01         1.41 
TCGA-ZJ-AAXU 
        0.16 

$`DEL PEAK 29(17Q25.3) WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-2W-A8YY 
       12.59        14.70         8.32         1.48         4.34        17.52 
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       36.56       144.16       177.04       173.29        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP 
       53.16        35.61         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
      155.77        94.95         9.34        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        95.11        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88        55.63       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       17.52         8.28        39.55        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.13        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       60.72        26.27        19.27         0.39         0.43         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL 
        0.13        40.96         0.30         4.24         1.87        47.77 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        1.64         0.07         0.49         0.89        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       15.22        19.79        15.55        12.23        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       16.11        36.26        16.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
       10.55         1.12        25.41        16.57        21.67        20.78 
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       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ 
       78.71        81.96        36.36        27.42         3.29        21.44 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       20.48        28.37         8.28        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A7HU 
       44.61        20.91        11.28         0.89         0.30        13.35 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A5YI 
       22.52        17.82        19.56         8.52        11.38        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
       19.96        54.81        35.05        20.84        17.23         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        93.99        12.16        69.50        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       32.42        23.97        19.96        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 
        4.73        33.37        58.45        15.68        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       27.12        24.30        46.92         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.87        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V5 
       18.25        67.20        18.84         5.16        18.25        16.24 
TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       15.42        29.26        67.59        19.13         3.91 

  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                        146.86                         210.67 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                         17.19                          23.97 
[1] "0.1 - 146.9 (17.2)" "0.1 - 210.7 (24.0)"
[1] "hr=" "1.3"
D55V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 29(17Q25.3) MUTATED    25  12   4   1
  DEL PEAK 29(17Q25.3) WILD-TYPE 110  58  17   7
D55V3, multiclass
    clus
vv   DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  T1                           25                            110
  T2                           12                             58
  T3                            4                             17
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                                cls
clus                               0   1
  DEL PEAK 29(17Q25.3) MUTATED    21  12
  DEL PEAK 29(17Q25.3) WILD-TYPE 108  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED     21   12
  DEL PEAK 29(17Q25.3) WILD-TYPE  108   44
   clus
vv  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  0                           21                            108
  1                           12                             44
[1] 2 2
[1] FALSE
D55V5, binary
                                cls
clus                              0  1
  DEL PEAK 29(17Q25.3) MUTATED   16  2
  DEL PEAK 29(17Q25.3) WILD-TYPE 92  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED     16    2
  DEL PEAK 29(17Q25.3) WILD-TYPE   92    8
   clus
vv  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  0                           16                             92
  1                            2                              8
[1] 2 2
[1] FALSE
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(17Q25.3) MUTATED     9  18
  DEL PEAK 29(17Q25.3) WILD-TYPE  44 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED      9   18
  DEL PEAK 29(17Q25.3) WILD-TYPE   44  107
     clus
vv    DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  NO                             9                             44
  YES                           18                            107
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(17Q25.3) MUTATED               0                               49
  DEL PEAK 29(17Q25.3) WILD-TYPE             6                              193
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 29(17Q25.3) MUTATED                                               0
  DEL PEAK 29(17Q25.3) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 29(17Q25.3) MUTATED                                     0
  DEL PEAK 29(17Q25.3) WILD-TYPE                                  21
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 29(17Q25.3) MUTATED                                           0
  DEL PEAK 29(17Q25.3) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 29(17Q25.3) MUTATED                                              2
  DEL PEAK 29(17Q25.3) WILD-TYPE                                           15
D55V7, multiclass
                                               clus
vv                                              DEL PEAK 29(17Q25.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              DEL PEAK 29(17Q25.3) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         193
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, continuous
D55V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(17Q25.3) MUTATED                                  3     3
  DEL PEAK 29(17Q25.3) WILD-TYPE                                5    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(17Q25.3) MUTATED                           3
  DEL PEAK 29(17Q25.3) WILD-TYPE                        25
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(17Q25.3) MUTATED                                           1
  DEL PEAK 29(17Q25.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 29(17Q25.3) MUTATED      37
  DEL PEAK 29(17Q25.3) WILD-TYPE   165
D55V10, multiclass
                                           clus
vv                                          DEL PEAK 29(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               37
                                           clus
vv                                          DEL PEAK 29(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                165
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, binary
                                cls
clus                               0   1
  DEL PEAK 29(17Q25.3) MUTATED     4  34
  DEL PEAK 29(17Q25.3) WILD-TYPE  19 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED      4   34
  DEL PEAK 29(17Q25.3) WILD-TYPE   19  129
                        clus
vv                       DEL PEAK 29(17Q25.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           34
                        clus
vv                       DEL PEAK 29(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            129
[1] 2 2
[1] FALSE
D55V12, continuous
D55V13, binary
                                cls
clus                               0   1
  DEL PEAK 29(17Q25.3) MUTATED    30  14
  DEL PEAK 29(17Q25.3) WILD-TYPE 163  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED     30   14
  DEL PEAK 29(17Q25.3) WILD-TYPE  163   62
            clus
vv           DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  TUMOR FREE                           30                            163
  WITH TUMOR                           14                             62
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 29(17Q25.3) MUTATED     1  19  26   0   3
  DEL PEAK 29(17Q25.3) WILD-TYPE  17 110  89   1  21
D55V14, multiclass
    clus
vv   DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  G1                            1                             17
  G2                           19                            110
  G3                           26                             89
  G4                            0                              1
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, continuous
D55V16, continuous
D55V17, continuous
D55V18, continuous
D55V19, binary
                                cls
clus                              0  1
  DEL PEAK 29(17Q25.3) MUTATED    4  0
  DEL PEAK 29(17Q25.3) WILD-TYPE 21  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED      4    0
  DEL PEAK 29(17Q25.3) WILD-TYPE   21    3
                         clus
vv                        DEL PEAK 29(17Q25.3) MUTATED
  COMPLETED AS PLANNED                               4
  TREATMENT NOT COMPLETED                            0
                         clus
vv                        DEL PEAK 29(17Q25.3) WILD-TYPE
  COMPLETED AS PLANNED                                21
  TREATMENT NOT COMPLETED                              3
[1] 2 2
[1] FALSE
D55V20, continuous
D55V21, continuous
D55V22, continuous
D55V23, continuous
D55V24, continuous
D55V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 29(17Q25.3) MUTATED                                     0
  DEL PEAK 29(17Q25.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 29(17Q25.3) MUTATED                                     2
  DEL PEAK 29(17Q25.3) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 29(17Q25.3) MUTATED                         7
  DEL PEAK 29(17Q25.3) WILD-TYPE                      29
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 29(17Q25.3) MUTATED                         0
  DEL PEAK 29(17Q25.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 29(17Q25.3) MUTATED                         3
  DEL PEAK 29(17Q25.3) WILD-TYPE                       7
D55V26, multiclass
                                     clus
vv                                    DEL PEAK 29(17Q25.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        7
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        3
                                     clus
vv                                    DEL PEAK 29(17Q25.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         29
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 29(17Q25.3) MUTATED                                               0
  DEL PEAK 29(17Q25.3) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 29(17Q25.3) MUTATED                                                3
  DEL PEAK 29(17Q25.3) WILD-TYPE                                             22
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 29(17Q25.3) MUTATED                                                                                  12
  DEL PEAK 29(17Q25.3) WILD-TYPE                                                                                70
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 29(17Q25.3) MUTATED                                                                                             21
  DEL PEAK 29(17Q25.3) WILD-TYPE                                                                                          100
D55V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 29(17Q25.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           21
                                                                                              clus
vv                                                                                             DEL PEAK 29(17Q25.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V28, binary
                                cls
clus                              0  1
  DEL PEAK 29(17Q25.3) MUTATED   12 13
  DEL PEAK 29(17Q25.3) WILD-TYPE 59 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED     12   13
  DEL PEAK 29(17Q25.3) WILD-TYPE   59   61
         clus
vv        DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  ABSENT                            12                             59
  PRESENT                           13                             61
[1] 2 2
[1] FALSE
D55V29, continuous
D55V30, continuous
D55V31, binary
                                cls
clus                              0  1
  DEL PEAK 29(17Q25.3) MUTATED   11 23
  DEL PEAK 29(17Q25.3) WILD-TYPE 38 94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED     11   23
  DEL PEAK 29(17Q25.3) WILD-TYPE   38   94
                                          clus
vv                                         DEL PEAK 29(17Q25.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           23
                                          clus
vv                                         DEL PEAK 29(17Q25.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             94
[1] 2 2
[1] FALSE
D55V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 29(17Q25.3) MUTATED              2           9         15
  DEL PEAK 29(17Q25.3) WILD-TYPE           13          45         70
D55V33, multiclass
              clus
vv             DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  CURRENT USER                            2                             13
  FORMER USER                             9                             45
  NEVER USED                             15                             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"
D55V34, continuous
D55V35, binary
                                cls
clus                              0  1
  DEL PEAK 29(17Q25.3) MUTATED   14  1
  DEL PEAK 29(17Q25.3) WILD-TYPE 78 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED     14    1
  DEL PEAK 29(17Q25.3) WILD-TYPE   78   17
         clus
vv        DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  ABSENT                            14                             78
  PRESENT                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 29(17Q25.3) MUTATED             1        17     0
  DEL PEAK 29(17Q25.3) WILD-TYPE           4        83     2
D55V36, multiclass
             clus
vv            DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             17                             83
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V37, continuous
D55V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 29(17Q25.3) MUTATED         0        0         0         1        8
  DEL PEAK 29(17Q25.3) WILD-TYPE       5        1         1         0       26
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 29(17Q25.3) MUTATED          10         9        2         1
  DEL PEAK 29(17Q25.3) WILD-TYPE        67        28        2         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 29(17Q25.3) MUTATED            1          0         5         0
  DEL PEAK 29(17Q25.3) WILD-TYPE          4          7        39         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 29(17Q25.3) MUTATED            1          8         1         2
  DEL PEAK 29(17Q25.3) WILD-TYPE          2         34         6        10
D55V39, multiclass
            clus
vv           DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              8                             26
  STAGE IB1                            10                             67
  STAGE IB2                             9                             28
  STAGE II                              2                              2
  STAGE IIA                             1                              7
  STAGE IIA1                            1                              4
  STAGE IIA2                            0                              7
  STAGE IIB                             5                             39
  STAGE III                             0                              1
  STAGE IIIA                            1                              2
  STAGE IIIB                            8                             34
  STAGE IVA                             1                              6
  STAGE IVB                             2                             10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 30(18Q21.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(18Q21.2) MUTATED    57  22
  DEL PEAK 30(18Q21.2) WILD-TYPE 157  46
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                            79                            203 
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                            22                             46 
$`DEL PEAK 30(18Q21.2) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME 
       12.59         4.34         0.69        31.40        35.01        57.73 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV 
       35.61         0.46        20.91        40.93        73.18        73.45 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UH 
       78.35        38.43        33.24       154.32        17.19       131.11 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-DG-A2KM TCGA-DR-A0ZL 
       13.61         2.73        45.83        99.91        63.98        87.75 
TCGA-DS-A0VN TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2H0 
      118.65        39.55        40.87        26.01        14.89        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2RL 
       26.27         6.64         1.51         0.39         0.59        47.77 
TCGA-EK-A2RM TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ 
        1.64         7.92        15.22        16.11         1.12        21.67 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A69B 
      137.16        66.81        78.71        81.96        24.56        28.37 
TCGA-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA41 TCGA-Q1-A5R1 
       21.11         0.89        12.49        13.35         9.17        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73P TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB 
       16.41         9.04        15.88        14.60        11.67        10.03 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH 
       23.97        19.96        65.49        53.59        36.13        39.78 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UI 
       40.14        58.45        51.32        43.40        24.30        45.11 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V3 
       47.87        41.52        26.07        67.20         5.16        17.75 
TCGA-ZJ-A8QQ 
       67.59 

$`DEL PEAK 30(18Q21.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-2W-A8YY TCGA-4J-AA1J 
      146.86        14.70         8.32         1.48        17.52        17.82 
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       210.67       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       155.77        94.95         9.34 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       50.99         8.35        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM 
       14.73         1.12        95.11        82.06        44.94        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76        55.63       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       17.52         8.28        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.13        24.82         7.46        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PI 
       27.25        27.22        24.00        13.48         0.36        19.27 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RN 
        4.24         0.07         1.87         1.74         0.43         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A69L 
        0.07         0.10         0.49         0.89        20.35        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55        12.23        23.84        19.04        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       20.98        26.14        16.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
       10.55        17.75        25.41        16.57        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LK TCGA-IR-A3LL 
        9.44       147.39       129.37        96.95        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
       27.42         3.29        21.44        20.48        15.58         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 
       18.15       209.59        44.61        20.91        11.28         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 
        0.82        22.52        20.28        17.82        19.56         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84        17.23         2.96        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PF 
       14.07         9.34        18.64        22.62        19.59        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 
       12.16        69.50        46.52        45.57        32.42        32.15 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        59.18        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 
       33.37        15.68        56.35        55.50        50.14        50.47 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ 
       48.39        28.50        29.95        27.12        46.92         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       14.53        27.25        47.47        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
       18.25        18.84        18.25        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        19.13         1.41         0.16         3.91 

  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                          0.39                           0.07 
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                        154.32                         210.67 
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                         26.27                          20.84 
[1] "0.4 - 154.3 (26.3)" "0.1 - 210.7 (20.8)"
[1] "hr=" "1.1"
D56V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 30(18Q21.2) MUTATED    35  16   7   3
  DEL PEAK 30(18Q21.2) WILD-TYPE 100  54  14   5
D56V3, multiclass
    clus
vv   DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  T1                           35                            100
  T2                           16                             54
  T3                            7                             14
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q21.2) MUTATED   35 11
  DEL PEAK 30(18Q21.2) WILD-TYPE 94 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED     35   11
  DEL PEAK 30(18Q21.2) WILD-TYPE   94   45
   clus
vv  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  0                           35                             94
  1                           11                             45
[1] 2 2
[1] FALSE
D56V5, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q21.2) MUTATED   29  5
  DEL PEAK 30(18Q21.2) WILD-TYPE 79  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED     29    5
  DEL PEAK 30(18Q21.2) WILD-TYPE   79    5
   clus
vv  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  0                           29                             79
  1                            5                              5
[1] 2 2
[1] FALSE
D56V6, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q21.2) MUTATED   13 36
  DEL PEAK 30(18Q21.2) WILD-TYPE 40 89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED     13   36
  DEL PEAK 30(18Q21.2) WILD-TYPE   40   89
     clus
vv    DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  NO                            13                             40
  YES                           36                             89
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(18Q21.2) MUTATED               0                               55
  DEL PEAK 30(18Q21.2) WILD-TYPE             6                              187
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 30(18Q21.2) MUTATED                                               1
  DEL PEAK 30(18Q21.2) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 30(18Q21.2) MUTATED                                    14
  DEL PEAK 30(18Q21.2) WILD-TYPE                                   7
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 30(18Q21.2) MUTATED                                           2
  DEL PEAK 30(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 30(18Q21.2) MUTATED                                             10
  DEL PEAK 30(18Q21.2) WILD-TYPE                                            7
D56V7, multiclass
                                               clus
vv                                              DEL PEAK 30(18Q21.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        55
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            10
                                               clus
vv                                              DEL PEAK 30(18Q21.2) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         187
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, continuous
D56V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(18Q21.2) MUTATED                                  2     4
  DEL PEAK 30(18Q21.2) WILD-TYPE                                6    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(18Q21.2) MUTATED                           9
  DEL PEAK 30(18Q21.2) WILD-TYPE                        19
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(18Q21.2) MUTATED                                           0
  DEL PEAK 30(18Q21.2) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 30(18Q21.2) MUTATED      61
  DEL PEAK 30(18Q21.2) WILD-TYPE   141
D56V10, multiclass
                                           clus
vv                                          DEL PEAK 30(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               61
                                           clus
vv                                          DEL PEAK 30(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  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"
D56V11, binary
                                cls
clus                               0   1
  DEL PEAK 30(18Q21.2) MUTATED     4  40
  DEL PEAK 30(18Q21.2) WILD-TYPE  19 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED      4   40
  DEL PEAK 30(18Q21.2) WILD-TYPE   19  123
                        clus
vv                       DEL PEAK 30(18Q21.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK 30(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            123
[1] 2 2
[1] FALSE
D56V12, continuous
D56V13, binary
                                cls
clus                               0   1
  DEL PEAK 30(18Q21.2) MUTATED    50  25
  DEL PEAK 30(18Q21.2) WILD-TYPE 143  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED     50   25
  DEL PEAK 30(18Q21.2) WILD-TYPE  143   51
            clus
vv           DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  TUMOR FREE                           50                            143
  WITH TUMOR                           25                             51
[1] 2 2
[1] FALSE
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 30(18Q21.2) MUTATED    4 33 32  1 10
  DEL PEAK 30(18Q21.2) WILD-TYPE 14 96 83  0 14
D56V14, multiclass
    clus
vv   DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  G1                            4                             14
  G2                           33                             96
  G3                           32                             83
  G4                            1                              0
  GX                           10                             14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, continuous
D56V16, continuous
D56V17, continuous
D56V18, continuous
D56V19, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q21.2) MUTATED    8  1
  DEL PEAK 30(18Q21.2) WILD-TYPE 17  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED      8    1
  DEL PEAK 30(18Q21.2) WILD-TYPE   17    2
                         clus
vv                        DEL PEAK 30(18Q21.2) MUTATED
  COMPLETED AS PLANNED                               8
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 30(18Q21.2) WILD-TYPE
  COMPLETED AS PLANNED                                17
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D56V20, continuous
D56V21, continuous
D56V22, continuous
D56V23, continuous
D56V24, continuous
D56V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 30(18Q21.2) MUTATED                                     0
  DEL PEAK 30(18Q21.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 30(18Q21.2) MUTATED                                     1
  DEL PEAK 30(18Q21.2) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 30(18Q21.2) MUTATED                        11
  DEL PEAK 30(18Q21.2) WILD-TYPE                      25
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 30(18Q21.2) MUTATED                         0
  DEL PEAK 30(18Q21.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 30(18Q21.2) MUTATED                         4
  DEL PEAK 30(18Q21.2) WILD-TYPE                       6
D56V26, multiclass
                                     clus
vv                                    DEL PEAK 30(18Q21.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                       11
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        4
                                     clus
vv                                    DEL PEAK 30(18Q21.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  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 30(18Q21.2) MUTATED                                               1
  DEL PEAK 30(18Q21.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 30(18Q21.2) MUTATED                                                8
  DEL PEAK 30(18Q21.2) WILD-TYPE                                             17
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 30(18Q21.2) MUTATED                                                                                  26
  DEL PEAK 30(18Q21.2) WILD-TYPE                                                                                56
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 30(18Q21.2) MUTATED                                                                                             31
  DEL PEAK 30(18Q21.2) WILD-TYPE                                                                                           90
D56V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 30(18Q21.2) 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)                                      26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           31
                                                                                              clus
vv                                                                                             DEL PEAK 30(18Q21.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        56
  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"
D56V28, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q21.2) MUTATED   22 12
  DEL PEAK 30(18Q21.2) WILD-TYPE 49 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED     22   12
  DEL PEAK 30(18Q21.2) WILD-TYPE   49   62
         clus
vv        DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  ABSENT                            22                             49
  PRESENT                           12                             62
[1] 2 2
[1] FALSE
D56V29, continuous
D56V30, continuous
D56V31, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q21.2) MUTATED   12 24
  DEL PEAK 30(18Q21.2) WILD-TYPE 37 93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED     12   24
  DEL PEAK 30(18Q21.2) WILD-TYPE   37   93
                                          clus
vv                                         DEL PEAK 30(18Q21.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           24
                                          clus
vv                                         DEL PEAK 30(18Q21.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             93
[1] 2 2
[1] FALSE
D56V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 30(18Q21.2) MUTATED              5          21         26
  DEL PEAK 30(18Q21.2) WILD-TYPE           10          33         59
D56V33, multiclass
              clus
vv             DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  CURRENT USER                            5                             10
  FORMER USER                            21                             33
  NEVER USED                             26                             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V34, continuous
D56V35, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q21.2) MUTATED   27  1
  DEL PEAK 30(18Q21.2) WILD-TYPE 65 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q21.2) MUTATED     27    1
  DEL PEAK 30(18Q21.2) WILD-TYPE   65   17
         clus
vv        DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  ABSENT                            27                             65
  PRESENT                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 30(18Q21.2) MUTATED             1        30     2
  DEL PEAK 30(18Q21.2) WILD-TYPE           4        70     0
D56V36, multiclass
             clus
vv            DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             30                             70
  OTHER                                  2                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V37, continuous
[1] "Remove cluster labels:"       "DEL PEAK 30(18Q21.2) MUTATED"
clus
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 30(18Q21.2) WILD-TYPE" "DEL PEAK 30(18Q21.2) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK 30(18Q21.2) WILD-TYPE" "DEL PEAK 30(18Q21.2) WILD-TYPE" 
                    TCGA-GH-A9DA                     TCGA-HM-A3JK 
"DEL PEAK 30(18Q21.2) WILD-TYPE" "DEL PEAK 30(18Q21.2) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-JX-A3Q8 
"DEL PEAK 30(18Q21.2) WILD-TYPE" "DEL PEAK 30(18Q21.2) WILD-TYPE" 
                    TCGA-MA-AA3W                     TCGA-MA-AA3Z 
"DEL PEAK 30(18Q21.2) WILD-TYPE" "DEL PEAK 30(18Q21.2) WILD-TYPE" 
                    TCGA-MA-AA42                     TCGA-MU-A51Y 
"DEL PEAK 30(18Q21.2) WILD-TYPE" "DEL PEAK 30(18Q21.2) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-MY-A913 
"DEL PEAK 30(18Q21.2) WILD-TYPE" "DEL PEAK 30(18Q21.2) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"DEL PEAK 30(18Q21.2) WILD-TYPE" 
D56V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 30(18Q21.2) MUTATED         1        1         0         0       11
  DEL PEAK 30(18Q21.2) WILD-TYPE       4        0         1         1       23
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 30(18Q21.2) MUTATED          26         5        2         2
  DEL PEAK 30(18Q21.2) WILD-TYPE        51        32        2         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 30(18Q21.2) MUTATED            2          0        15         0
  DEL PEAK 30(18Q21.2) WILD-TYPE          3          7        29         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 30(18Q21.2) MUTATED            2          6         1         5
  DEL PEAK 30(18Q21.2) WILD-TYPE          1         36         6         7
D56V39, multiclass
            clus
vv           DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             11                             23
  STAGE IB1                            26                             51
  STAGE IB2                             5                             32
  STAGE II                              2                              2
  STAGE IIA                             2                              6
  STAGE IIA1                            2                              3
  STAGE IIA2                            0                              7
  STAGE IIB                            15                             29
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                            6                             36
  STAGE IVA                             1                              6
  STAGE IVB                             5                              7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 31(19P13.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(19P13.3) MUTATED    68  31
  DEL PEAK 31(19P13.3) WILD-TYPE 146  37
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            99                            183 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            31                             37 
$`DEL PEAK 31(19P13.3) MUTATED`
TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN 
        4.34         0.69        23.67        11.44        18.74         5.46 
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       31.40        30.21        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL 
        0.46        20.91        40.93        52.01        18.02        15.48 
TCGA-C5-A7CO TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      147.35         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A907 TCGA-DS-A0VM TCGA-DS-A0VN 
       99.91        23.51        27.52        14.73       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3Y4 TCGA-EA-A411 
       16.83        17.52         8.28        40.87        36.89        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       31.73        26.01        25.91        27.25        27.22        24.00 
TCGA-EA-A97N TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 
        0.36         6.64        19.27         0.39         0.43         0.89 
TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ 
        1.45        40.96         1.74         1.64         2.33         0.10 
TCGA-EK-A3GN TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A9SC 
        0.89        19.79        23.84        10.55        17.75        16.57 
TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JX-A3PZ TCGA-JX-A5QV 
       14.93       129.37        24.56        20.48        21.11        20.91 
TCGA-LP-A4AX TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A73S TCGA-RA-A741 
       12.49        17.23         2.96        15.95        22.62        14.60 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       12.16        10.03        19.96        32.15        53.59        36.13 
TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 
       59.18        16.64         4.73        40.14        55.50        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM 
       43.40        48.39        24.30        45.11        14.53        27.25 
TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 
       47.47        15.85        18.84         5.16        17.75        16.24 
TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       15.42        67.59        19.13 

$`DEL PEAK 31(19P13.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-2W-A8YY 
      146.86        12.59        14.70         8.32         1.48        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
       17.82        49.48        57.04        68.84        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      177.04       173.29        82.85        19.86        67.46        46.32 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       38.99         2.43         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF 
       83.05        78.35       100.14        38.43        33.24        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM 
       20.42       210.67       154.32       101.82       134.33        20.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8XI TCGA-C5-A8YT 
       17.19       155.77       131.11        94.95         8.35        20.81 
TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WF 
       87.75        58.88        36.76        55.63        22.98        16.18 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       25.02        26.40        12.13        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG 
       26.79        27.29        13.48        60.72        26.27         1.51 
TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.59         0.13         0.30         4.24         0.07         1.87 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.43        47.77         0.07         0.49        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.22        15.55        12.23        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26        20.98        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 
       35.44         1.12        25.41        21.67        20.78         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      147.39       137.16        66.81        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VL 
       29.85        36.36        27.42         3.29        21.44        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
       28.37         8.28        18.15       209.59        44.61        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89         0.30         0.82        13.35        22.52        20.28 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         9.17         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       34.62        19.96        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
        9.34        18.64        19.59        11.67        93.99        69.50 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8QC 
       46.52        45.57        32.42        23.97        65.49        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 
       39.78        31.27        40.87        33.37        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       56.35        50.14        50.47        28.50        29.95        27.12 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU 
       46.92         1.71        47.87        41.52        26.07        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V2 TCGA-WL-A834 TCGA-XS-A8TJ 
        3.42        18.25        67.20        18.25        26.01        29.26 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                        147.35                         210.67 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                         19.96                          25.41 
[1] "0.1 - 147.3 (20.0)" "0.1 - 210.7 (25.4)"
[1] "hr=" "2"  
D57V2, continuous
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 31(19P13.3) MUTATED   48 20  9  3
  DEL PEAK 31(19P13.3) WILD-TYPE 87 50 12  5
D57V3, multiclass
    clus
vv   DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  T1                           48                             87
  T2                           20                             50
  T3                            9                             12
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   41 19
  DEL PEAK 31(19P13.3) WILD-TYPE 88 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     41   19
  DEL PEAK 31(19P13.3) WILD-TYPE   88   37
   clus
vv  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  0                           41                             88
  1                           19                             37
[1] 2 2
[1] FALSE
D57V5, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   33  4
  DEL PEAK 31(19P13.3) WILD-TYPE 75  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     33    4
  DEL PEAK 31(19P13.3) WILD-TYPE   75    6
   clus
vv  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  0                           33                             75
  1                            4                              6
[1] 2 2
[1] FALSE
D57V6, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   17 51
  DEL PEAK 31(19P13.3) WILD-TYPE 36 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     17   51
  DEL PEAK 31(19P13.3) WILD-TYPE   36   74
     clus
vv    DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  NO                            17                             36
  YES                           51                             74
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(19P13.3) MUTATED               2                               90
  DEL PEAK 31(19P13.3) WILD-TYPE             4                              152
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 31(19P13.3) MUTATED                                               1
  DEL PEAK 31(19P13.3) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 31(19P13.3) MUTATED                                     4
  DEL PEAK 31(19P13.3) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 31(19P13.3) MUTATED                                           0
  DEL PEAK 31(19P13.3) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 31(19P13.3) MUTATED                                              8
  DEL PEAK 31(19P13.3) WILD-TYPE                                            9
D57V7, multiclass
                                               clus
vv                                              DEL PEAK 31(19P13.3) MUTATED
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        90
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             8
                                               clus
vv                                              DEL PEAK 31(19P13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              4
  CERVICAL SQUAMOUS CELL CARCINOMA                                         152
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, continuous
D57V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(19P13.3) MUTATED                                  1     7
  DEL PEAK 31(19P13.3) WILD-TYPE                                7    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(19P13.3) MUTATED                           8
  DEL PEAK 31(19P13.3) WILD-TYPE                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(19P13.3) MUTATED                                           2
  DEL PEAK 31(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 31(19P13.3) MUTATED      80
  DEL PEAK 31(19P13.3) WILD-TYPE   122
D57V10, multiclass
                                           clus
vv                                          DEL PEAK 31(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               80
                                           clus
vv                                          DEL PEAK 31(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D57V11, binary
                                cls
clus                               0   1
  DEL PEAK 31(19P13.3) MUTATED     4  61
  DEL PEAK 31(19P13.3) WILD-TYPE  19 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED      4   61
  DEL PEAK 31(19P13.3) WILD-TYPE   19  102
                        clus
vv                       DEL PEAK 31(19P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 31(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            102
[1] 2 2
[1] FALSE
D57V12, continuous
D57V13, binary
                                cls
clus                               0   1
  DEL PEAK 31(19P13.3) MUTATED    56  38
  DEL PEAK 31(19P13.3) WILD-TYPE 137  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     56   38
  DEL PEAK 31(19P13.3) WILD-TYPE  137   38
            clus
vv           DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  TUMOR FREE                           56                            137
  WITH TUMOR                           38                             38
[1] 2 2
[1] FALSE
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 31(19P13.3) MUTATED    3 40 49  0  8
  DEL PEAK 31(19P13.3) WILD-TYPE 15 89 66  1 16
D57V14, multiclass
    clus
vv   DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  G1                            3                             15
  G2                           40                             89
  G3                           49                             66
  G4                            0                              1
  GX                            8                             16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, continuous
D57V16, continuous
D57V17, continuous
D57V18, continuous
D57V19, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   10  1
  DEL PEAK 31(19P13.3) WILD-TYPE 15  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     10    1
  DEL PEAK 31(19P13.3) WILD-TYPE   15    2
                         clus
vv                        DEL PEAK 31(19P13.3) MUTATED
  COMPLETED AS PLANNED                              10
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 31(19P13.3) WILD-TYPE
  COMPLETED AS PLANNED                                15
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D57V20, continuous
D57V21, continuous
D57V22, continuous
D57V23, continuous
D57V24, continuous
D57V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 31(19P13.3) MUTATED                                     0
  DEL PEAK 31(19P13.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 31(19P13.3) MUTATED                                     2
  DEL PEAK 31(19P13.3) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 31(19P13.3) MUTATED                        14
  DEL PEAK 31(19P13.3) WILD-TYPE                      22
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 31(19P13.3) MUTATED                         0
  DEL PEAK 31(19P13.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 31(19P13.3) MUTATED                         2
  DEL PEAK 31(19P13.3) WILD-TYPE                       8
D57V26, multiclass
                                     clus
vv                                    DEL PEAK 31(19P13.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                       14
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 31(19P13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                         22
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 31(19P13.3) MUTATED                                               2
  DEL PEAK 31(19P13.3) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 31(19P13.3) MUTATED                                                9
  DEL PEAK 31(19P13.3) WILD-TYPE                                             16
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 31(19P13.3) MUTATED                                                                                  23
  DEL PEAK 31(19P13.3) WILD-TYPE                                                                                59
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 31(19P13.3) MUTATED                                                                                             41
  DEL PEAK 31(19P13.3) WILD-TYPE                                                                                           80
D57V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 31(19P13.3) MUTATED
  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)                                      23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           41
                                                                                              clus
vv                                                                                             DEL PEAK 31(19P13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        59
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D57V28, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   20 25
  DEL PEAK 31(19P13.3) WILD-TYPE 51 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     20   25
  DEL PEAK 31(19P13.3) WILD-TYPE   51   49
         clus
vv        DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  ABSENT                            20                             51
  PRESENT                           25                             49
[1] 2 2
[1] FALSE
D57V29, continuous
D57V30, continuous
D57V31, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   19 36
  DEL PEAK 31(19P13.3) WILD-TYPE 30 81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     19   36
  DEL PEAK 31(19P13.3) WILD-TYPE   30   81
                                          clus
vv                                         DEL PEAK 31(19P13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           36
                                          clus
vv                                         DEL PEAK 31(19P13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             81
[1] 2 2
[1] FALSE
D57V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 31(19P13.3) MUTATED              5          20         29
  DEL PEAK 31(19P13.3) WILD-TYPE           10          34         56
D57V33, multiclass
              clus
vv             DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  CURRENT USER                            5                             10
  FORMER USER                            20                             34
  NEVER USED                             29                             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"
D57V34, continuous
D57V35, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   27  5
  DEL PEAK 31(19P13.3) WILD-TYPE 65 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     27    5
  DEL PEAK 31(19P13.3) WILD-TYPE   65   13
         clus
vv        DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  ABSENT                            27                             65
  PRESENT                            5                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 31(19P13.3) MUTATED             2        40     0
  DEL PEAK 31(19P13.3) WILD-TYPE           3        60     2
D57V36, multiclass
             clus
vv            DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  CARBOPLATIN                            2                              3
  CISPLATIN                             40                             60
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V37, continuous
D57V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 31(19P13.3) MUTATED         1        0         0         0       12
  DEL PEAK 31(19P13.3) WILD-TYPE       4        1         1         1       22
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 31(19P13.3) MUTATED          30        14        1         3
  DEL PEAK 31(19P13.3) WILD-TYPE        47        23        3         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 31(19P13.3) MUTATED            2          2        17         0
  DEL PEAK 31(19P13.3) WILD-TYPE          3          5        27         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 31(19P13.3) MUTATED            2         13         1         5
  DEL PEAK 31(19P13.3) WILD-TYPE          1         29         6         7
D57V39, multiclass
            clus
vv           DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                             12                             22
  STAGE IB1                            30                             47
  STAGE IB2                            14                             23
  STAGE II                              1                              3
  STAGE IIA                             3                              5
  STAGE IIA1                            2                              3
  STAGE IIA2                            2                              5
  STAGE IIB                            17                             27
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                           13                             29
  STAGE IVA                             1                              6
  STAGE IVB                             5                              7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 32(19Q13.33) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(19Q13.33) MUTATED    25  12
  DEL PEAK 32(19Q13.33) WILD-TYPE 189  56
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                             37                             245 
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                             12                              56 
$`DEL PEAK 32(19Q13.33) MUTATED`
TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1ML 
        4.34         0.69        30.21        35.01         0.46        20.91 
TCGA-C5-A7CM TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A8YQ TCGA-DG-A2KJ TCGA-DS-A0VN 
       20.35        94.95         2.73        23.51        95.11       118.65 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A556 TCGA-EK-A2IP TCGA-EK-A2PM TCGA-EK-A3GJ 
       40.87        30.90        14.89         6.64         0.59         0.10 
TCGA-FU-A3NI TCGA-GH-A9DA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VI 
       20.98        17.75       129.37        78.71        81.96        24.56 
TCGA-JW-A5VK TCGA-JX-A3Q8 TCGA-MY-A5BD TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EJ 
       20.48        44.61        54.81         9.04        32.42        19.96 
TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A957 TCGA-VS-A9U7 TCGA-VS-A9UM TCGA-VS-A9V0 
       53.59        39.78        55.50        48.39        27.25        18.84 
TCGA-VS-A9V5 
       16.24 

$`DEL PEAK 32(19Q13.33) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-2W-A8YY 
      146.86        12.59        14.70         8.32         1.48        17.52 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.82        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME 
        5.46        19.86        67.46        31.40        46.32        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99        35.61         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
      210.67       154.32       101.82       134.33        15.48       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
       17.19       155.77       131.11         9.34        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       45.83         8.35        99.91        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       14.73         1.12        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76        55.63       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        39.55        37.35        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       31.73        26.01        12.13        24.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
        0.36        60.72        26.27         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL 
        4.24         0.07         1.87         1.74         0.43        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        1.64         2.33         0.07         0.49         0.89        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        7.92        15.22        19.79        15.55        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
       19.04        16.11        31.36        36.26        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
       28.31        14.01        35.44        10.55         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      137.16        66.81        96.95        29.85        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        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        20.91        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         9.17         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       19.96        35.05        20.84        17.23         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        69.50        10.03        46.52        45.57 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       23.97        65.49        32.15        36.13        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       58.45        15.68        56.35        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       43.40        28.50        29.95        27.12        24.30        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
       45.11         1.71        14.53        47.87        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       26.07        15.85        14.53         3.42        18.25        67.20 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
        5.16        18.25        17.75        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                         129.37                          210.67 
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                          24.56                           21.67 
[1] "0.1 - 129.4 (24.6)" "0.1 - 210.7 (21.7)"
[1] "hr=" "1.3"
D58V2, continuous
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 32(19Q13.33) MUTATED    17  10   3   1
  DEL PEAK 32(19Q13.33) WILD-TYPE 118  60  18   7
D58V3, multiclass
    clus
vv   DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  T1                            17                             118
  T2                            10                              60
  T3                             3                              18
  T4                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                                 cls
clus                                0   1
  DEL PEAK 32(19Q13.33) MUTATED    16   6
  DEL PEAK 32(19Q13.33) WILD-TYPE 113  50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED     16    6
  DEL PEAK 32(19Q13.33) WILD-TYPE  113   50
   clus
vv  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  0                            16                             113
  1                             6                              50
[1] 2 2
[1] FALSE
D58V5, binary
                                 cls
clus                               0  1
  DEL PEAK 32(19Q13.33) MUTATED   13  2
  DEL PEAK 32(19Q13.33) WILD-TYPE 95  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED     13    2
  DEL PEAK 32(19Q13.33) WILD-TYPE   95    8
   clus
vv  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  0                            13                              95
  1                             2                               8
[1] 2 2
[1] FALSE
D58V6, binary
                                 cls
clus                                0   1
  DEL PEAK 32(19Q13.33) MUTATED     8  18
  DEL PEAK 32(19Q13.33) WILD-TYPE  45 107
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED      8   18
  DEL PEAK 32(19Q13.33) WILD-TYPE   45  107
     clus
vv    DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  NO                              8                              45
  YES                            18                             107
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 32(19Q13.33) MUTATED               0
  DEL PEAK 32(19Q13.33) WILD-TYPE             6
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(19Q13.33) MUTATED                                 27
  DEL PEAK 32(19Q13.33) WILD-TYPE                              215
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 32(19Q13.33) MUTATED                                               1
  DEL PEAK 32(19Q13.33) WILD-TYPE                                             5
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 32(19Q13.33) MUTATED                                     4
  DEL PEAK 32(19Q13.33) WILD-TYPE                                  17
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 32(19Q13.33) MUTATED                                           1
  DEL PEAK 32(19Q13.33) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 32(19Q13.33) MUTATED                                              5
  DEL PEAK 32(19Q13.33) WILD-TYPE                                           12
D58V7, multiclass
                                               clus
vv                                              DEL PEAK 32(19Q13.33) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              5
                                               clus
vv                                              DEL PEAK 32(19Q13.33) WILD-TYPE
  ADENOSQUAMOUS                                                               6
  CERVICAL SQUAMOUS CELL CARCINOMA                                          215
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, continuous
D58V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(19Q13.33) MUTATED                                  1     1
  DEL PEAK 32(19Q13.33) WILD-TYPE                                7    18
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(19Q13.33) MUTATED                           4
  DEL PEAK 32(19Q13.33) WILD-TYPE                        24
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 32(19Q13.33) MUTATED                                           1
  DEL PEAK 32(19Q13.33) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 32(19Q13.33) MUTATED      27
  DEL PEAK 32(19Q13.33) WILD-TYPE   175
D58V10, multiclass
                                           clus
vv                                          DEL PEAK 32(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 1
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                27
                                           clus
vv                                          DEL PEAK 32(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  18
  BLACK OR AFRICAN AMERICAN                                              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 175
[1] 5 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 32(19Q13.33) MUTATED     3  15
  DEL PEAK 32(19Q13.33) WILD-TYPE  20 148
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED      3   15
  DEL PEAK 32(19Q13.33) WILD-TYPE   20  148
                        clus
vv                       DEL PEAK 32(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            15
                        clus
vv                       DEL PEAK 32(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             148
[1] 2 2
[1] FALSE
D58V12, continuous
D58V13, binary
                                 cls
clus                                0   1
  DEL PEAK 32(19Q13.33) MUTATED    24  11
  DEL PEAK 32(19Q13.33) WILD-TYPE 169  65
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED     24   11
  DEL PEAK 32(19Q13.33) WILD-TYPE  169   65
            clus
vv           DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  TUMOR FREE                            24                             169
  WITH TUMOR                            11                              65
[1] 2 2
[1] FALSE
                                 vv
clus                               G1  G2  G3  G4  GX
  DEL PEAK 32(19Q13.33) MUTATED     1  16  18   1   1
  DEL PEAK 32(19Q13.33) WILD-TYPE  17 113  97   0  23
D58V14, multiclass
    clus
vv   DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  G1                             1                              17
  G2                            16                             113
  G3                            18                              97
  G4                             1                               0
  GX                             1                              23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, continuous
D58V16, continuous
D58V17, continuous
D58V18, continuous
D58V19, binary
                                 cls
clus                               0  1
  DEL PEAK 32(19Q13.33) MUTATED    3  0
  DEL PEAK 32(19Q13.33) WILD-TYPE 22  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED      3    0
  DEL PEAK 32(19Q13.33) WILD-TYPE   22    3
                         clus
vv                        DEL PEAK 32(19Q13.33) MUTATED
  COMPLETED AS PLANNED                                3
  TREATMENT NOT COMPLETED                             0
                         clus
vv                        DEL PEAK 32(19Q13.33) WILD-TYPE
  COMPLETED AS PLANNED                                 22
  TREATMENT NOT COMPLETED                               3
[1] 2 2
[1] FALSE
D58V20, continuous
D58V21, continuous
D58V22, continuous
D58V23, continuous
D58V24, continuous
D58V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 32(19Q13.33) MUTATED                                     0
  DEL PEAK 32(19Q13.33) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 32(19Q13.33) MUTATED                                     1
  DEL PEAK 32(19Q13.33) WILD-TYPE                                   6
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 32(19Q13.33) MUTATED                         6
  DEL PEAK 32(19Q13.33) WILD-TYPE                      30
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 32(19Q13.33) MUTATED                         0
  DEL PEAK 32(19Q13.33) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 32(19Q13.33) MUTATED                         2
  DEL PEAK 32(19Q13.33) WILD-TYPE                       8
D58V26, multiclass
                                     clus
vv                                    DEL PEAK 32(19Q13.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         6
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         2
                                     clus
vv                                    DEL PEAK 32(19Q13.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               6
  OTHER LOCATION, SPECIFY                                          30
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 32(19Q13.33) MUTATED                                               1
  DEL PEAK 32(19Q13.33) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 32(19Q13.33) MUTATED                                                3
  DEL PEAK 32(19Q13.33) WILD-TYPE                                             22
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 32(19Q13.33) MUTATED                                                                                  13
  DEL PEAK 32(19Q13.33) WILD-TYPE                                                                                69
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 32(19Q13.33) MUTATED                                                                                             12
  DEL PEAK 32(19Q13.33) WILD-TYPE                                                                                          109
D58V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 32(19Q13.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            12
                                                                                              clus
vv                                                                                             DEL PEAK 32(19Q13.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         69
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V28, binary
                                 cls
clus                               0  1
  DEL PEAK 32(19Q13.33) MUTATED    8  8
  DEL PEAK 32(19Q13.33) WILD-TYPE 63 66
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED      8    8
  DEL PEAK 32(19Q13.33) WILD-TYPE   63   66
         clus
vv        DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  ABSENT                              8                              63
  PRESENT                             8                              66
[1] 2 2
[1] FALSE
D58V29, continuous
D58V30, continuous
D58V31, binary
                                 cls
clus                                0   1
  DEL PEAK 32(19Q13.33) MUTATED     5  10
  DEL PEAK 32(19Q13.33) WILD-TYPE  44 107
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED      5   10
  DEL PEAK 32(19Q13.33) WILD-TYPE   44  107
                                          clus
vv                                         DEL PEAK 32(19Q13.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            10
                                          clus
vv                                         DEL PEAK 32(19Q13.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             107
[1] 2 2
[1] FALSE
D58V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 32(19Q13.33) MUTATED              2           5         12
  DEL PEAK 32(19Q13.33) WILD-TYPE           13          49         73
D58V33, multiclass
              clus
vv             DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  CURRENT USER                             2                              13
  FORMER USER                              5                              49
  NEVER USED                              12                              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"
D58V34, continuous
D58V35, binary
                                 cls
clus                               0  1
  DEL PEAK 32(19Q13.33) MUTATED   14  1
  DEL PEAK 32(19Q13.33) WILD-TYPE 78 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(19Q13.33) MUTATED     14    1
  DEL PEAK 32(19Q13.33) WILD-TYPE   78   17
         clus
vv        DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  ABSENT                             14                              78
  PRESENT                             1                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 32(19Q13.33) MUTATED             1        14     1
  DEL PEAK 32(19Q13.33) WILD-TYPE           4        86     1
D58V36, multiclass
             clus
vv            DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  CARBOPLATIN                             1                               4
  CISPLATIN                              14                              86
  OTHER                                   1                               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"
D58V37, continuous
D58V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 32(19Q13.33) MUTATED         1        0         0         0        3
  DEL PEAK 32(19Q13.33) WILD-TYPE       4        1         1         1       31
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 32(19Q13.33) MUTATED          17         3        2         0
  DEL PEAK 32(19Q13.33) WILD-TYPE        60        34        2         8
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 32(19Q13.33) MUTATED            1          0         6         0
  DEL PEAK 32(19Q13.33) WILD-TYPE          4          7        38         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 32(19Q13.33) MUTATED            0          2         1         2
  DEL PEAK 32(19Q13.33) WILD-TYPE          3         40         6        10
D58V39, multiclass
            clus
vv           DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                               3                              31
  STAGE IB1                             17                              60
  STAGE IB2                              3                              34
  STAGE II                               2                               2
  STAGE IIA                              0                               8
  STAGE IIA1                             1                               4
  STAGE IIA2                             0                               7
  STAGE IIB                              6                              38
  STAGE III                              0                               1
  STAGE IIIA                             0                               3
  STAGE IIIB                             2                              40
  STAGE IVA                              1                               6
  STAGE IVB                              2                              10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK 33(20P12.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(20P12.1) MUTATED    22  12
  DEL PEAK 33(20P12.1) WILD-TYPE 192  56
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            34                            248 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            12                             56 
$`DEL PEAK 33(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        82.06        40.87        24.56         7.46        60.72 
TCGA-EK-A2PI TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A770 TCGA-GH-A9DA 
       19.27         7.92        16.11        31.36         1.12        17.75 
TCGA-IR-A3LB TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX 
       66.81        29.85        24.56        21.11        20.91        12.49 
TCGA-MU-A5YI TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8Q9 TCGA-VS-A94Y 
       34.62        17.23        14.60        11.67        53.59         4.73 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       18.84         5.16        15.42        67.59 

$`DEL PEAK 33(20P12.1) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-ZJ-AAX4 TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
        0.69        17.52        17.82        57.04        23.67        11.44 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74        36.56       144.16       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
       19.86        67.46        46.32        30.21        35.01        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
        9.34         2.73        50.99         8.35        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52        20.81        20.91        14.73         1.12        95.11 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        39.55        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B 
       13.05        25.02        36.89        26.40        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.13        24.82        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 
       27.25        27.22        24.00        13.48         0.36        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51         0.39         0.43         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        1.87         1.74         0.43        47.77         1.64         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 
        0.07         0.10         0.49         0.89        20.35        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HZ 
       19.79        15.55        12.23        23.84        19.04        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       20.98        26.14        16.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       10.55        25.41        16.57        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       129.37        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        28.37         8.28        18.15       209.59        44.61 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       11.28         0.89         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       20.28        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       28.08        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        69.50        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA 
       32.42        23.97        19.96        65.49        32.15        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       29.95        27.12        24.30        46.92        45.11         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        47.87        47.47        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V2 
       15.85        14.53         3.42        18.25        67.20        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       17.75        16.24        26.01        29.26        19.13         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                          1.12                           0.07 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                        177.04                         210.67 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                        22.835                         22.570 
[1] "1.1 - 177.0 (22.8)" "0.1 - 210.7 (22.6)"
[1] "hr=" "1.6"
D59V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 33(20P12.1) MUTATED    20   7   1   1
  DEL PEAK 33(20P12.1) WILD-TYPE 115  63  20   7
D59V3, multiclass
    clus
vv   DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  T1                           20                            115
  T2                            7                             63
  T3                            1                             20
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                                cls
clus                               0   1
  DEL PEAK 33(20P12.1) MUTATED    18   6
  DEL PEAK 33(20P12.1) WILD-TYPE 111  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     18    6
  DEL PEAK 33(20P12.1) WILD-TYPE  111   50
   clus
vv  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  0                           18                            111
  1                            6                             50
[1] 2 2
[1] FALSE
D59V5, binary
                                cls
clus                              0  1
  DEL PEAK 33(20P12.1) MUTATED   14  1
  DEL PEAK 33(20P12.1) WILD-TYPE 94  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     14    1
  DEL PEAK 33(20P12.1) WILD-TYPE   94    9
   clus
vv  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  0                           14                             94
  1                            1                              9
[1] 2 2
[1] FALSE
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(20P12.1) MUTATED    10  14
  DEL PEAK 33(20P12.1) WILD-TYPE  43 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     10   14
  DEL PEAK 33(20P12.1) WILD-TYPE   43  111
     clus
vv    DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  NO                            10                             43
  YES                           14                            111
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(20P12.1) MUTATED               0                               29
  DEL PEAK 33(20P12.1) WILD-TYPE             6                              213
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 33(20P12.1) MUTATED                                               1
  DEL PEAK 33(20P12.1) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 33(20P12.1) MUTATED                                     4
  DEL PEAK 33(20P12.1) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 33(20P12.1) MUTATED                                           0
  DEL PEAK 33(20P12.1) WILD-TYPE                                         3
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 33(20P12.1) MUTATED                                              2
  DEL PEAK 33(20P12.1) WILD-TYPE                                           15
D59V7, multiclass
                                               clus
vv                                              DEL PEAK 33(20P12.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        29
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              DEL PEAK 33(20P12.1) WILD-TYPE
  ADENOSQUAMOUS                                                              6
  CERVICAL SQUAMOUS CELL CARCINOMA                                         213
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, continuous
D59V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(20P12.1) MUTATED                                  2     3
  DEL PEAK 33(20P12.1) WILD-TYPE                                6    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(20P12.1) MUTATED                           4
  DEL PEAK 33(20P12.1) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 33(20P12.1) MUTATED                                           0
  DEL PEAK 33(20P12.1) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 33(20P12.1) MUTATED      24
  DEL PEAK 33(20P12.1) WILD-TYPE   178
D59V10, multiclass
                                           clus
vv                                          DEL PEAK 33(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               24
                                           clus
vv                                          DEL PEAK 33(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                178
[1] 5 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 33(20P12.1) MUTATED     2  19
  DEL PEAK 33(20P12.1) WILD-TYPE  21 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED      2   19
  DEL PEAK 33(20P12.1) WILD-TYPE   21  144
                        clus
vv                       DEL PEAK 33(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       DEL PEAK 33(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            144
[1] 2 2
[1] FALSE
D59V12, continuous
D59V13, binary
                                cls
clus                               0   1
  DEL PEAK 33(20P12.1) MUTATED    20  15
  DEL PEAK 33(20P12.1) WILD-TYPE 173  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     20   15
  DEL PEAK 33(20P12.1) WILD-TYPE  173   61
            clus
vv           DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  TUMOR FREE                           20                            173
  WITH TUMOR                           15                             61
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 33(20P12.1) MUTATED     2  16  13   0   3
  DEL PEAK 33(20P12.1) WILD-TYPE  16 113 102   1  21
D59V14, multiclass
    clus
vv   DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  G1                            2                             16
  G2                           16                            113
  G3                           13                            102
  G4                            0                              1
  GX                            3                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V15, continuous
D59V16, continuous
D59V17, continuous
D59V18, continuous
D59V19, binary
                                cls
clus                              0  1
  DEL PEAK 33(20P12.1) MUTATED    2  1
  DEL PEAK 33(20P12.1) WILD-TYPE 23  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED      2    1
  DEL PEAK 33(20P12.1) WILD-TYPE   23    2
                         clus
vv                        DEL PEAK 33(20P12.1) MUTATED
  COMPLETED AS PLANNED                               2
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 33(20P12.1) WILD-TYPE
  COMPLETED AS PLANNED                                23
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D59V20, continuous
D59V21, continuous
D59V22, continuous
D59V23, continuous
D59V24, continuous
D59V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 33(20P12.1) MUTATED                                     0
  DEL PEAK 33(20P12.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 33(20P12.1) MUTATED                                     1
  DEL PEAK 33(20P12.1) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 33(20P12.1) MUTATED                         6
  DEL PEAK 33(20P12.1) WILD-TYPE                      30
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 33(20P12.1) MUTATED                         1
  DEL PEAK 33(20P12.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 33(20P12.1) MUTATED                         1
  DEL PEAK 33(20P12.1) WILD-TYPE                       9
D59V26, multiclass
                                     clus
vv                                    DEL PEAK 33(20P12.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        6
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 33(20P12.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              6
  OTHER LOCATION, SPECIFY                                         30
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 33(20P12.1) MUTATED                                               0
  DEL PEAK 33(20P12.1) WILD-TYPE                                             3
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 33(20P12.1) MUTATED                                                2
  DEL PEAK 33(20P12.1) WILD-TYPE                                             23
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 33(20P12.1) MUTATED                                                                                  12
  DEL PEAK 33(20P12.1) WILD-TYPE                                                                                70
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 33(20P12.1) MUTATED                                                                                             16
  DEL PEAK 33(20P12.1) WILD-TYPE                                                                                          105
D59V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 33(20P12.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           16
                                                                                              clus
vv                                                                                             DEL PEAK 33(20P12.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V28, binary
                                cls
clus                              0  1
  DEL PEAK 33(20P12.1) MUTATED    9  9
  DEL PEAK 33(20P12.1) WILD-TYPE 62 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED      9    9
  DEL PEAK 33(20P12.1) WILD-TYPE   62   65
         clus
vv        DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  ABSENT                             9                             62
  PRESENT                            9                             65
[1] 2 2
[1] FALSE
D59V29, continuous
D59V30, continuous
D59V31, binary
                                cls
clus                               0   1
  DEL PEAK 33(20P12.1) MUTATED     7  12
  DEL PEAK 33(20P12.1) WILD-TYPE  42 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED      7   12
  DEL PEAK 33(20P12.1) WILD-TYPE   42  105
                                          clus
vv                                         DEL PEAK 33(20P12.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           12
                                          clus
vv                                         DEL PEAK 33(20P12.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            105
[1] 2 2
[1] FALSE
D59V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 33(20P12.1) MUTATED              3           9          8
  DEL PEAK 33(20P12.1) WILD-TYPE           12          45         77
D59V33, multiclass
              clus
vv             DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                             9                             45
  NEVER USED                              8                             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"
D59V34, continuous
D59V35, binary
                                cls
clus                              0  1
  DEL PEAK 33(20P12.1) MUTATED   13  3
  DEL PEAK 33(20P12.1) WILD-TYPE 79 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     13    3
  DEL PEAK 33(20P12.1) WILD-TYPE   79   15
         clus
vv        DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  ABSENT                            13                             79
  PRESENT                            3                             15
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 33(20P12.1) MUTATED             1        11     0
  DEL PEAK 33(20P12.1) WILD-TYPE           4        89     2
D59V36, multiclass
             clus
vv            DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  CARBOPLATIN                            1                              4
  CISPLATIN                             11                             89
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V37, continuous
[1] "Remove cluster labels:"       "DEL PEAK 33(20P12.1) MUTATED"
clus
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                             2                             15 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 33(20P12.1) WILD-TYPE" "DEL PEAK 33(20P12.1) WILD-TYPE" 
                    TCGA-C5-A1ML                     TCGA-C5-A1MN 
"DEL PEAK 33(20P12.1) WILD-TYPE" "DEL PEAK 33(20P12.1) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK 33(20P12.1) WILD-TYPE" "DEL PEAK 33(20P12.1) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 33(20P12.1) WILD-TYPE" "DEL PEAK 33(20P12.1) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MA-AA3W 
"DEL PEAK 33(20P12.1) WILD-TYPE" "DEL PEAK 33(20P12.1) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK 33(20P12.1) WILD-TYPE" "DEL PEAK 33(20P12.1) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 33(20P12.1) WILD-TYPE" "DEL PEAK 33(20P12.1) WILD-TYPE" 
                    TCGA-ZX-AA5X 
"DEL PEAK 33(20P12.1) WILD-TYPE" 
D59V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 33(20P12.1) MUTATED         0        0         1         0        6
  DEL PEAK 33(20P12.1) WILD-TYPE       5        1         0         1       28
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 33(20P12.1) MUTATED           9         3        0         1
  DEL PEAK 33(20P12.1) WILD-TYPE        68        34        4         7
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 33(20P12.1) MUTATED            0          0         9         0
  DEL PEAK 33(20P12.1) WILD-TYPE          5          7        35         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 33(20P12.1) MUTATED            0          4         1         2
  DEL PEAK 33(20P12.1) WILD-TYPE          3         38         6        10
D59V39, multiclass
            clus
vv           DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IA1                             1                              0
  STAGE IA2                             0                              1
  STAGE IB                              6                             28
  STAGE IB1                             9                             68
  STAGE IB2                             3                             34
  STAGE II                              0                              4
  STAGE IIA                             1                              7
  STAGE IIA1                            0                              5
  STAGE IIA2                            0                              7
  STAGE IIB                             9                             35
  STAGE III                             0                              1
  STAGE IIIA                            0                              3
  STAGE IIIB                            4                             38
  STAGE IVA                             1                              6
  STAGE IVB                             2                             10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 34(21Q11.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(21Q11.2) MUTATED    36  20
  DEL PEAK 34(21Q11.2) WILD-TYPE 178  48
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                            56                            226 
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                            20                             48 
$`DEL PEAK 34(21Q11.2) MUTATED`
TCGA-EK-A2GZ TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1M9 TCGA-C5-A1MJ 
       12.59        57.04        23.67        11.44        35.01         0.46 
TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CJ TCGA-C5-A7X3 TCGA-C5-A8YQ 
       40.93        73.18        73.45       101.82         9.34        23.51 
TCGA-C5-A8YR TCGA-DG-A2KJ TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A3HR TCGA-EA-A411 
       27.52        95.11        87.75        55.63        30.90        24.56 
TCGA-EA-A439 TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2PK 
       31.73         7.46        14.89         0.36         1.51         0.39 
TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-FU-A23L 
        1.45         1.74        47.77         0.89        15.22        23.84 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3LB TCGA-JW-A5VG 
       31.36        20.98        21.67         9.44        66.81        27.42 
TCGA-LP-A4AW TCGA-LP-A7HU TCGA-PN-A8MA TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH 
        0.89        13.35         2.96        12.16        10.03        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 
       23.97        19.96        53.59         4.73        40.14        15.68 
TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UL 
       55.50        51.32        50.47        24.30        46.92        14.53 
TCGA-VS-A9UP TCGA-WL-A834 
       47.47        26.01 

$`DEL PEAK 34(21Q11.2) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 
      146.86        14.70         8.32         1.48         4.34         0.69 
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        17.82        49.48        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-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         2.43        20.91         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        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK 
       18.02        17.85        20.42       210.67       154.32       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       99.91        20.81        20.91        14.73         1.12        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       44.94        63.98        58.88        36.76       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       40.87        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A5FO 
       36.89        26.40        26.01        12.13        24.82        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM 
       60.72        26.27         6.64        19.27         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.89         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.87         0.43         1.64         2.33         0.07         0.10 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        0.49        20.35         7.92        19.79        15.55        12.23 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       19.04        16.11        36.26        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       14.01        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC 
       16.57        20.78        14.93       147.39       137.16       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH 
       96.95        78.71        81.96        29.85        36.36         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
       12.49         0.30         0.82        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         9.17         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
       19.96        54.81        35.05        20.84        17.23        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL 
       11.67        93.99        69.50        46.52        45.57        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        36.13        11.51        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       40.87        16.64        33.37        58.45        56.35        50.14 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UI 
       43.40        48.39        28.50        29.95        27.12        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
        1.71        27.25        47.87        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       18.25        17.75        16.24        15.42        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         1.41         0.16         3.91 

  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                          0.36                           0.07 
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                        101.82                         210.67 
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                        23.905                         21.010 
[1] "0.4 - 101.8 (23.9)" "0.1 - 210.7 (21.0)"
[1] "hr=" "1.9"
D60V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(21Q11.2) MUTATED    24  14   9   3
  DEL PEAK 34(21Q11.2) WILD-TYPE 111  56  12   5
D60V3, multiclass
    clus
vv   DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  T1                           24                            111
  T2                           14                             56
  T3                            9                             12
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                                cls
clus                               0   1
  DEL PEAK 34(21Q11.2) MUTATED    21  14
  DEL PEAK 34(21Q11.2) WILD-TYPE 108  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     21   14
  DEL PEAK 34(21Q11.2) WILD-TYPE  108   42
   clus
vv  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  0                           21                            108
  1                           14                             42
[1] 2 2
[1] FALSE
D60V5, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED   23  3
  DEL PEAK 34(21Q11.2) WILD-TYPE 85  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     23    3
  DEL PEAK 34(21Q11.2) WILD-TYPE   85    7
   clus
vv  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  0                           23                             85
  1                            3                              7
[1] 2 2
[1] FALSE
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(21Q11.2) MUTATED     6  25
  DEL PEAK 34(21Q11.2) WILD-TYPE  47 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED      6   25
  DEL PEAK 34(21Q11.2) WILD-TYPE   47  100
     clus
vv    DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  NO                             6                             47
  YES                           25                            100
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(21Q11.2) MUTATED               1                               49
  DEL PEAK 34(21Q11.2) WILD-TYPE             5                              193
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 34(21Q11.2) MUTATED                                               1
  DEL PEAK 34(21Q11.2) WILD-TYPE                                             5
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 34(21Q11.2) MUTATED                                     5
  DEL PEAK 34(21Q11.2) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 34(21Q11.2) MUTATED                                           1
  DEL PEAK 34(21Q11.2) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 34(21Q11.2) MUTATED                                              1
  DEL PEAK 34(21Q11.2) WILD-TYPE                                           16
D60V7, multiclass
                                               clus
vv                                              DEL PEAK 34(21Q11.2) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK 34(21Q11.2) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         193
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, continuous
D60V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(21Q11.2) MUTATED                                  1     5
  DEL PEAK 34(21Q11.2) WILD-TYPE                                7    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(21Q11.2) MUTATED                           9
  DEL PEAK 34(21Q11.2) WILD-TYPE                        19
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 34(21Q11.2) MUTATED                                           0
  DEL PEAK 34(21Q11.2) WILD-TYPE                                         2
                                vv
clus                             WHITE
  DEL PEAK 34(21Q11.2) MUTATED      36
  DEL PEAK 34(21Q11.2) WILD-TYPE   166
D60V10, multiclass
                                           clus
vv                                          DEL PEAK 34(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               36
                                           clus
vv                                          DEL PEAK 34(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              2
  WHITE                                                                166
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                                cls
clus                               0   1
  DEL PEAK 34(21Q11.2) MUTATED     1  35
  DEL PEAK 34(21Q11.2) WILD-TYPE  22 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED      1   35
  DEL PEAK 34(21Q11.2) WILD-TYPE   22  128
                        clus
vv                       DEL PEAK 34(21Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       DEL PEAK 34(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE
D60V12, continuous
D60V13, binary
                                cls
clus                               0   1
  DEL PEAK 34(21Q11.2) MUTATED    35  19
  DEL PEAK 34(21Q11.2) WILD-TYPE 158  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     35   19
  DEL PEAK 34(21Q11.2) WILD-TYPE  158   57
            clus
vv           DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  TUMOR FREE                           35                            158
  WITH TUMOR                           19                             57
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 34(21Q11.2) MUTATED     2  18  33   0   5
  DEL PEAK 34(21Q11.2) WILD-TYPE  16 111  82   1  19
D60V14, multiclass
    clus
vv   DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  G1                            2                             16
  G2                           18                            111
  G3                           33                             82
  G4                            0                              1
  GX                            5                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, continuous
[1] "Remove cluster labels:"       "DEL PEAK 34(21Q11.2) MUTATED"
clus
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                             2                             41 
                    TCGA-EX-A69M                     TCGA-FU-A3TX 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-VS-A9V4                     TCGA-ZJ-AAX4 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-2W-A8YY                     TCGA-BI-A0VR 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1BJ                     TCGA-C5-A1BL 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1BQ                     TCGA-C5-A1ME 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1MF                     TCGA-C5-A1MH 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A2M2                     TCGA-C5-A3HD 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A7CM                     TCGA-C5-A7CO 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A8XH                     TCGA-C5-A907 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-DG-A2KK                     TCGA-DS-A3LQ 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-EK-A2RA                     TCGA-FU-A2QG 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-FU-A3WB                     TCGA-HM-A3JK 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-HM-A4S6                     TCGA-IR-A3L7 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-IR-A3LH                     TCGA-JX-A3Q0 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-MA-AA43                     TCGA-MU-A5YI 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-Q1-A6DW 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-Q1-A73S                     TCGA-RA-A741 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-VS-A8QF                     TCGA-VS-A94Z 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-VS-A9V0                     TCGA-ZJ-A8QR 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-ZJ-AAXA                     TCGA-ZJ-AAXT 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-ZJ-AB0I 
"DEL PEAK 34(21Q11.2) WILD-TYPE" 
D60V16, continuous
D60V17, continuous
D60V18, continuous
D60V19, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED    4  1
  DEL PEAK 34(21Q11.2) WILD-TYPE 21  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED      4    1
  DEL PEAK 34(21Q11.2) WILD-TYPE   21    2
                         clus
vv                        DEL PEAK 34(21Q11.2) MUTATED
  COMPLETED AS PLANNED                               4
  TREATMENT NOT COMPLETED                            1
                         clus
vv                        DEL PEAK 34(21Q11.2) WILD-TYPE
  COMPLETED AS PLANNED                                21
  TREATMENT NOT COMPLETED                              2
[1] 2 2
[1] FALSE
D60V20, continuous
D60V21, continuous
D60V22, continuous
D60V23, continuous
D60V24, continuous
D60V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 34(21Q11.2) MUTATED                                     0
  DEL PEAK 34(21Q11.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 34(21Q11.2) MUTATED                                     3
  DEL PEAK 34(21Q11.2) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 34(21Q11.2) MUTATED                         6
  DEL PEAK 34(21Q11.2) WILD-TYPE                      30
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 34(21Q11.2) MUTATED                         1
  DEL PEAK 34(21Q11.2) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 34(21Q11.2) MUTATED                         0
  DEL PEAK 34(21Q11.2) WILD-TYPE                      10
D60V26, multiclass
                                     clus
vv                                    DEL PEAK 34(21Q11.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                        6
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        0
                                     clus
vv                                    DEL PEAK 34(21Q11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                         30
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                         10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 34(21Q11.2) MUTATED                                               1
  DEL PEAK 34(21Q11.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 34(21Q11.2) MUTATED                                                4
  DEL PEAK 34(21Q11.2) WILD-TYPE                                             21
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 34(21Q11.2) MUTATED                                                                                  17
  DEL PEAK 34(21Q11.2) WILD-TYPE                                                                                65
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 34(21Q11.2) MUTATED                                                                                             25
  DEL PEAK 34(21Q11.2) WILD-TYPE                                                                                           96
D60V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 34(21Q11.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           25
                                                                                              clus
vv                                                                                             DEL PEAK 34(21Q11.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        65
  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"
D60V28, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED   13 15
  DEL PEAK 34(21Q11.2) WILD-TYPE 58 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     13   15
  DEL PEAK 34(21Q11.2) WILD-TYPE   58   59
         clus
vv        DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  ABSENT                            13                             58
  PRESENT                           15                             59
[1] 2 2
[1] FALSE
D60V29, continuous
D60V30, continuous
D60V31, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED    8 24
  DEL PEAK 34(21Q11.2) WILD-TYPE 41 93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED      8   24
  DEL PEAK 34(21Q11.2) WILD-TYPE   41   93
                                          clus
vv                                         DEL PEAK 34(21Q11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           24
                                          clus
vv                                         DEL PEAK 34(21Q11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             93
[1] 2 2
[1] FALSE
D60V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 34(21Q11.2) MUTATED              3           9         22
  DEL PEAK 34(21Q11.2) WILD-TYPE           12          45         63
D60V33, multiclass
              clus
vv             DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  CURRENT USER                            3                             12
  FORMER USER                             9                             45
  NEVER USED                             22                             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"
D60V34, continuous
D60V35, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED   17  5
  DEL PEAK 34(21Q11.2) WILD-TYPE 75 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     17    5
  DEL PEAK 34(21Q11.2) WILD-TYPE   75   13
         clus
vv        DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  ABSENT                            17                             75
  PRESENT                            5                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 34(21Q11.2) MUTATED             0        21     0
  DEL PEAK 34(21Q11.2) WILD-TYPE           5        79     2
D60V36, multiclass
             clus
vv            DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  CARBOPLATIN                            0                              5
  CISPLATIN                             21                             79
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V37, continuous
[1] "Remove cluster labels:"       "DEL PEAK 34(21Q11.2) MUTATED"
clus
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                             1                             16 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1ML                     TCGA-C5-A1MP 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-GH-A9DA 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-JX-A3Q8                     TCGA-MA-AA3W 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-MA-AA3Z                     TCGA-MA-AA42 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
                    TCGA-MY-A913                     TCGA-ZX-AA5X 
"DEL PEAK 34(21Q11.2) WILD-TYPE" "DEL PEAK 34(21Q11.2) WILD-TYPE" 
D60V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 34(21Q11.2) MUTATED         0        1         0         0        7
  DEL PEAK 34(21Q11.2) WILD-TYPE       5        0         1         1       27
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 34(21Q11.2) MUTATED          12         6        2         3
  DEL PEAK 34(21Q11.2) WILD-TYPE        65        31        2         5
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 34(21Q11.2) MUTATED            3          0         6         0
  DEL PEAK 34(21Q11.2) WILD-TYPE          2          7        38         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 34(21Q11.2) MUTATED            2         10         3         1
  DEL PEAK 34(21Q11.2) WILD-TYPE          1         32         4        11
D60V39, multiclass
            clus
vv           DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              1                              0
  STAGE IA1                             0                              1
  STAGE IA2                             0                              1
  STAGE IB                              7                             27
  STAGE IB1                            12                             65
  STAGE IB2                             6                             31
  STAGE II                              2                              2
  STAGE IIA                             3                              5
  STAGE IIA1                            3                              2
  STAGE IIA2                            0                              7
  STAGE IIB                             6                             38
  STAGE III                             0                              1
  STAGE IIIA                            2                              1
  STAGE IIIB                           10                             32
  STAGE IVA                             3                              4
  STAGE IVB                             1                             11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 35(22Q13.32) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(22Q13.32) MUTATED    60  22
  DEL PEAK 35(22Q13.32) WILD-TYPE 154  46
  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE 
                             82                             200 
  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE 
                             22                              46 
$`DEL PEAK 35(22Q13.32) MUTATED`
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1BF 
       12.59         4.34         0.69        17.82        23.67        18.74 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MJ 
      173.29         5.46        31.40        30.21        57.73         0.46 
TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7X3 TCGA-C5-A7X8 
       40.93        73.18        83.05        52.01         9.34         2.73 
TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VN TCGA-EA-A1QT 
       27.52         1.12        95.11        44.94       118.65        40.87 
TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A6QX 
       30.90        24.56        31.73        12.13        14.89        24.00 
TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RJ 
        0.36         1.51         0.39         0.89         1.45         1.74 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3HY TCGA-GH-A9DA 
        2.33         0.10        15.55        12.23        31.36        17.75 
TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-JW-A5VG 
       21.67        14.93       137.16        66.81       129.37        27.42 
TCGA-JW-A5VI TCGA-JW-A852 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A7HU TCGA-MA-AA3W 
       24.56         8.28        20.91         0.89        13.35        22.52 
TCGA-MA-AA3X TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V 
       20.28        17.23        15.58        16.41         9.04        19.59 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       11.67        12.16        46.52        23.97        19.96        65.49 
TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 TCGA-VS-A953 
       53.59        39.78        16.64         4.73        58.45        15.68 
TCGA-VS-A957 TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM 
       55.50        29.95        24.30        45.11        14.53        27.25 
TCGA-VS-A9UT TCGA-VS-A9V0 TCGA-XS-A8TJ TCGA-ZJ-AAXA 
       15.85        18.84        29.26         1.41 

$`DEL PEAK 35(22Q13.32) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-2W-A8YY TCGA-BI-A0VR 
      146.86        14.70         8.32         1.48        17.52        49.48 
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       57.04        11.44        68.84        36.56       144.16       177.04 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MF 
       82.85        19.86        67.46        46.32        35.01        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         2.43        20.91         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       73.45        78.35       100.14        38.43        33.24        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK 
       94.95        13.61        50.99        45.83         8.35        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KM 
       23.51        20.81        20.91        14.73        82.06        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       87.75        58.88        36.76        55.63       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18        17.52         8.28        39.55        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       26.01        24.82         7.46        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       27.25        27.22        13.48        60.72        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
       19.27         0.43         0.59         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM 
        4.24         0.07         1.87         0.43        47.77         1.64 
TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.49         0.89        20.35         7.92        15.22 
TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI 
       19.79        23.84        19.04        16.11        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.12        25.41        16.57        20.78         9.44       147.39 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH 
       96.95        78.71        81.96        29.85        36.36         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        20.48        15.58        28.37        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
      209.59        44.61        11.28        12.49         0.30         0.82 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         9.17         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB 
       18.64        22.62        14.60        93.99        69.50        10.03 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       45.57        32.42        32.15        36.13        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A958 
       31.27        40.87        33.37        40.14        56.35        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC 
       51.32        50.47        43.40        48.39        28.50        27.12 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       46.92         1.71        47.87        47.47        41.52        26.07 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 
       14.53         3.42        18.25        67.20         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       17.75        16.24        15.42        26.01        67.59        19.13 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE 
                         173.29                          210.67 
  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE 
                         19.775                          24.920 
[1] "0.1 - 173.3 (19.8)" "0.1 - 210.7 (24.9)"
[1] "hr=" "1.4"
D61V2, continuous
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 35(22Q13.32) MUTATED   39 20 10  2
  DEL PEAK 35(22Q13.32) WILD-TYPE 96 50 11  6
D61V3, multiclass
    clus
vv   DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  T1                            39                              96
  T2                            20                              50
  T3                            10                              11
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.32) MUTATED   36 20
  DEL PEAK 35(22Q13.32) WILD-TYPE 93 36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED     36   20
  DEL PEAK 35(22Q13.32) WILD-TYPE   93   36
   clus
vv  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  0                            36                              93
  1                            20                              36
[1] 2 2
[1] FALSE
D61V5, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.32) MUTATED   37  2
  DEL PEAK 35(22Q13.32) WILD-TYPE 71  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED     37    2
  DEL PEAK 35(22Q13.32) WILD-TYPE   71    8
   clus
vv  DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  0                            37                              71
  1                             2                               8
[1] 2 2
[1] FALSE
D61V6, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.32) MUTATED   12 38
  DEL PEAK 35(22Q13.32) WILD-TYPE 41 87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED     12   38
  DEL PEAK 35(22Q13.32) WILD-TYPE   41   87
     clus
vv    DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  NO                             12                              41
  YES                            38                              87
[1] 2 2
[1] FALSE
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 35(22Q13.32) MUTATED               1
  DEL PEAK 35(22Q13.32) WILD-TYPE             5
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(22Q13.32) MUTATED                                 72
  DEL PEAK 35(22Q13.32) WILD-TYPE                              170
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 35(22Q13.32) MUTATED                                               0
  DEL PEAK 35(22Q13.32) WILD-TYPE                                             6
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 35(22Q13.32) MUTATED                                     5
  DEL PEAK 35(22Q13.32) WILD-TYPE                                  16
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 35(22Q13.32) MUTATED                                           2
  DEL PEAK 35(22Q13.32) WILD-TYPE                                         1
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 35(22Q13.32) MUTATED                                              7
  DEL PEAK 35(22Q13.32) WILD-TYPE                                           10
D61V7, multiclass
                                               clus
vv                                              DEL PEAK 35(22Q13.32) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         72
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              7
                                               clus
vv                                              DEL PEAK 35(22Q13.32) WILD-TYPE
  ADENOSQUAMOUS                                                               5
  CERVICAL SQUAMOUS CELL CARCINOMA                                          170
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, continuous
D61V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(22Q13.32) MUTATED                                  3     5
  DEL PEAK 35(22Q13.32) WILD-TYPE                                5    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(22Q13.32) MUTATED                           9
  DEL PEAK 35(22Q13.32) WILD-TYPE                        19
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 35(22Q13.32) MUTATED                                           1
  DEL PEAK 35(22Q13.32) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 35(22Q13.32) MUTATED      60
  DEL PEAK 35(22Q13.32) WILD-TYPE   142
D61V10, multiclass
                                           clus
vv                                          DEL PEAK 35(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                60
                                           clus
vv                                          DEL PEAK 35(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        5
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              19
  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"
D61V11, binary
                                 cls
clus                                0   1
  DEL PEAK 35(22Q13.32) MUTATED     7  44
  DEL PEAK 35(22Q13.32) WILD-TYPE  16 119
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED      7   44
  DEL PEAK 35(22Q13.32) WILD-TYPE   16  119
                        clus
vv                       DEL PEAK 35(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            44
                        clus
vv                       DEL PEAK 35(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                  16
  NOT HISPANIC OR LATINO                             119
[1] 2 2
[1] FALSE
D61V12, continuous
D61V13, binary
                                 cls
clus                                0   1
  DEL PEAK 35(22Q13.32) MUTATED    55  22
  DEL PEAK 35(22Q13.32) WILD-TYPE 138  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED     55   22
  DEL PEAK 35(22Q13.32) WILD-TYPE  138   54
            clus
vv           DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  TUMOR FREE                            55                             138
  WITH TUMOR                            22                              54
[1] 2 2
[1] FALSE
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 35(22Q13.32) MUTATED    5 34 40  0  6
  DEL PEAK 35(22Q13.32) WILD-TYPE 13 95 75  1 18
D61V14, multiclass
    clus
vv   DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  G1                             5                              13
  G2                            34                              95
  G3                            40                              75
  G4                             0                               1
  GX                             6                              18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, continuous
D61V16, continuous
D61V17, continuous
D61V18, continuous
D61V19, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.32) MUTATED   10  0
  DEL PEAK 35(22Q13.32) WILD-TYPE 15  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED     10    0
  DEL PEAK 35(22Q13.32) WILD-TYPE   15    3
                         clus
vv                        DEL PEAK 35(22Q13.32) MUTATED
  COMPLETED AS PLANNED                               10
  TREATMENT NOT COMPLETED                             0
                         clus
vv                        DEL PEAK 35(22Q13.32) WILD-TYPE
  COMPLETED AS PLANNED                                 15
  TREATMENT NOT COMPLETED                               3
[1] 2 2
[1] FALSE
D61V20, continuous
D61V21, continuous
D61V22, continuous
D61V23, continuous
D61V24, continuous
D61V25, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 35(22Q13.32) MUTATED                                     0
  DEL PEAK 35(22Q13.32) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 35(22Q13.32) MUTATED                                     1
  DEL PEAK 35(22Q13.32) WILD-TYPE                                   6
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 35(22Q13.32) MUTATED                        11
  DEL PEAK 35(22Q13.32) WILD-TYPE                      25
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 35(22Q13.32) MUTATED                         0
  DEL PEAK 35(22Q13.32) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 35(22Q13.32) MUTATED                         3
  DEL PEAK 35(22Q13.32) WILD-TYPE                       7
D61V26, multiclass
                                     clus
vv                                    DEL PEAK 35(22Q13.32) 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 35(22Q13.32) 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)
  DEL PEAK 35(22Q13.32) MUTATED                                               2
  DEL PEAK 35(22Q13.32) WILD-TYPE                                             1
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 35(22Q13.32) MUTATED                                                5
  DEL PEAK 35(22Q13.32) WILD-TYPE                                             20
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 35(22Q13.32) MUTATED                                                                                  30
  DEL PEAK 35(22Q13.32) WILD-TYPE                                                                                52
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 35(22Q13.32) MUTATED                                                                                             33
  DEL PEAK 35(22Q13.32) WILD-TYPE                                                                                           88
D61V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 35(22Q13.32) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            33
                                                                                              clus
vv                                                                                             DEL PEAK 35(22Q13.32) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         52
  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"
D61V28, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.32) MUTATED   19 26
  DEL PEAK 35(22Q13.32) WILD-TYPE 52 48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED     19   26
  DEL PEAK 35(22Q13.32) WILD-TYPE   52   48
         clus
vv        DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  ABSENT                             19                              52
  PRESENT                            26                              48
[1] 2 2
[1] FALSE
D61V29, continuous
D61V30, continuous
D61V31, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.32) MUTATED   14 37
  DEL PEAK 35(22Q13.32) WILD-TYPE 35 80
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED     14   37
  DEL PEAK 35(22Q13.32) WILD-TYPE   35   80
                                          clus
vv                                         DEL PEAK 35(22Q13.32) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            37
                                          clus
vv                                         DEL PEAK 35(22Q13.32) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              80
[1] 2 2
[1] FALSE
D61V32, continuous
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 35(22Q13.32) MUTATED              5          16         28
  DEL PEAK 35(22Q13.32) WILD-TYPE           10          38         57
D61V33, multiclass
              clus
vv             DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  CURRENT USER                             5                              10
  FORMER USER                             16                              38
  NEVER USED                              28                              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V34, continuous
D61V35, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.32) MUTATED   31  3
  DEL PEAK 35(22Q13.32) WILD-TYPE 61 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.32) MUTATED     31    3
  DEL PEAK 35(22Q13.32) WILD-TYPE   61   15
         clus
vv        DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  ABSENT                             31                              61
  PRESENT                             3                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 35(22Q13.32) MUTATED             0        32     1
  DEL PEAK 35(22Q13.32) WILD-TYPE           5        68     1
D61V36, multiclass
             clus
vv            DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  CARBOPLATIN                             0                               5
  CISPLATIN                              32                              68
  OTHER                                   1                               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"
D61V37, continuous
D61V38, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 35(22Q13.32) MUTATED         1        1         0         0       11
  DEL PEAK 35(22Q13.32) WILD-TYPE       4        0         1         1       23
                                 vv
clus                              STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 35(22Q13.32) MUTATED          27         6        3         4
  DEL PEAK 35(22Q13.32) WILD-TYPE        50        31        1         4
                                 vv
clus                              STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 35(22Q13.32) MUTATED            1          0        12         0
  DEL PEAK 35(22Q13.32) WILD-TYPE          4          7        32         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 35(22Q13.32) MUTATED            1         15         2         1
  DEL PEAK 35(22Q13.32) WILD-TYPE          2         27         5        11
D61V39, multiclass
            clus
vv           DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               1                               0
  STAGE IA1                              0                               1
  STAGE IA2                              0                               1
  STAGE IB                              11                              23
  STAGE IB1                             27                              50
  STAGE IB2                              6                              31
  STAGE II                               3                               1
  STAGE IIA                              4                               4
  STAGE IIA1                             1                               4
  STAGE IIA2                             0                               7
  STAGE IIB                             12                              32
  STAGE III                              0                               1
  STAGE IIIA                             1                               2
  STAGE IIIB                            15                              27
  STAGE IVA                              2                               5
  STAGE IVB                              1                              11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = DEL PEAK 36(XP11.3) MUTATION ANALYSIS
D62V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 36(XP11.3) MUTATED    51  19
  DEL PEAK 36(XP11.3) WILD-TYPE 163  49
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                           70                           212 
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                           19                            49 
$`DEL PEAK 36(XP11.3) MUTATED`
TCGA-ZJ-AAX4 TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BK TCGA-C5-A1BN 
        0.69        57.04        23.67        11.44       177.04         5.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LV 
       46.32        30.21        53.16        20.91        40.93        73.45 
TCGA-C5-A3HD TCGA-C5-A7UH TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-DS-A0VN TCGA-DS-A3LQ 
       52.01       131.11        99.91        23.51       118.65        22.98 
TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QE TCGA-EA-A43B TCGA-EA-A44S 
       16.18        40.87        30.90        25.02        26.01        12.13 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
       14.89        27.22        60.72         1.51         0.43         0.59 
TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 
        0.30         1.87         0.43         0.10         0.49        20.35 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV TCGA-IR-A3LA TCGA-IR-A3LB 
       19.04        31.36        20.98        10.55       137.16        66.81 
TCGA-IR-A3LK TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MA-AA42 
       29.85        21.11        44.61         0.89         0.82         8.52 
TCGA-MY-A5BF TCGA-Q1-A6DT TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI 
       20.84         9.04        69.50        10.03        32.42        23.97 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 
       11.51        59.18        16.64         4.73        40.14        15.68 
TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UC TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UR 
       50.47        48.39        27.12        27.25        47.87        26.07 
TCGA-VS-A9UT TCGA-VS-A9V5 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       15.85        16.24        67.59        19.13 

$`DEL PEAK 36(XP11.3) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-VS-A9V4 
      146.86        12.59        14.70         8.32         1.48         4.34 
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        17.82        49.48        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      144.16       173.29        82.85        19.86        67.46        31.40 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       35.01        57.73        38.99        35.61         0.46         2.43 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        3.58        44.22        73.18        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43        33.24        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-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-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       17.19       155.77        94.95         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       50.99        45.83         8.35        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       14.73         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A5RQ 
       87.75        58.88        36.76        55.63       117.99        16.83 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       17.52         8.28        39.55        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA 
       13.05        36.89        26.40        24.56        31.73        24.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
        7.46        26.79        25.91        27.29        27.25        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK 
       13.48         0.36        26.27         6.64        19.27         0.39 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.89         1.45         0.13        40.96         4.24         0.07 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        1.74        47.77         1.64         2.33         0.07         0.89 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        7.92        15.22        19.79        15.55        12.23        23.84 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       16.11        36.26        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44         1.12        17.75        25.41        16.57        21.67 
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       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU 
      209.59        20.91        11.28        12.49         0.30        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 
       22.52        20.28        17.82        19.56         9.17        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 
       28.08        34.62        19.96        54.81        35.05        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        15.58        16.41        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EG 
       14.60        11.67        93.99        12.16        46.52        45.57 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH 
       19.96        65.49        32.15        53.59        36.13        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       31.27        40.87        33.37        58.45        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UD 
       50.14        51.32        43.40        28.50        29.95        24.30 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UQ 
       46.92        45.11         1.71        14.53        47.47        41.52 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA 
       18.25        17.75        15.42        26.01        29.26         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                       177.04                        210.67 
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                       23.590                        21.555 
[1] "0.1 - 177.0 (23.6)" "0.1 - 210.7 (21.6)"
[1] "hr=" "1.2"
D62V2, continuous
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 36(XP11.3) MUTATED    34  15   6   1
  DEL PEAK 36(XP11.3) WILD-TYPE 101  55  15   7
D62V3, multiclass
    clus
vv   DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  T1                          34                           101
  T2                          15                            55
  T3                           6                            15
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                               cls
clus                             0  1
  DEL PEAK 36(XP11.3) MUTATED   32 11
  DEL PEAK 36(XP11.3) WILD-TYPE 97 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED     32   11
  DEL PEAK 36(XP11.3) WILD-TYPE   97   45
   clus
vv  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  0                          32                            97
  1                          11                            45
[1] 2 2
[1] FALSE
D62V5, binary
                               cls
clus                             0  1
  DEL PEAK 36(XP11.3) MUTATED   24  1
  DEL PEAK 36(XP11.3) WILD-TYPE 84  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED     24    1
  DEL PEAK 36(XP11.3) WILD-TYPE   84    9
   clus
vv  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  0                          24                            84
  1                           1                             9
[1] 2 2
[1] FALSE
D62V6, binary
                               cls
clus                             0  1
  DEL PEAK 36(XP11.3) MUTATED    9 28
  DEL PEAK 36(XP11.3) WILD-TYPE 44 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED      9   28
  DEL PEAK 36(XP11.3) WILD-TYPE   44   97
     clus
vv    DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  NO                            9                            44
  YES                          28                            97
[1] 2 2
[1] FALSE
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(XP11.3) MUTATED               1                               60
  DEL PEAK 36(XP11.3) WILD-TYPE             5                              182
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 36(XP11.3) MUTATED                                               1
  DEL PEAK 36(XP11.3) WILD-TYPE                                             5
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 36(XP11.3) MUTATED                                     3
  DEL PEAK 36(XP11.3) WILD-TYPE                                  18
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 36(XP11.3) MUTATED                                           3
  DEL PEAK 36(XP11.3) WILD-TYPE                                         0
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 36(XP11.3) MUTATED                                              4
  DEL PEAK 36(XP11.3) WILD-TYPE                                           13
D62V7, multiclass
                                               clus
vv                                              DEL PEAK 36(XP11.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       60
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
                                               clus
vv                                              DEL PEAK 36(XP11.3) WILD-TYPE
  ADENOSQUAMOUS                                                             5
  CERVICAL SQUAMOUS CELL CARCINOMA                                        182
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, continuous
D62V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(XP11.3) MUTATED                                  0     5
  DEL PEAK 36(XP11.3) WILD-TYPE                                8    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(XP11.3) MUTATED                           8
  DEL PEAK 36(XP11.3) WILD-TYPE                        20
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 36(XP11.3) MUTATED                                           2    51
  DEL PEAK 36(XP11.3) WILD-TYPE                                         0   151
D62V10, multiclass
                                           clus
vv                                          DEL PEAK 36(XP11.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              51
                                           clus
vv                                          DEL PEAK 36(XP11.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      8
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               151
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, binary
                               cls
clus                              0   1
  DEL PEAK 36(XP11.3) MUTATED     2  42
  DEL PEAK 36(XP11.3) WILD-TYPE  21 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED      2   42
  DEL PEAK 36(XP11.3) WILD-TYPE   21  121
                        clus
vv                       DEL PEAK 36(XP11.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       DEL PEAK 36(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           121
[1] 2 2
[1] FALSE
D62V12, continuous
D62V13, binary
                               cls
clus                              0   1
  DEL PEAK 36(XP11.3) MUTATED    45  21
  DEL PEAK 36(XP11.3) WILD-TYPE 148  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED     45   21
  DEL PEAK 36(XP11.3) WILD-TYPE  148   55
            clus
vv           DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  TUMOR FREE                          45                           148
  WITH TUMOR                          21                            55
[1] 2 2
[1] FALSE
                               vv
clus                             G1  G2  G3  G4  GX
  DEL PEAK 36(XP11.3) MUTATED     3  27  32   0   8
  DEL PEAK 36(XP11.3) WILD-TYPE  15 102  83   1  16
D62V14, multiclass
    clus
vv   DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  G1                           3                            15
  G2                          27                           102
  G3                          32                            83
  G4                           0                             1
  GX                           8                            16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, continuous
D62V16, continuous
D62V17, continuous
D62V18, continuous
D62V19, binary
                               cls
clus                             0  1
  DEL PEAK 36(XP11.3) MUTATED    8  2
  DEL PEAK 36(XP11.3) WILD-TYPE 17  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED      8    2
  DEL PEAK 36(XP11.3) WILD-TYPE   17    1
                         clus
vv                        DEL PEAK 36(XP11.3) MUTATED
  COMPLETED AS PLANNED                              8
  TREATMENT NOT COMPLETED                           2
                         clus
vv                        DEL PEAK 36(XP11.3) WILD-TYPE
  COMPLETED AS PLANNED                               17
  TREATMENT NOT COMPLETED                             1
[1] 2 2
[1] FALSE
D62V20, continuous
D62V21, continuous
D62V22, continuous
D62V23, continuous
D62V24, continuous
D62V25, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 36(XP11.3) MUTATED                                     0
  DEL PEAK 36(XP11.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 36(XP11.3) MUTATED                                     4
  DEL PEAK 36(XP11.3) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 36(XP11.3) MUTATED                         8                       0
  DEL PEAK 36(XP11.3) WILD-TYPE                      28                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 36(XP11.3) MUTATED                         2
  DEL PEAK 36(XP11.3) WILD-TYPE                       8
D62V26, multiclass
                                     clus
vv                                    DEL PEAK 36(XP11.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                       8
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK 36(XP11.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                        28
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 36(XP11.3) MUTATED                                               1
  DEL PEAK 36(XP11.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 36(XP11.3) MUTATED                                                9
  DEL PEAK 36(XP11.3) WILD-TYPE                                             16
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 36(XP11.3) MUTATED                                                                                  17
  DEL PEAK 36(XP11.3) WILD-TYPE                                                                                65
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 36(XP11.3) MUTATED                                                                                             32
  DEL PEAK 36(XP11.3) WILD-TYPE                                                                                           89
D62V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 36(XP11.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          32
                                                                                              clus
vv                                                                                             DEL PEAK 36(XP11.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            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"
D62V28, binary
                               cls
clus                             0  1
  DEL PEAK 36(XP11.3) MUTATED   18 17
  DEL PEAK 36(XP11.3) WILD-TYPE 53 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED     18   17
  DEL PEAK 36(XP11.3) WILD-TYPE   53   57
         clus
vv        DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  ABSENT                           18                            53
  PRESENT                          17                            57
[1] 2 2
[1] FALSE
D62V29, continuous
D62V30, continuous
D62V31, binary
                               cls
clus                             0  1
  DEL PEAK 36(XP11.3) MUTATED   15 22
  DEL PEAK 36(XP11.3) WILD-TYPE 34 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED     15   22
  DEL PEAK 36(XP11.3) WILD-TYPE   34   95
                                          clus
vv                                         DEL PEAK 36(XP11.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          22
                                          clus
vv                                         DEL PEAK 36(XP11.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            95
[1] 2 2
[1] FALSE
D62V32, continuous
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 36(XP11.3) MUTATED              3          11         32
  DEL PEAK 36(XP11.3) WILD-TYPE           12          43         53
D62V33, multiclass
              clus
vv             DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  CURRENT USER                           3                            12
  FORMER USER                           11                            43
  NEVER USED                            32                            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"
D62V34, continuous
D62V35, binary
                               cls
clus                             0  1
  DEL PEAK 36(XP11.3) MUTATED   24  1
  DEL PEAK 36(XP11.3) WILD-TYPE 68 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED     24    1
  DEL PEAK 36(XP11.3) WILD-TYPE   68   17
         clus
vv        DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  ABSENT                           24                            68
  PRESENT                           1                            17
[1] 2 2
[1] FALSE
                               vv
clus                            CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 36(XP11.3) MUTATED             1        24     0
  DEL PEAK 36(XP11.3) WILD-TYPE           4        76     2
D62V36, multiclass
             clus
vv            DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  CARBOPLATIN                           1                             4
  CISPLATIN                            24                            76
  OTHER                                 0                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V37, continuous
D62V38, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 36(XP11.3) MUTATED         2        1         0         1        9
  DEL PEAK 36(XP11.3) WILD-TYPE       3        0         1         0       25
                               vv
clus                            STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 36(XP11.3) MUTATED          16         8        2         2
  DEL PEAK 36(XP11.3) WILD-TYPE        61        29        2         6
                               vv
clus                            STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 36(XP11.3) MUTATED            0          1        15         0
  DEL PEAK 36(XP11.3) WILD-TYPE          5          6        29         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 36(XP11.3) MUTATED            1          8         2         2
  DEL PEAK 36(XP11.3) WILD-TYPE          2         34         5        10
D62V39, multiclass
            clus
vv           DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IA1                            0                             1
  STAGE IA2                            1                             0
  STAGE IB                             9                            25
  STAGE IB1                           16                            61
  STAGE IB2                            8                            29
  STAGE II                             2                             2
  STAGE IIA                            2                             6
  STAGE IIA1                           0                             5
  STAGE IIA2                           1                             6
  STAGE IIB                           15                            29
  STAGE III                            0                             1
  STAGE IIIA                           1                             2
  STAGE IIIB                           8                            34
  STAGE IVA                            2                             5
  STAGE IVB                            2                            10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 37(XQ21.33) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(XQ21.33) MUTATED    40  18
  DEL PEAK 37(XQ21.33) WILD-TYPE 174  50
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                            58                            224 
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                            18                             50 
$`DEL PEAK 37(XQ21.33) MUTATED`
TCGA-EX-A69M TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BQ TCGA-C5-A1M5 
        8.32        17.82        23.67        11.44        19.86        67.46 
TCGA-C5-A1M8 TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LX TCGA-C5-A3HD 
       30.21         2.43        20.91        40.93        83.05        52.01 
TCGA-C5-A7CJ TCGA-C5-A7CO TCGA-C5-A7X5 TCGA-C5-A8XK TCGA-DS-A0VK TCGA-DS-A0VN 
      101.82       147.35        13.61        99.91        36.76       118.65 
TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EK-A2IP 
       16.18        40.87        12.13        14.89        27.25         6.64 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 
        0.43         0.59         0.43         0.10         0.49        20.35 
TCGA-EX-A1H6 TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A5XV TCGA-IR-A3LK TCGA-JW-A5VL 
        7.92        19.04        31.36        10.55        29.85        15.58 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A5U3 TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MY-A5BF 
       21.11        44.61         0.82         9.17         8.52        20.84 
TCGA-Q1-A73Q TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8QA TCGA-VS-A94Y TCGA-VS-A9U6 
        9.34        69.50        10.03        36.13         4.73        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UC TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9V0 
       48.39        27.12        47.87        26.07        15.85        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V5 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
        5.16        16.24        29.26        19.13 

$`DEL PEAK 37(XQ21.33) WILD-TYPE`
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A449 TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-ZJ-AAX4 
      146.86        12.59        14.70         1.48         4.34         0.69 
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        49.48        57.04        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 
      144.16       177.04       173.29        82.85         5.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       46.32        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY 
        0.46         3.58        44.22        73.18        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        33.24        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC 
      210.67       154.32       134.33        15.48        20.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
      155.77       131.11        94.95         9.34         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       45.83         8.35        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       14.73         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       87.75        58.88        55.63       117.99        22.98        16.83 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       31.73        26.01        24.82         7.46        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 
       27.29        27.22        24.00        13.48         0.36        60.72 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         1.51        19.27         0.39         0.89         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        40.96         0.30         4.24         0.07         1.87 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        1.74        47.77         1.64         2.33         0.07         0.89 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       15.22        19.79        15.55        12.23        23.84        16.11 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26        20.98        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44         1.12        17.75        25.41        16.57        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-A3LL TCGA-JW-A5VG 
      129.37        96.95        78.71        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        21.44        20.48        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       18.15       209.59        20.91        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30        13.35        22.52        20.28        17.82        19.56 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       17.23         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        17.56        14.07        15.88        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EC 
       19.59        14.60        11.67        93.99        12.16        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       45.57        32.42        23.97        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        11.51        59.18        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       16.64        33.37        40.14        58.45        15.68        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UB 
       55.50        50.14        51.32        50.47        28.50        29.95 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       47.47        41.52        14.53         3.42        18.25        67.20 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       18.25        17.75        15.42        26.01        67.59         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                        147.35                         210.67 
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                        19.495                         23.985 
[1] "0.1 - 147.3 (19.5)" "0.1 - 210.7 (24.0)"
[1] "hr=" "1.6"
D63V2, continuous
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 37(XQ21.33) MUTATED    31  12   3   1
  DEL PEAK 37(XQ21.33) WILD-TYPE 104  58  18   7
D63V3, multiclass
    clus
vv   DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  T1                           31                            104
  T2                           12                             58
  T3                            3                             18
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                                cls
clus                               0   1
  DEL PEAK 37(XQ21.33) MUTATED    25  13
  DEL PEAK 37(XQ21.33) WILD-TYPE 104  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED     25   13
  DEL PEAK 37(XQ21.33) WILD-TYPE  104   43
   clus
vv  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  0                           25                            104
  1                           13                             43
[1] 2 2
[1] FALSE
D63V5, binary
                                cls
clus                              0  1
  DEL PEAK 37(XQ21.33) MUTATED   17  3
  DEL PEAK 37(XQ21.33) WILD-TYPE 91  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED     17    3
  DEL PEAK 37(XQ21.33) WILD-TYPE   91    7
   clus
vv  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  0                           17                             91
  1                            3                              7
[1] 2 2
[1] FALSE
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(XQ21.33) MUTATED    11  25
  DEL PEAK 37(XQ21.33) WILD-TYPE  42 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED     11   25
  DEL PEAK 37(XQ21.33) WILD-TYPE   42  100
     clus
vv    DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  NO                            11                             42
  YES                           25                            100
[1] 2 2
[1] FALSE
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(XQ21.33) MUTATED               1                               47
  DEL PEAK 37(XQ21.33) WILD-TYPE             5                              195
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 37(XQ21.33) MUTATED                                               0
  DEL PEAK 37(XQ21.33) WILD-TYPE                                             6
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 37(XQ21.33) MUTATED                                     3
  DEL PEAK 37(XQ21.33) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 37(XQ21.33) MUTATED                                           2
  DEL PEAK 37(XQ21.33) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 37(XQ21.33) MUTATED                                              6
  DEL PEAK 37(XQ21.33) WILD-TYPE                                           11
D63V7, multiclass
                                               clus
vv                                              DEL PEAK 37(XQ21.33) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        47
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             6
                                               clus
vv                                              DEL PEAK 37(XQ21.33) WILD-TYPE
  ADENOSQUAMOUS                                                              5
  CERVICAL SQUAMOUS CELL CARCINOMA                                         195
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, continuous
D63V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(XQ21.33) MUTATED                                  1     4
  DEL PEAK 37(XQ21.33) WILD-TYPE                                7    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(XQ21.33) MUTATED                           5
  DEL PEAK 37(XQ21.33) WILD-TYPE                        23
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 37(XQ21.33) MUTATED                                           2
  DEL PEAK 37(XQ21.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 37(XQ21.33) MUTATED      42
  DEL PEAK 37(XQ21.33) WILD-TYPE   160
D63V10, multiclass
                                           clus
vv                                          DEL PEAK 37(XQ21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               42
                                           clus
vv                                          DEL PEAK 37(XQ21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                160
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, binary
                                cls
clus                               0   1
  DEL PEAK 37(XQ21.33) MUTATED     5  31
  DEL PEAK 37(XQ21.33) WILD-TYPE  18 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED      5   31
  DEL PEAK 37(XQ21.33) WILD-TYPE   18  132
                        clus
vv                       DEL PEAK 37(XQ21.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       DEL PEAK 37(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            132
[1] 2 2
[1] FALSE
D63V12, continuous
D63V13, binary
                                cls
clus                               0   1
  DEL PEAK 37(XQ21.33) MUTATED    34  21
  DEL PEAK 37(XQ21.33) WILD-TYPE 159  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED     34   21
  DEL PEAK 37(XQ21.33) WILD-TYPE  159   55
            clus
vv           DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  TUMOR FREE                           34                            159
  WITH TUMOR                           21                             55
[1] 2 2
[1] FALSE
                                vv
clus                              G1  G2  G3  G4  GX
  DEL PEAK 37(XQ21.33) MUTATED     4  20  26   0   7
  DEL PEAK 37(XQ21.33) WILD-TYPE  14 109  89   1  17
D63V14, multiclass
    clus
vv   DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  G1                            4                             14
  G2                           20                            109
  G3                           26                             89
  G4                            0                              1
  GX                            7                             17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, continuous
D63V16, continuous
D63V17, continuous
D63V18, continuous
D63V19, binary
                                cls
clus                              0  1
  DEL PEAK 37(XQ21.33) MUTATED    6  2
  DEL PEAK 37(XQ21.33) WILD-TYPE 19  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED      6    2
  DEL PEAK 37(XQ21.33) WILD-TYPE   19    1
                         clus
vv                        DEL PEAK 37(XQ21.33) MUTATED
  COMPLETED AS PLANNED                               6
  TREATMENT NOT COMPLETED                            2
                         clus
vv                        DEL PEAK 37(XQ21.33) WILD-TYPE
  COMPLETED AS PLANNED                                19
  TREATMENT NOT COMPLETED                              1
[1] 2 2
[1] FALSE
D63V20, continuous
D63V21, continuous
D63V22, continuous
D63V23, continuous
D63V24, continuous
D63V25, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 37(XQ21.33) MUTATED                                     0
  DEL PEAK 37(XQ21.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 37(XQ21.33) MUTATED                                     4
  DEL PEAK 37(XQ21.33) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 37(XQ21.33) MUTATED                         6
  DEL PEAK 37(XQ21.33) WILD-TYPE                      30
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 37(XQ21.33) MUTATED                         0
  DEL PEAK 37(XQ21.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 37(XQ21.33) MUTATED                         4
  DEL PEAK 37(XQ21.33) WILD-TYPE                       6
D63V26, multiclass
                                     clus
vv                                    DEL PEAK 37(XQ21.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                        6
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        4
                                     clus
vv                                    DEL PEAK 37(XQ21.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              3
  OTHER LOCATION, SPECIFY                                         30
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 37(XQ21.33) MUTATED                                               2
  DEL PEAK 37(XQ21.33) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 37(XQ21.33) MUTATED                                                5
  DEL PEAK 37(XQ21.33) WILD-TYPE                                             20
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 37(XQ21.33) MUTATED                                                                                  14
  DEL PEAK 37(XQ21.33) WILD-TYPE                                                                                68
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 37(XQ21.33) MUTATED                                                                                             27
  DEL PEAK 37(XQ21.33) WILD-TYPE                                                                                           94
D63V27, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 37(XQ21.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           27
                                                                                              clus
vv                                                                                             DEL PEAK 37(XQ21.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        68
  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"
D63V28, binary
                                cls
clus                              0  1
  DEL PEAK 37(XQ21.33) MUTATED   13 14
  DEL PEAK 37(XQ21.33) WILD-TYPE 58 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED     13   14
  DEL PEAK 37(XQ21.33) WILD-TYPE   58   60
         clus
vv        DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  ABSENT                            13                             58
  PRESENT                           14                             60
[1] 2 2
[1] FALSE
D63V29, continuous
D63V30, continuous
D63V31, binary
                                cls
clus                              0  1
  DEL PEAK 37(XQ21.33) MUTATED   16 20
  DEL PEAK 37(XQ21.33) WILD-TYPE 33 97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED     16   20
  DEL PEAK 37(XQ21.33) WILD-TYPE   33   97
                                          clus
vv                                         DEL PEAK 37(XQ21.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           20
                                          clus
vv                                         DEL PEAK 37(XQ21.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             97
[1] 2 2
[1] FALSE
D63V32, continuous
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 37(XQ21.33) MUTATED              4          11         21
  DEL PEAK 37(XQ21.33) WILD-TYPE           11          43         64
D63V33, multiclass
              clus
vv             DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  CURRENT USER                            4                             11
  FORMER USER                            11                             43
  NEVER USED                             21                             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"
D63V34, continuous
D63V35, binary
                                cls
clus                              0  1
  DEL PEAK 37(XQ21.33) MUTATED   21  1
  DEL PEAK 37(XQ21.33) WILD-TYPE 71 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED     21    1
  DEL PEAK 37(XQ21.33) WILD-TYPE   71   17
         clus
vv        DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  ABSENT                            21                             71
  PRESENT                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CARBOPLATIN CISPLATIN OTHER
  DEL PEAK 37(XQ21.33) MUTATED             3        21     0
  DEL PEAK 37(XQ21.33) WILD-TYPE           2        79     2
D63V36, multiclass
             clus
vv            DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  CARBOPLATIN                            3                              2
  CISPLATIN                             21                             79
  OTHER                                  0                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V37, continuous
D63V38, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB
  DEL PEAK 37(XQ21.33) MUTATED         2        0         0         1        7
  DEL PEAK 37(XQ21.33) WILD-TYPE       3        1         1         0       27
                                vv
clus                             STAGE IB1 STAGE IB2 STAGE II STAGE IIA
  DEL PEAK 37(XQ21.33) MUTATED          16         9        0         2
  DEL PEAK 37(XQ21.33) WILD-TYPE        61        28        4         6
                                vv
clus                             STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  DEL PEAK 37(XQ21.33) MUTATED            0          1         9         0
  DEL PEAK 37(XQ21.33) WILD-TYPE          5          6        35         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  DEL PEAK 37(XQ21.33) MUTATED            0          8         0         3
  DEL PEAK 37(XQ21.33) WILD-TYPE          3         34         7         9
D63V39, multiclass
            clus
vv           DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              0                              1
  STAGE IA1                             0                              1
  STAGE IA2                             1                              0
  STAGE IB                              7                             27
  STAGE IB1                            16                             61
  STAGE IB2                             9                             28
  STAGE II                              0                              4
  STAGE IIA                             2                              6
  STAGE IIA1                            0                              5
  STAGE IIA2                            1                              6
  STAGE IIB                             9                             35
  STAGE III                             0                              1
  STAGE IIIA                            0                              3
  STAGE IIIB                            8                             34
  STAGE IVA                             0                              7
  STAGE IVB                             3                              9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
