[1] "ofn"      "-oTOV-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/OV-TP/22507289/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/22534546/transformed.cor.cli.txt"

nPatients in clinical file=590, in cluster file=579, common to both=573
[1]  73 573
[1] "AMP PEAK  1(1P34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          291                           282 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          291                           282 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          364                           209 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          364                           209 
[1] "AMP PEAK  3(1Q42.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                          317                           256 
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                          317                           256 
[1] "AMP PEAK  4(2P23.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                          247                           326 
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                          247                           326 
[1] "AMP PEAK  5(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                          259                           314 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                          259                           314 
[1] "AMP PEAK  6(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          479                            94 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          479                            94 
[1] "AMP PEAK  7(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                          162                           411 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                          162                           411 
[1] "AMP PEAK  8(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                          113                           460 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                          113                           460 
[1] "AMP PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           305                            268 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           305                            268 
[1] "AMP PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          300                           273 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          300                           273 
[1] "AMP PEAK 11(7Q36.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                          316                           257 
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                          316                           257 
[1] "AMP PEAK 12(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           210                            363 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           210                            363 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           455                            118 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           455                            118 
[1] "AMP PEAK 14(10P15.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                           250                            323 
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                           250                            323 
[1] "AMP PEAK 15(10Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                           182                            391 
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                           182                            391 
[1] "AMP PEAK 16(11Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                           252                            321 
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                           252                            321 
[1] "AMP PEAK 17(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                            328                             245 
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                            328                             245 
[1] "AMP PEAK 18(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                           311                            262 
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                           311                            262 
[1] "AMP PEAK 19(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         221                          352 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         221                          352 
[1] "AMP PEAK 20(14Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                           146                            427 
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                           146                            427 
[1] "AMP PEAK 21(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                            156                             417 
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                            156                             417 
[1] "AMP PEAK 22(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           160                            413 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           160                            413 
[1] "AMP PEAK 23(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           212                            361 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           212                            361 
[1] "AMP PEAK 24(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           139                            434 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           139                            434 
[1] "AMP PEAK 25(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                            314                             259 
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                            314                             259 
[1] "AMP PEAK 26(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         319                          254 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         319                          254 
[1] "AMP PEAK 27(19Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                           242                            331 
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                           242                            331 
[1] "AMP PEAK 28(20P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                         315                          258 
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                         315                          258 
[1] "AMP PEAK 29(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                            344                             229 
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                            344                             229 
[1] "AMP PEAK 30(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            399                             174 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            399                             174 
[1] "AMP PEAK 31(22Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                            91                            482 
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                            91                            482 
[1] "AMP PEAK 32(XP11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                           159                            414 
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                           159                            414 
[1] "AMP PEAK 33(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                        217                         356 
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                        217                         356 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           266                            307 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           266                            307 
[1] "DEL PEAK  2(1Q41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                         95                         478 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                         95                         478 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                          120                           453 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                          120                           453 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          133                           440 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          133                           440 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          172                           401 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          172                           401 
[1] "DEL PEAK  6(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          208                           365 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          208                           365 
[1] "DEL PEAK  7(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            84                            489 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            84                            489 
[1] "DEL PEAK  8(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                          390                           183 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                          390                           183 
[1] "DEL PEAK  9(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          416                           157 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          416                           157 
[1] "DEL PEAK 10(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          350                           223 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          350                           223 
[1] "DEL PEAK 11(5Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                          414                           159 
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                          414                           159 
[1] "DEL PEAK 12(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        375                         198 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        375                         198 
[1] "DEL PEAK 13(7P22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE 
                          251                           322 
  DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE 
                          251                           322 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          384                           189 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          384                           189 
[1] "DEL PEAK 15(8P21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                          401                           172 
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                          401                           172 
[1] "DEL PEAK 16(9P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                          259                           314 
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                          259                           314 
[1] "DEL PEAK 17(9Q34.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                           341                            232 
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                           341                            232 
[1] "DEL PEAK 18(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           117                            456 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           117                            456 
[1] "DEL PEAK 19(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            222                             351 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            222                             351 
[1] "DEL PEAK 20(10Q25.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE 
                           238                            335 
  DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE 
                           238                            335 
[1] "DEL PEAK 21(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           340                            233 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           340                            233 
[1] "DEL PEAK 22(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                         200                          373 
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                         200                          373 
[1] "DEL PEAK 23(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE 
                           193                            380 
  DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE 
                           193                            380 
[1] "DEL PEAK 24(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                            214                             359 
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                            214                             359 
[1] "DEL PEAK 25(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                           359                            214 
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                           359                            214 
[1] "DEL PEAK 26(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE 
                           303                            270 
  DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE 
                           303                            270 
[1] "DEL PEAK 27(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE 
                           296                            277 
  DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE 
                           296                            277 
[1] "DEL PEAK 28(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE 
                           359                            214 
  DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE 
                           359                            214 
[1] "DEL PEAK 29(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           309                            264 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           309                            264 
[1] "DEL PEAK 30(16Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE 
                           457                            116 
  DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE 
                           457                            116 
[1] "DEL PEAK 31(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                           447                            126 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                           447                            126 
[1] "DEL PEAK 32(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                         486                           87 
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                         486                           87 
[1] "DEL PEAK 33(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                           467                            106 
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                           467                            106 
[1] "DEL PEAK 34(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         377                          196 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         377                          196 
[1] "DEL PEAK 35(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE 
                           506                             67 
  DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE 
                           506                             67 
[1] "DEL PEAK 36(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE 
                            296                             277 
  DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE 
                            296                             277 
[1] "DEL PEAK 37(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE 
                            282                             291 
  DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE 
                            282                             291 
[1] "DEL PEAK 38(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE 
                           224                            349 
  DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE 
                           224                            349 
[1] "DEL PEAK 39(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE 
                            499                              74 
  DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE 
                            499                              74 
[1] "DEL PEAK 40(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                          354                           219 
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                          354                           219 
[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] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_GRADE"                         
[16] "TUMOR_STAGE"                         
[17] "DAYS_TO_TUMOR_RECURRENCE"            
[18] "CHEMO_THERAPY"                       
[19] "RESIDUAL_TUMOR"                      
[20] "ETHNICITY"                           

Input Data has 20 rows and 573 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=302,	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=211,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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=22,	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:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'TUMOR_GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_GRADE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'TUMOR_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'DAYS_TO_TUMOR_RECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_TUMOR_RECURRENCE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'CHEMO_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CHEMO_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 19:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	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] "****** SUMMARY ***** "
Output Data has 573 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "TUMOR_TISSUE_SITE"          
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "RESIDUAL_TUMOR"              "ETHNICITY"                  
YEARS_TO_BIRTH, nv=55, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=3, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P34.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P34.3) MUTATED   130 156
  AMP PEAK  1(1P34.3) WILD-TYPE  98 175
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          286                           273 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          156                           175 
$`AMP PEAK  1(1P34.3) MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1336 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       11.87        41.00        49.15         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       65.52        63.09        65.46         0.53        49.28        32.52 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
       76.57       103.40        82.39        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1649 TCGA-09-1667 
       38.37       119.08        29.10        55.43        64.64        61.87 
TCGA-09-1670 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2048 TCGA-09-2049 
       17.98         3.02        97.55         6.18         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       71.11        63.09        39.75        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 
       81.17        28.54        83.31        81.01        32.35        87.06 
TCGA-13-1482 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       61.71        52.44       125.56        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       66.15        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       44.68        80.02        78.48        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       70.45         8.42        23.05        25.94        26.20        27.52 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 
       19.10        16.70        40.54        15.39        26.83        49.41 
TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 
        8.81        18.90        51.35        68.68        86.01       129.96 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 TCGA-24-0966 TCGA-24-0979 
      115.89        91.66        49.84         4.70         7.63        41.56 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 
       22.32        63.55         7.82         7.99         0.76         6.02 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
        4.83        17.39        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14         9.11         3.45         1.18        22.22 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       56.58        51.91        58.09        39.88        19.53        44.09 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 
       25.87        17.23        48.33        38.24         8.32         3.81 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2026 
        9.80        30.21        11.05        81.11       152.02        34.82 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 
       55.92        18.48        57.07        36.16         0.36        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 
       70.45        44.61         0.82        36.23        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 TCGA-25-1329 
       53.26         1.02        26.96        52.04        65.00        15.02 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1633 TCGA-25-1634 
       18.58        17.03        12.95        20.61        62.17        35.87 
TCGA-25-1635 TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 
       52.04        49.05         1.02        12.00        45.01        42.02 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1707 
       48.33       101.79        68.32        16.93        23.93        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 
       31.27        17.36        62.93        39.42        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       17.33        12.36        12.30        14.93         7.23         5.36 
TCGA-29-2425 TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       65.00        42.25        21.47        35.77        38.07        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        2.47        15.68        44.91        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 
        1.22        24.26        30.05        48.79        45.57        18.77 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       42.51         2.20        28.77        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       24.69        20.98        20.52        14.17         6.05        16.18 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       47.57        28.93        42.02        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       22.32        25.02       180.20       116.12         9.40         2.14 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       44.81         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        28.47        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1899 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 
       33.67         8.42        34.13        31.30        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       67.76        15.75        38.17         5.52        14.50         4.01 
TCGA-61-2012 TCGA-61-2088 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       30.64         4.77        60.62         6.48        76.87        20.68 
TCGA-61-2111 TCGA-OY-A56P TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
      125.75        39.68        29.16         9.47        57.76        17.98 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
       18.51        34.19        32.88        39.58         2.73        31.20 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       55.17        11.18        11.38       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0794 TCGA-13-0797 TCGA-13-0802 TCGA-13-0803 
       58.65        40.24        63.09        69.73        51.02        43.86 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 
       13.61        68.94       107.18       153.37        92.42       145.45 
TCGA-13-0893 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0911 
       43.36        50.37       123.16       118.98        60.59        44.55 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       58.68        48.79        48.76        83.74 

$`AMP PEAK  1(1P34.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 
       13.81        20.52        43.92         1.81         2.01        46.62 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1362 TCGA-04-1364 TCGA-04-1514 
       48.76        21.57        63.98        44.32        33.67        56.55 
TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
       84.20        48.89        27.88        28.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1674 
       41.62        57.60        55.36        30.51         5.85         8.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2054 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 
        6.12        35.15        20.94        55.23        57.27        17.46 
TCGA-13-1477 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       54.64        29.42       124.44        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1494 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1511 
       83.93        93.90       115.07        13.97        43.20        54.25 
TCGA-13-1512 TCGA-20-0996 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       14.53        72.20        25.38         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1027 TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 
       49.68        32.09        29.13         2.76        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1121 TCGA-23-2078 TCGA-23-2081 
       31.20        19.46        33.30         6.38        87.48        77.00 
TCGA-23-2641 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 
        2.76         4.50        11.64        21.80         7.66        54.12 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 
       47.41         6.31         6.38         7.86         6.25         5.95 
TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1467 TCGA-24-1544 TCGA-24-1545 
        5.36        28.37        18.64       105.99        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 
       64.27        16.21        41.06        41.39        88.50        70.62 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 
       45.50        47.70        10.26        90.15        88.37         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 
        3.72         4.37        11.28         5.79         5.52        22.68 
TCGA-24-1927 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
       16.44         4.87        44.84        58.16       109.71        14.43 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2261 TCGA-24-2267 TCGA-24-2289 
       28.18        64.01        44.52         0.79        47.54        67.36 
TCGA-24-2293 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 
       16.64        33.01        42.05         2.01        34.98        37.97 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 
       33.96         2.99        12.99        27.62        38.20         0.30 
TCGA-25-1632 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       59.15        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       38.04         3.02        19.99         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       26.99        78.90        47.61        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 
       31.20        36.36        59.67        18.25        34.62        86.60 
TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 
       66.81        31.30        22.98        11.84         8.38        36.30 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 
       86.17        62.47        45.11        13.84        11.47         9.76 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1880 TCGA-31-1946 TCGA-31-1951 
       36.26         0.26        48.10        57.57        30.18        22.49 
TCGA-31-1953 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        6.71        44.12        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
        8.55        30.08        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 
       25.91        25.08        23.80        21.60         2.24        18.31 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       11.47        23.74        10.42        40.77         1.48        24.03 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 
       29.00        25.08        80.12        22.32        34.39         5.42 
TCGA-61-1721 TCGA-61-1736 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 
       11.11        48.79        43.69         1.45         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 TCGA-61-1995 
       13.02         9.07        37.05        42.51        43.43         2.01 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98        30.64        39.85         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
        4.80        51.72        71.74        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       55.50        44.52        22.22         6.35        31.07         8.61 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
       18.94         0.79         9.99        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       81.86        14.66         6.71        35.44        36.92        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0727 
       20.91         6.21        24.59        44.55        12.39        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0792 TCGA-13-0793 
       17.82         2.50        11.54        38.01       118.42       107.28 
TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 
       20.35        83.34        87.48        45.99        35.28        35.31 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 
      111.39        66.67        95.15       102.84        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
      134.04        19.36       127.79       116.65        37.64       109.32 
TCGA-13-0919 TCGA-13-0924 TCGA-13-2071 
       84.53        85.94        25.41 

  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                         0.36                          0.26 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                       180.20                        134.04 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                       34.485                        31.000 
[1] "0.4 - 180.2 (34.5)" "0.3 - 134.0 (31.0)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  1(1P34.3) MUTATED         2   283                1
  AMP PEAK  1(1P34.3) WILD-TYPE       1   275                1
D1V3, multiclass
                  clus
vv                 AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    283                           275
  PERITONEUM OVARY                           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"
D1V4, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED   274   3
  AMP PEAK  1(1P34.3) WILD-TYPE 267   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED    274    3
  AMP PEAK  1(1P34.3) WILD-TYPE  267    2
     clus
vv    AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  NO                          274                           267
  YES                           3                             2
[1] 2 2
[1] FALSE
D1V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  1(1P34.3) MUTATED    8  8  3  1
  AMP PEAK  1(1P34.3) WILD-TYPE  7 18  2  2
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  R0                           8                             7
  R1                           8                            18
  R2                           3                             2
  RX                           1                             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"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED     5 167
  AMP PEAK  1(1P34.3) WILD-TYPE   5 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED      5  167
  AMP PEAK  1(1P34.3) WILD-TYPE    5  160
                        clus
vv                       AMP PEAK  1(1P34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         167
                        clus
vv                       AMP PEAK  1(1P34.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           160
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED   136 217
  AMP PEAK  2(1Q21.3) WILD-TYPE  92 114
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          353                           206 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          217                           114 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1341 
       20.52        11.87        43.92        41.00        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 
       18.51        11.87        65.52        63.09        48.76        65.46 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       49.28        44.32        33.67        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
        0.79        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       64.64        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       38.43        41.62        61.87        55.36        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 
        3.02         8.55         6.18        35.15       112.41        63.09 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       20.94        26.93        12.46        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 
       81.01        17.46        54.64        87.06        61.71       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 
       20.68        22.39        70.82        83.93        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
      127.27        66.15       115.07        34.82        65.69        34.16 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       80.15        44.68        54.25        14.53        80.02        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       77.88        76.90        65.52         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       26.20        25.38        19.10         2.66        47.54        49.68 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1031 TCGA-23-1114 TCGA-23-1117 TCGA-23-1119 
       15.39        26.83        18.90        68.68        33.30       129.96 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
        6.38        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
       49.84         4.70         4.50        41.56        22.32        63.55 
TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.31         7.82         7.99         0.76         6.25         6.02 
TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
        4.83        18.64        18.67        43.53         8.55        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         9.11         1.18        22.22        26.96 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       16.21        56.58        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       45.50        25.87        10.26        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
        8.32         3.81        11.28         5.52         9.80        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2038 
       34.82       109.71        14.43        55.92        18.48        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
       57.07         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 
        0.82        67.36        33.11        26.96        33.01        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 
        2.01        34.98        65.00        37.97        33.96        12.99 
TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       15.02        17.03        12.95        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 
       14.96        24.99        24.00        85.05         1.02         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99        42.02        29.03        31.00        26.99 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1701 TCGA-29-1702 
       47.61        48.33       101.79        40.41        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        31.27        34.62        17.36 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       66.81        62.93        39.42        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       12.36        12.30         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        45.11        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
        9.76        35.77        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
       15.68         0.26        48.10        44.91         6.12        36.62 
TCGA-30-1867 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 
        1.22         6.71        44.12         2.20        29.10        21.53 
TCGA-36-1571 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       22.85        30.08        27.85        24.23        24.69        35.05 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       18.31        20.52        14.17        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       23.74        28.93        42.02         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 
       21.14         1.74        22.32        25.02       180.20       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1728 
        9.40         2.14        44.81         8.09        20.94        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
        4.34        31.79        28.47        35.80         2.43        33.67 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       43.69         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 
       34.13        31.30        42.51        56.61        15.75        38.17 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 
       14.50         4.01        30.64        39.85        30.64        45.40 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
        4.77        51.72        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
        6.48        76.87       125.75         6.35         8.61        39.68 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        9.99        29.16         9.47        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       54.31        34.19        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
       36.92        20.91        24.59        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17        11.18        11.54        38.01 
TCGA-13-0762 TCGA-13-0768 TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
      111.78        58.65        40.24        63.09        20.35        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0883 
       83.34        87.48        51.02        43.86        13.61        68.94 
TCGA-13-0885 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
      111.39        92.42       145.45       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 
       66.15       134.04        19.36        50.37       123.16       116.65 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       44.55        84.53        48.79        48.76        83.74 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1349 TCGA-04-1350 
       13.81         1.81        49.15         2.01        21.57        63.98 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1644 
        0.53        32.52        76.57       103.40        82.39        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1669 
       27.88        28.64        89.33        74.93        57.60        30.51 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 TCGA-09-2050 TCGA-09-2053 TCGA-13-1403 
       97.55         6.12         4.54        71.11        39.75        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1412 TCGA-13-1483 TCGA-13-1491 TCGA-13-1492 
       81.17        28.54        32.35        29.42        52.44       125.56 
TCGA-13-1494 TCGA-13-1500 TCGA-13-1501 TCGA-13-1507 TCGA-13-A5FT TCGA-20-0996 
       93.90        13.97        43.20        65.52        70.45        72.20 
TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 
       27.52        16.70         2.93        40.54        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
        8.81        29.13         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-2078 
       31.20        19.46        86.01         4.27        39.09        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       91.66        77.00         2.76         7.63        11.64        21.80 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1419 TCGA-24-1425 
        7.66        54.12        47.41         6.38         7.86         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1463 TCGA-24-1470 TCGA-24-1545 
        5.36        17.39        28.37        72.92         3.45        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       64.27        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       47.70        17.23        90.15         3.48         3.72         4.37 
TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 
        5.79        22.68        16.44        28.18        64.01        36.16 
TCGA-24-2261 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        0.79        36.23        16.64        55.86        53.26         1.02 
TCGA-25-1315 TCGA-25-1322 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1630 
       52.04         2.99        18.58        27.62        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 
        0.30        59.15        13.02        49.05        38.04        12.00 
TCGA-25-2401 TCGA-29-1688 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
        2.96        78.90        39.02        33.93        31.20        68.32 
TCGA-29-1699 TCGA-29-1762 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1778 
       36.36        86.60        31.30        22.98        11.84        14.93 
TCGA-29-1781 TCGA-29-2427 TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        8.38        62.47        34.78        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 
       48.79        45.57        30.18        18.77        22.49        42.51 
TCGA-36-1568 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-2530 TCGA-36-2532 
       28.77        22.55         8.55        25.74        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2549 TCGA-42-2590 TCGA-42-2591 TCGA-57-1992 TCGA-57-1993 
       20.98         6.05        10.42        40.77        29.00        25.08 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1725 
       80.12        22.32        34.39         5.42        11.11        31.43 
TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 TCGA-61-1895 TCGA-61-1910 TCGA-61-1913 
       18.54        48.79        44.84         1.45        37.05        48.92 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2016 
       67.76        43.43         2.01         5.52        17.98         1.18 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2094 TCGA-61-2095 TCGA-61-2109 TCGA-61-2110 
       45.96         4.80        71.74        61.64        20.68        44.52 
TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-10-0926 TCGA-10-0927 
       22.22        31.07        18.94         0.79        25.91        81.86 
TCGA-10-0928 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0755 
       18.51        19.99         6.21        44.55        12.39         2.50 
TCGA-13-0758 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0801 
       11.38        61.84        56.71       118.42       107.28        45.99 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       35.28        35.31       107.18       153.37        66.67        95.15 
TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      127.79       118.98        60.59        37.64       109.32        58.68 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.26                          0.30 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       180.20                        153.37 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        33.67                         31.25 
[1] "0.3 - 180.2 (33.7)" "0.3 - 153.4 (31.2)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  2(1Q21.3) MUTATED         1   354                2
  AMP PEAK  2(1Q21.3) WILD-TYPE       2   204                0
D2V3, multiclass
                  clus
vv                 AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  OMENTUM                                    1                             2
  OVARY                                    354                           204
  PERITONEUM OVARY                           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"
D2V4, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   345   2
  AMP PEAK  2(1Q21.3) WILD-TYPE 196   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    345    2
  AMP PEAK  2(1Q21.3) WILD-TYPE  196    3
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                          345                           196
  YES                           2                             3
[1] 2 2
[1] FALSE
D2V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  2(1Q21.3) MUTATED   11 14  4  0
  AMP PEAK  2(1Q21.3) WILD-TYPE  4 12  1  3
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  R0                          11                             4
  R1                          14                            12
  R2                           4                             1
  RX                           0                             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"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     6 202
  AMP PEAK  2(1Q21.3) WILD-TYPE   4 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      6  202
  AMP PEAK  2(1Q21.3) WILD-TYPE    4  125
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         202
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           125
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q42.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q42.2) MUTATED   116 190
  AMP PEAK  3(1Q42.2) WILD-TYPE 112 141
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                          306                           253 
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                          190                           141 
$`AMP PEAK  3(1Q42.2) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1341 TCGA-04-1342 
       13.81        20.52        11.87        43.92         1.08        18.51 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1353 TCGA-04-1356 TCGA-04-1364 TCGA-04-1514 
       65.52        63.09         0.53        49.28        33.67        56.55 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       19.99         0.79        38.37       119.08        84.20        55.43 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       64.64        31.86        47.70        45.37         9.99        38.43 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 
       57.60        61.87        55.36        17.98         5.85         8.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15         4.54       112.41        63.09        39.75 
TCGA-09-2054 TCGA-09-2056 TCGA-13-1403 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       20.94        12.46        77.10        55.23        57.27        81.01 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       32.35        54.64        87.06       124.44        20.68        22.39 
TCGA-13-1488 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1504 TCGA-13-1511 
       70.82        90.38       127.27        66.15        34.82        54.25 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU 
       14.53        80.02        77.88        76.90        70.45         8.42 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-23-1021 TCGA-23-1026 
       25.94        26.20        25.38        19.10        47.54        26.83 
TCGA-23-1027 TCGA-23-1030 TCGA-23-1031 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       32.09        29.13        18.90        68.68        33.30        86.01 
TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
      129.96         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2641 TCGA-23-2643 TCGA-24-0982 TCGA-24-1105 
       24.95       115.89         2.76         4.70        22.32        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 TCGA-24-1469 TCGA-24-1471 
        6.02        18.64         8.55        12.46         9.11         1.18 
TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1552 TCGA-24-1553 
       26.96        64.27        16.21        56.58        41.39        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 
       70.62        39.88        19.53        44.09        45.50        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       10.26        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1845 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        3.48         3.81         5.52         9.80        22.68        30.21 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 
       81.11         4.87       152.02        58.16        34.82        14.43 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       64.01        44.52         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
       44.61        67.36        36.23        16.64        33.11        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1634 
       15.02        17.03        12.95        20.61        38.20        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 
       52.04        14.96        24.99        24.00        85.05         1.02 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 
        3.02        45.01        42.02        29.03        31.00        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 
       47.61       101.79        40.41        68.32        16.93        23.93 
TCGA-29-1703 TCGA-29-1710 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       59.67        31.27        86.60        66.81        62.93        39.42 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 
       22.98        24.36        17.33        12.36        14.93         7.23 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 
       86.17        65.00        62.47        13.84        21.47        11.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       35.77        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.12        36.62         1.22         2.20        28.77        29.10 
TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 
       22.85        30.08        24.23        24.69        35.05        29.82 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
        2.24        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 
       11.47        47.57        23.74        42.02        10.42         1.48 
TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 
       11.38         1.74        22.32        25.08        25.02        80.12 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-61-1722 TCGA-61-1727 
      116.12         9.40         2.14        44.81         8.09        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 
        4.34        31.79        28.47        44.84         2.43        33.67 
TCGA-61-1743 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1917 
       43.69        13.02         9.07        34.13        42.51        43.43 
TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2088 
       38.17         4.01        30.64        39.85         1.18         4.77 
TCGA-61-2092 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       51.72        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       76.87        20.68       125.75        31.07         8.61        39.68 
TCGA-VG-A8LO TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0930 
        0.79         9.47        17.98        35.57        54.31        34.19 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 
       14.66         6.71        35.44        36.92        20.91        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 TCGA-13-0799 
        2.50        11.18        11.54       111.78        20.35        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 
       87.48        45.99        51.02        68.94       153.37        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
       92.42       145.45        71.74        66.15        19.36        50.37 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
      118.98       116.65        44.55        84.53        48.76        83.74 

$`AMP PEAK  3(1Q42.2) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       41.00         1.81        49.15         2.01        46.62        11.87 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 
       48.76        21.57        63.98        65.46        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1536 TCGA-04-1644 
       76.57       103.40        82.39        41.59        29.10        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       27.88        28.64        36.23        89.33        74.93        41.62 
TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2050 TCGA-09-2055 
       30.51         3.02        97.55         6.18        71.11        26.93 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1482 TCGA-13-1483 
       81.17        28.54        83.31        17.46        61.71        29.42 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1499 
       83.93        52.44       125.56        93.90         4.24       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       13.97        43.20        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-2059 TCGA-13-2065 TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 
       44.68        78.48        65.52        23.05        72.20        27.52 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       16.70         2.93         2.66        49.68        40.54        15.39 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       49.41         8.81         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1120 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       31.20        19.46         4.27        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       49.84         4.50         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1417 TCGA-24-1425 TCGA-24-1426 
        7.66        54.12        63.55         7.82         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 
        4.83        17.39        28.37        18.67        43.53        72.92 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 TCGA-24-1550 
       45.14       105.99         3.45        22.22        57.40        41.06 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1563 TCGA-24-1567 TCGA-24-1844 TCGA-24-1846 
       51.91        88.50        47.70        17.23         3.72         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1927 TCGA-24-1928 TCGA-24-2023 TCGA-24-2027 
       11.28         5.79        16.44        11.05        44.84       109.71 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       55.92        18.48        28.18        57.07        36.16         0.79 
TCGA-24-2288 TCGA-24-2297 TCGA-25-1623 TCGA-25-1625 TCGA-25-1631 TCGA-25-1632 
        0.82        55.86        18.58        27.62         0.30        59.15 
TCGA-25-1633 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 
       62.17        13.02        49.05        38.04        12.00        19.99 
TCGA-25-2401 TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 
        2.96        26.99        48.33        39.02        33.93        31.20 
TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1768 
       36.36        18.25        41.98        34.62        17.36        31.30 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 
       22.55        11.84        12.30         8.38         5.36        36.30 
TCGA-29-2428 TCGA-29-2431 TCGA-29-2436 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       45.11        42.25         9.76         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       34.78        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-2530 
       21.53        22.55         8.55        25.74        27.85        33.01 
TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       29.49        25.91        25.08        23.80        21.60        20.98 
TCGA-42-2588 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 TCGA-59-2348 
       28.93        40.77        24.03        21.14        29.00       180.20 
TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
       22.32        34.39         5.42        11.11        20.94        31.43 
TCGA-61-1728 TCGA-61-1736 TCGA-61-1738 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       27.88        48.79        35.80         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       11.41        31.30        37.05        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2012 
       15.75         2.01         5.52        14.50        17.98        30.64 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2095 TCGA-61-2110 
       45.96        45.40         4.80        71.74        61.64        44.52 
TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        18.94         9.99        29.16        57.76 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0937 TCGA-13-0714 
       25.91        81.86        18.51        32.88        19.99         6.21 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       44.55        12.39        11.38        38.01        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
       58.65        40.24       118.42       107.28        63.09        69.73 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        35.31        13.61       107.18       111.39 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 
       95.15       102.84        43.36       134.04       127.79       123.16 
TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 
       60.59        37.64       109.32        58.68        48.79        85.94 
TCGA-13-2071 
       25.41 

  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                         0.36                          0.26 
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                       153.37                        180.20 
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                        32.22                         33.01 
[1] "0.4 - 153.4 (32.2)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  3(1Q42.2) MUTATED         3   304                2
  AMP PEAK  3(1Q42.2) WILD-TYPE       0   254                0
D3V3, multiclass
                  clus
vv                 AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE
  OMENTUM                                    3                             0
  OVARY                                    304                           254
  PERITONEUM OVARY                           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"
D3V4, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.2) MUTATED   297   1
  AMP PEAK  3(1Q42.2) WILD-TYPE 244   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.2) MUTATED    297    1
  AMP PEAK  3(1Q42.2) WILD-TYPE  244    4
     clus
vv    AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE
  NO                          297                           244
  YES                           1                             4
[1] 2 2
[1] FALSE
D3V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  3(1Q42.2) MUTATED   10 15  4  2
  AMP PEAK  3(1Q42.2) WILD-TYPE  5 11  1  1
D3V6, multiclass
    clus
vv   AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE
  R0                          10                             5
  R1                          15                            11
  R2                           4                             1
  RX                           2                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.2) MUTATED     4 171
  AMP PEAK  3(1Q42.2) WILD-TYPE   6 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.2) MUTATED      4  171
  AMP PEAK  3(1Q42.2) WILD-TYPE    6  156
                        clus
vv                       AMP PEAK  3(1Q42.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         171
                        clus
vv                       AMP PEAK  3(1Q42.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           156
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P23.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P23.2) MUTATED    99 143
  AMP PEAK  4(2P23.2) WILD-TYPE 129 188
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                          242                           317 
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                          143                           188 
$`AMP PEAK  4(2P23.2) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1336 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 
       20.52        11.87        49.15         1.08        18.51        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1371 
       21.57        63.98        49.28        32.52        33.67        82.39 
TCGA-04-1525 TCGA-04-1646 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 
       38.37        27.88        45.37         9.99        38.43        41.62 
TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 
       61.87        17.98         5.85         8.55         6.18        35.15 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 
       63.09        39.75        20.94        77.10        28.54        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1481 TCGA-13-1495 TCGA-13-1497 
       55.23        57.27        32.35        87.06        90.38       127.27 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 
       34.82        65.69        34.16        54.25        80.02        78.48 
TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 
       77.88         8.42        23.05        27.52        19.10         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1028 TCGA-23-1029 TCGA-23-1114 
        2.66        47.54        15.39        49.41         8.81        68.68 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1124 TCGA-23-2072 
       33.30        86.01       129.96        39.09        58.13        24.95 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2645 TCGA-24-0970 TCGA-24-0982 TCGA-24-1417 
       87.48        91.66         4.50        11.64        22.32         7.82 
TCGA-24-1418 TCGA-24-1424 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1467 
        7.99         6.02        18.64        18.67        43.53       105.99 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1550 TCGA-24-1551 
        9.11         1.18        22.22        26.96        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1560 TCGA-24-1563 TCGA-24-1604 TCGA-24-1614 
       41.39        58.09        44.09        47.70        88.37        48.33 
TCGA-24-1616 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1928 TCGA-24-2019 
       38.24         3.81        11.28         5.52        11.05         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 TCGA-24-2033 TCGA-24-2261 
      152.02        44.84        34.82        14.43        18.48         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 
        0.36        47.54        44.61         0.82        67.36        33.11 
TCGA-25-1312 TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
        1.02        52.04         2.01        34.98        65.00        37.97 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 
       12.99        15.02        18.58        27.62        17.03        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 
       38.20         0.30        35.87        14.96        24.00        85.05 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2404 TCGA-25-2409 
       49.05        38.04        12.00        45.01        29.03        26.99 
TCGA-29-1691 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1711 TCGA-29-1761 
       48.33        68.32        16.93        23.93        34.62        17.36 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 
       66.81        62.93        24.36        17.33        12.36        14.93 
TCGA-29-1781 TCGA-29-1784 TCGA-29-2425 TCGA-29-2429 TCGA-29-A5NZ TCGA-30-1714 
        8.38         5.36        65.00        13.84        35.77        38.07 
TCGA-30-1853 TCGA-30-1859 TCGA-30-1862 TCGA-30-1867 TCGA-31-1946 TCGA-31-1950 
       36.26        48.10         6.12         1.22        30.18        18.77 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 
        6.71        42.51         2.20        28.77        22.85         8.55 
TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2538 TCGA-36-2543 
       30.08        24.69        35.05        33.01        25.08         2.24 
TCGA-36-2544 TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       20.98         6.05        11.47        23.74        28.93        42.02 
TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2352 
       11.38         1.74        22.32        25.02       180.20         9.40 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       44.81         8.09        31.43        27.88         4.34        31.79 
TCGA-61-1741 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1906 TCGA-61-1913 
       33.67         8.42         5.79        13.02        34.13        48.92 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 
       15.75        38.17         5.52        14.50         4.01        39.85 
TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
        4.77        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
       20.68       125.75        22.22         6.35         8.61        39.68 
TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       18.94         9.99        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 
       35.57        81.86        34.19        32.88        14.66        35.44 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0761 
       39.58         2.73        17.82        55.17        11.18        38.01 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 
       56.71        40.24        63.09        87.48        51.02        43.86 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
      107.18       153.37        92.42       145.45        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0906 TCGA-13-0913 TCGA-13-0919 
       66.15       134.04        19.36       118.98       109.32        84.53 
TCGA-13-0921 TCGA-13-2071 
       48.76        25.41 

$`AMP PEAK  4(2P23.2) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 
       13.81        43.92        41.00         1.81         2.01        46.62 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 TCGA-04-1362 
       11.87        65.52        48.76        65.46         0.53        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
       76.57       103.40        56.55        41.59        19.99         0.79 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
      119.08        29.10        84.20        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 
       64.64        36.23        31.86        47.70        89.33        74.93 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       57.60        55.36        30.51         3.02        97.55         6.12 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2055 TCGA-09-2056 TCGA-13-1404 
        4.54       112.41        71.11        26.93        12.46        81.17 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       81.01        17.46        54.64        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       20.68        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       93.90         4.24        66.15       115.07        13.97        43.20 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 
       65.52        80.15        44.68        14.53        76.90        65.52 
TCGA-13-A5FT TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 
       70.45        25.94        26.20        72.20        25.38        16.70 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1030 TCGA-23-1031 
       49.68        40.54        26.83        32.09        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
        2.76        51.35        54.51         3.22        31.20        19.46 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 
        4.27         6.38        33.47         0.53       115.89        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 
       49.84         2.76         4.70         7.63        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.86         0.76         6.25         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       17.39        28.37         8.55        72.92        12.46        45.14 
TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1555 
        3.45        57.40        64.27        16.21        56.58        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       70.62        39.88        19.53        45.50        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       17.23        90.15         8.32         3.48         3.72         4.37 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         9.80        22.68        30.21        16.44        81.11 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       58.16       109.71        55.92        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 
       57.07        36.16        31.63        70.45        36.23        16.64 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1321 
       55.86        53.26        26.96        33.01        42.05        33.96 
TCGA-25-1322 TCGA-25-1627 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 
        2.99        12.95        59.15        62.17        52.04        24.99 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       13.02         1.02         3.02        19.99        42.02         2.96 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       31.00        78.90        47.61       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       33.93        31.20        36.36        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       31.27        86.60        39.42        31.30        22.98        22.55 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       11.84        12.30         7.23        36.30        86.17        62.47 
TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1718 
       45.11        42.25        21.47        11.47         9.76        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
        2.47        15.68         0.26        44.91        34.78        36.62 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1951 
       57.57        24.26        30.05        48.79        45.57        22.49 
TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 
       44.12        29.10        21.53        22.55        25.74        27.85 
TCGA-36-1580 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 
       24.23        29.49        29.82        25.91        23.80        21.60 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2590 
       18.31        20.52        14.17        16.18        47.57        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 
       40.77         1.48        24.03        21.14        29.00        25.08 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32       116.12        34.39         2.14         5.42 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       11.11        20.94        18.54        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1904 
       35.80         2.43        43.69         1.45        11.41         9.07 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       31.30        37.05        42.51        56.61        67.76        43.43 
TCGA-61-1995 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
        2.01        17.98        30.64        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.40         4.80        51.72        71.74        61.64        58.39 
TCGA-61-2110 TCGA-61-2613 TCGA-VG-A8LO TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
       44.52        31.07         0.79        54.31        25.91        18.51 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        6.71        36.92        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0758 
       44.55        12.39        31.20        15.19         2.50        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 
       11.54       111.78        61.84        58.65       118.42       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 
       20.35        69.73        83.34        45.99        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       13.61        68.94       111.39        66.67        95.15       102.84 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
      127.79        50.37       123.16        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       37.64        58.68        48.79        83.74        85.94 

  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                         0.30                          0.26 
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                       180.20                        127.79 
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                       32.435                        33.470 
[1] "0.3 - 180.2 (32.4)" "0.3 - 127.8 (33.5)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  4(2P23.2) MUTATED         1   241                1
  AMP PEAK  4(2P23.2) WILD-TYPE       2   317                1
D4V3, multiclass
                  clus
vv                 AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE
  OMENTUM                                    1                             2
  OVARY                                    241                           317
  PERITONEUM OVARY                           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"
D4V4, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P23.2) MUTATED   235   2
  AMP PEAK  4(2P23.2) WILD-TYPE 306   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P23.2) MUTATED    235    2
  AMP PEAK  4(2P23.2) WILD-TYPE  306    3
     clus
vv    AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE
  NO                          235                           306
  YES                           2                             3
[1] 2 2
[1] FALSE
D4V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  4(2P23.2) MUTATED    5 11  3  1
  AMP PEAK  4(2P23.2) WILD-TYPE 10 15  2  2
D4V6, multiclass
    clus
vv   AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE
  R0                           5                            10
  R1                          11                            15
  R2                           3                             2
  RX                           1                             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"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P23.2) MUTATED     4 139
  AMP PEAK  4(2P23.2) WILD-TYPE   6 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P23.2) MUTATED      4  139
  AMP PEAK  4(2P23.2) WILD-TYPE    6  188
                        clus
vv                       AMP PEAK  4(2P23.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         139
                        clus
vv                       AMP PEAK  4(2P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           188
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(2Q31.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(2Q31.2) MUTATED    96 154
  AMP PEAK  5(2Q31.2) WILD-TYPE 132 177
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                          250                           309 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                          154                           177 
$`AMP PEAK  5(2Q31.2) MUTATED`
TCGA-59-A5PD TCGA-04-1342 TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 
       20.52        18.51        48.76        63.98        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 
       44.32        33.67        41.59        19.99        29.10        84.20 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
       64.64        31.86        45.37        38.43        89.33        41.62 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-2043 TCGA-09-2048 
       55.36        17.98         5.85         3.02         6.18         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 
      112.41        71.11        39.75        81.17        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       57.27        81.01        17.46        87.06        61.71        29.42 
TCGA-13-1488 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1501 TCGA-13-1504 
       70.82        90.38         4.24       127.27        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 
       65.69        34.16        44.68        54.25        80.02        77.88 
TCGA-20-0987 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 
       23.05        19.10        16.70        47.54        49.68        15.39 
TCGA-23-1026 TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1111 TCGA-23-1114 
       26.83        49.41        18.90         2.76         3.22        68.68 
TCGA-23-1117 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
       33.30        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0982 
      115.89        77.00         2.76         4.70         4.50        22.32 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 
        7.99         0.76         5.95        17.39        28.37        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 
       43.53         8.55        45.14       105.99         9.11         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 TCGA-24-1556 
       22.22        26.96        64.27        16.21        58.09        70.62 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       39.88        44.09        88.37        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 
        3.72         3.81         5.52         9.80        30.21        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2030 TCGA-24-2033 TCGA-24-2261 TCGA-24-2262 
       81.11       152.02        55.92        18.48         0.79         0.36 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 
       47.54        70.45        44.61         0.82        67.36        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1319 
       53.26         1.02        26.96        33.01         2.01        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1626 TCGA-25-1630 TCGA-25-1634 
       37.97        33.96         2.99        17.03        38.20        35.87 
TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 
       14.96        24.00        85.05        13.02         1.02         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-29-1688 TCGA-29-1691 
       12.00        45.01        42.02         2.96        78.90        48.33 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1702 TCGA-29-1705 
       39.02        40.41        33.93        68.32        23.93        18.25 
TCGA-29-1707 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 
       41.98        17.36        66.81        62.93        39.42        22.98 
TCGA-29-1770 TCGA-29-1775 TCGA-29-1781 TCGA-29-1783 TCGA-29-2425 TCGA-29-2429 
       24.36        12.36         8.38         7.23        65.00        13.84 
TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 
       21.47        11.47        38.07        51.91         2.47        48.10 
TCGA-30-1862 TCGA-30-1866 TCGA-31-1950 TCGA-31-1951 TCGA-36-1575 TCGA-36-1576 
        6.12        36.62        18.77        22.49         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2534 TCGA-36-2544 
       25.74        27.85        24.69        33.01        29.82        20.98 
TCGA-36-2547 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2591 TCGA-42-2593 
       20.52        16.18        11.47        23.74        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 
       24.03        11.38         1.74        22.32        25.02       180.20 
TCGA-59-2352 TCGA-61-1722 TCGA-61-1724 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
        9.40         8.09        20.94         4.34        31.79        28.47 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1906 
        2.43        33.67        43.69         8.42         5.79        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1915 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 
       31.30        37.05        67.76        38.17         4.01        30.64 
TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 
       30.64        45.40         4.77        60.62        55.50         6.48 
TCGA-61-2104 TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0365 
       76.87        22.22         6.35        39.68        18.94         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 
       57.76        17.98        35.57        81.86        14.66        35.44 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 
       20.91        24.59        39.58         2.73        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0800 TCGA-13-0803 
       11.18        11.38        11.54       111.78        87.48        43.86 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 
       68.94       107.18       111.39        66.67        92.42       102.84 
TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 
       43.36        19.36       127.79        50.37       118.98        60.59 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-2071 
       58.68        84.53        48.79        25.41 

$`AMP PEAK  5(2Q31.2) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        2.01        46.62         1.08        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       21.57        65.46         0.53        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 
       56.55         0.79        38.37       119.08        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-1659 TCGA-09-1664 
       27.88        28.64        36.23        47.70         9.99        74.93 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       57.60        61.87        30.51         8.55        97.55         6.12 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       35.15        63.09        20.94        26.93        12.46        77.10 
TCGA-13-1405 TCGA-13-1412 TCGA-13-1477 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       28.54        32.35        54.64       124.44        20.68        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1498 TCGA-13-1499 
       83.93        52.44       125.56        93.90        66.15       115.07 
TCGA-13-1500 TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 
       13.97        65.52        80.15        14.53        78.48        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       65.52        70.45         8.42        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 TCGA-23-1027 
       27.52        25.38         2.93         2.66        40.54        32.09 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1116 
        8.81        29.13        51.35        54.51        31.20        19.46 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-2078 TCGA-23-2079 
       86.01       129.96         4.27         6.38        87.48        91.66 
TCGA-23-2084 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
       49.84         7.63        11.64        21.80        41.56         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1431 
        7.86         6.25         6.02         5.36         4.83        18.64 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 
       72.92        12.46         3.45        57.40        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1562 TCGA-24-1563 
       51.91        41.39        88.50        19.53        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1846 
       25.87        10.26        17.23        90.15        48.33         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 TCGA-24-2023 
       11.28         5.79        22.68        16.44         4.87        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 
       58.16        34.82       109.71        14.43        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2271 TCGA-24-2290 TCGA-24-2293 
       44.52        57.07        36.16        31.63        36.23        16.64 
TCGA-24-2297 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1323 TCGA-25-1329 
       55.86        52.04        42.05        34.98        12.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       18.58        27.62        12.95        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 TCGA-25-2391 TCGA-25-2393 TCGA-25-2399 
       62.17        52.04        24.99        49.05        38.04        19.99 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1693 TCGA-29-1697 
       29.03        31.00        26.99        47.61       101.79        31.20 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 
       36.36        16.93        59.67        31.27        34.62        86.60 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       31.30        22.55        17.33        11.84        12.30        14.93 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 
        5.36        36.30        86.17        62.47        45.11        42.25 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
        9.76        35.77        36.26        15.68         0.26        44.91 
TCGA-30-1861 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       34.78         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       45.57        30.18         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1580 
       28.77        29.10        21.53        22.85        22.55        24.23 
TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       35.05        29.49        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 
        2.24        18.31        14.17         6.05        47.57        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 
       42.02        10.42        21.14        29.00        25.08        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       22.32       116.12        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 
       11.11        31.43        18.54        27.88        48.79        44.84 
TCGA-61-1738 TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1911 
       35.80         1.45        11.41        13.02         9.07        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        43.43        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
       14.50        17.98        39.85         1.18        45.96         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2109 
       51.72        71.74        61.64        58.39        65.52        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO TCGA-WR-A838 
       44.52       125.75        31.07         8.61         0.79         9.99 
TCGA-09-0364 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       29.16        54.31        25.91        18.51        34.19        32.88 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 
        6.71        36.92        19.99         6.21        44.55        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       31.20        15.19         2.50        38.01        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       58.65        40.24       118.42       107.28        63.09        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
       69.73        83.34        45.99        51.02        35.28        35.31 
TCGA-13-0807 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 
       13.61       153.37        95.15       145.45        71.74        66.15 
TCGA-13-0900 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      134.04       123.16       116.65        44.55        37.64       109.32 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       48.76        83.74        85.94 

  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                         0.36                          0.26 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                       180.20                        153.37 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                        32.19                         34.19 
[1] "0.4 - 180.2 (32.2)" "0.3 - 153.4 (34.2)"
[1] "hr=" "1.1"
D5V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  5(2Q31.2) MUTATED         0   252                1
  AMP PEAK  5(2Q31.2) WILD-TYPE       3   306                1
D5V3, multiclass
                  clus
vv                 AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  OMENTUM                                    0                             3
  OVARY                                    252                           306
  PERITONEUM OVARY                           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"
D5V4, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q31.2) MUTATED   243   3
  AMP PEAK  5(2Q31.2) WILD-TYPE 298   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.2) MUTATED    243    3
  AMP PEAK  5(2Q31.2) WILD-TYPE  298    2
     clus
vv    AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  NO                          243                           298
  YES                           3                             2
[1] 2 2
[1] FALSE
D5V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  5(2Q31.2) MUTATED    4 10  2  1
  AMP PEAK  5(2Q31.2) WILD-TYPE 11 16  3  2
D5V6, multiclass
    clus
vv   AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  R0                           4                            11
  R1                          10                            16
  R2                           2                             3
  RX                           1                             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"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q31.2) MUTATED     6 139
  AMP PEAK  5(2Q31.2) WILD-TYPE   4 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.2) MUTATED      6  139
  AMP PEAK  5(2Q31.2) WILD-TYPE    4  188
                        clus
vv                       AMP PEAK  5(2Q31.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         139
                        clus
vv                       AMP PEAK  5(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           188
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(3Q26.2) MUTATED   191 276
  AMP PEAK  6(3Q26.2) WILD-TYPE  37  55
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          467                            92 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          276                            55 
$`AMP PEAK  6(3Q26.2) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       65.52        63.09        48.76        21.57        63.98         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 
       29.10        84.20        48.89        27.88        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-13-1403 
        4.54       112.41        71.11        63.09        39.75        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       17.46        32.35        87.06        29.42       124.44        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        83.93        52.44       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24       127.27        66.15       115.07        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       65.69        34.16        65.52        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       14.53        80.02        78.48        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       70.45         8.42        23.05        25.94        26.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       49.68        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.76        51.35        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68        19.46        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       24.95       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 
        2.76         4.70         4.50        11.64        41.56         7.66 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       22.32        63.55         6.31         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         6.02         5.36         4.83        17.39 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
       18.64        18.67        43.53         8.55        72.92        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1562 
       58.09        88.50        70.62        39.88        19.53        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       47.70        25.87        17.23        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         3.81        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 
       81.11         4.87       152.02        44.84        34.82       109.71 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       55.92        18.48        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       53.26         1.02        26.96         2.01        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       37.97        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       59.15        35.87        52.04        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2391 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       85.05        49.05         3.02        45.01        19.99        42.02 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       29.03        26.99        78.90        48.33       101.79        39.02 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       40.41        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 
       59.67        18.25        31.27        34.62        17.36        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 
       62.93        39.42        22.98        24.36        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 
       12.30        14.93         7.23         5.36        36.30        65.00 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ 
       45.11        13.84        42.25        21.47        11.47        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       48.10        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       22.49         6.71        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       21.53        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.08        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       14.17        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 
       42.02        10.42        40.77         1.48        24.03        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 
       22.32       116.12         9.40        34.39         2.14        44.81 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
        8.09        20.94        31.43        18.54        27.88        31.79 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 
       48.79        44.84        35.80         2.43        33.67         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       43.43        15.75        38.17         5.52        14.50         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2087 TCGA-61-2094 
       30.64        39.85        30.64         1.18         4.80        71.74 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 
       60.62        65.52         6.48        76.87        20.68       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        0.79        29.16         9.47        57.76        17.98        35.57 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       18.51        34.19        14.66         6.71        35.44        36.92 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
       19.99         6.21        24.59        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.20        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        38.01       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       58.65        40.24       118.42       107.28        63.09        20.35 
TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       69.73        87.48        45.99        51.02        43.86        35.28 
TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       13.61       107.18       111.39       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       95.15       145.45        43.36        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       19.36        50.37       118.98        60.59       116.65        44.55 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-2071 
       84.53        48.79        48.76        83.74        25.41 

$`AMP PEAK  6(3Q26.2) WILD-TYPE`
TCGA-04-1351 TCGA-04-1519 TCGA-04-1638 TCGA-04-1648 TCGA-09-1664 TCGA-09-1675 
       65.46         0.79        55.43        28.64        74.93        97.55 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 
       20.94        26.93        12.46        54.64        61.71        20.68 
TCGA-13-1500 TCGA-20-0996 TCGA-23-1111 TCGA-24-0966 TCGA-24-0975 TCGA-24-1103 
       13.97        72.20         3.22         7.63        21.80        54.12 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1425 TCGA-24-1430 TCGA-24-1464 TCGA-24-1546 
       47.41         6.38         5.95        28.37        12.46        64.27 
TCGA-24-1560 TCGA-24-1565 TCGA-24-1603 TCGA-24-1846 TCGA-24-2024 TCGA-24-2029 
       44.09        10.26        90.15         4.37        58.16        14.43 
TCGA-24-2035 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1633 TCGA-25-2042 
       28.18        33.01        52.04        42.05        62.17        13.02 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2401 TCGA-25-2408 TCGA-29-1690 
        1.02        38.04        12.00         2.96        31.00        47.61 
TCGA-29-1696 TCGA-29-1707 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 
       33.93        41.98        86.60        31.30        22.55        17.33 
TCGA-29-1781 TCGA-29-2414 TCGA-29-2427 TCGA-29-2436 TCGA-30-1880 TCGA-31-1955 
        8.38        86.17        62.47         9.76        57.57        42.51 
TCGA-36-1571 TCGA-36-2537 TCGA-36-2540 TCGA-36-2549 TCGA-57-1583 TCGA-59-2349 
       22.85        25.91        23.80         6.05        11.38        80.12 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1730 TCGA-61-1734 TCGA-61-1743 TCGA-61-1995 
        5.42        11.11         4.34        28.47        43.69         2.01 
TCGA-61-2002 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 
       17.98        45.96        45.40         4.77        51.72        61.64 
TCGA-61-2096 TCGA-61-2101 TCGA-61-2110 TCGA-WR-A838 TCGA-10-0925 TCGA-10-0926 
       58.39        55.50        44.52         9.99        54.31        25.91 
TCGA-10-0927 TCGA-10-0931 TCGA-10-0938 TCGA-13-0720 TCGA-13-0799 TCGA-13-0805 
       81.86        32.88        20.91        44.55        83.34        35.31 
TCGA-13-0883 TCGA-13-0891 TCGA-13-0903 TCGA-13-0905 TCGA-13-0912 TCGA-13-0913 
       68.94       102.84       127.79       123.16        37.64       109.32 
TCGA-13-0916 TCGA-13-0924 
       58.68        85.94 

  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                         0.26                          0.79 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                       180.20                        127.79 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                        32.09                         34.62 
[1] "0.3 - 180.2 (32.1)" "0.8 - 127.8 (34.6)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  6(3Q26.2) MUTATED         3   466                2
  AMP PEAK  6(3Q26.2) WILD-TYPE       0    92                0
D6V3, multiclass
                  clus
vv                 AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  OMENTUM                                    3                             0
  OVARY                                    466                            92
  PERITONEUM OVARY                           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"
D6V4, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED   454   3
  AMP PEAK  6(3Q26.2) WILD-TYPE  87   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED    454    3
  AMP PEAK  6(3Q26.2) WILD-TYPE   87    2
     clus
vv    AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  NO                          454                            87
  YES                           3                             2
[1] 2 2
[1] FALSE
D6V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  6(3Q26.2) MUTATED   12 22  5  3
  AMP PEAK  6(3Q26.2) WILD-TYPE  3  4  0  0
D6V6, multiclass
    clus
vv   AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  R0                          12                             3
  R1                          22                             4
  R2                           5                             0
  RX                           3                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED     8 279
  AMP PEAK  6(3Q26.2) WILD-TYPE   2  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED      8  279
  AMP PEAK  6(3Q26.2) WILD-TYPE    2   48
                        clus
vv                       AMP PEAK  6(3Q26.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         279
                        clus
vv                       AMP PEAK  6(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            48
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4P16.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(4P16.3) MUTATED    59  98
  AMP PEAK  7(4P16.3) WILD-TYPE 169 233
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                          157                           402 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           98                           233 
$`AMP PEAK  7(4P16.3) MUTATED`
TCGA-5X-AA5U TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 
       11.87        48.76        21.57        65.46        49.28        33.67 
TCGA-04-1365 TCGA-04-1519 TCGA-04-1530 TCGA-04-1646 TCGA-09-1666 TCGA-09-1668 
       76.57         0.79       119.08        27.88        57.60        55.36 
TCGA-09-1675 TCGA-09-2048 TCGA-09-2055 TCGA-13-1405 TCGA-13-1412 TCGA-13-1481 
       97.55         4.54        26.93        28.54        32.35        87.06 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 
       93.90         4.24       127.27       115.07        43.20        65.69 
TCGA-13-2060 TCGA-13-A5FU TCGA-23-1026 TCGA-23-1028 TCGA-23-1032 TCGA-23-1109 
       77.88         8.42        26.83        49.41         2.76        51.35 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 
       54.51        68.68        39.09        33.47        58.13       115.89 
TCGA-23-2079 TCGA-23-2643 TCGA-24-0966 TCGA-24-1428 TCGA-24-1430 TCGA-24-1464 
       91.66         4.70         7.63        17.39        28.37        12.46 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1550 TCGA-24-1553 TCGA-24-1556 
       22.22        26.96        57.40        41.06        58.09        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 
       39.88        19.53        47.70        90.15        88.37         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1928 
        3.72         3.81         4.37         5.79         9.80        11.05 
TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2280 TCGA-24-2289 
       34.82        18.48        28.18        57.07        70.45        67.36 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1313 TCGA-25-1315 TCGA-25-1320 TCGA-25-1321 
       33.11        55.86        26.96        52.04        37.97        33.96 
TCGA-25-1322 TCGA-25-1628 TCGA-25-1630 TCGA-25-1635 TCGA-25-1870 TCGA-25-1877 
        2.99        20.61        38.20        52.04        14.96        24.00 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       49.05         1.02        38.04         3.02        12.00        45.01 
TCGA-29-1691 TCGA-29-1701 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 
       48.33        16.93        18.25        34.62        17.36        66.81 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 
       62.93        31.30        22.98        24.36        17.33        12.36 
TCGA-29-1785 TCGA-29-2429 TCGA-29-2431 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       36.30        13.84        42.25        35.77        38.07        51.91 
TCGA-30-1855 TCGA-30-1866 TCGA-36-1569 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 
        2.47        36.62        29.10        27.85        35.05        33.01 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2551 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
        2.24        20.98        16.18        28.93        42.02        10.42 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-61-1722 
       40.77        24.03         1.74        25.08        25.02         8.09 
TCGA-61-1724 TCGA-61-1728 TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 
       20.94        27.88        31.79        35.80         2.43        43.69 
TCGA-61-1900 TCGA-61-1907 TCGA-61-1915 TCGA-61-1918 TCGA-61-2009 TCGA-61-2012 
        5.79        31.30        67.76        15.75        39.85        30.64 
TCGA-61-2094 TCGA-61-2102 TCGA-61-2614 TCGA-10-0925 TCGA-10-0926 TCGA-10-0936 
       71.74         6.48         8.61        54.31        25.91        36.92 
TCGA-10-0937 TCGA-13-0717 TCGA-13-0726 TCGA-13-0758 TCGA-13-0791 TCGA-13-0799 
       19.99        24.59        31.20        11.38        40.24        83.34 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 
       87.48        51.02        68.94       107.18        66.67        92.42 
TCGA-13-0893 TCGA-13-0901 TCGA-13-0905 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 
       43.36        19.36       123.16       109.32        48.79        48.76 
TCGA-13-2071 
       25.41 

$`AMP PEAK  7(4P16.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
        2.01        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1350 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1367 
       63.09        63.98         0.53        32.52        44.32       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 
       82.39        56.55        41.59        19.99        38.37        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       84.20        55.43        48.89        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       74.93        41.62        61.87        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        3.02         8.55         6.18         6.12        35.15       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-13-1403 
       71.11        63.09        39.75        20.94        12.46        77.10 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       81.17        83.31        55.23        57.27        81.01        17.46 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       54.64        61.71        29.42       124.44        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1498 
       70.82        83.93        52.44       125.56        90.38        66.15 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       13.97        34.82        34.16        65.52        80.15        44.68 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
       54.25        14.53        80.02        78.48        76.90        65.52 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       70.45        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 
       49.68        40.54        15.39        32.09         8.81        29.13 
TCGA-23-1031 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       18.90         3.22        31.20        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 
      129.96         4.27         6.38         0.53        24.95        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 
       77.00        49.84         2.76         4.50        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1431 
        6.25         6.02         5.95         5.36         4.83        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 
       18.67        43.53         8.55        72.92        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        9.11         3.45         1.18        64.27        16.21        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 
       51.91        41.39        88.50        44.09        45.50        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1847 
       10.26        17.23        48.33        38.24         8.32        11.28 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        5.52        22.68        30.21        16.44        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
      152.02        44.84        58.16       109.71        14.43        55.92 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       64.01        44.52        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       31.63        44.61         0.82        36.23        16.64        53.26 
TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
        1.02        33.01        42.05         2.01        34.98        65.00 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.99        15.02        18.58        27.62        17.03        12.95 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1871 TCGA-25-1878 
        0.30        59.15        62.17        35.87        24.99        85.05 
TCGA-25-2042 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       13.02        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       26.99        78.90        47.61       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 
       33.93        31.20        68.32        36.36        23.93        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 TCGA-29-1766 TCGA-29-1771 TCGA-29-1776 
       41.98        31.27        86.60        39.42        22.55        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 
       12.30        14.93         8.38         7.23         5.36        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       65.00        62.47        45.11        21.47        11.47         9.76 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
       36.26        15.68         0.26        48.10        44.91        34.78 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
        6.12         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12         2.20        28.77        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2532 
        8.55        30.08        25.74        24.23        24.69        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2545 
       29.82        25.91        25.08        23.80        21.60        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       20.52        14.17         6.05        11.47        47.57        23.74 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 
        1.48        11.38        21.14        22.32        29.00       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
        5.42        44.81        11.11        31.43        18.54         4.34 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       28.47        48.79        44.84        33.67         1.45         8.42 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02         9.07        34.13        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        43.43        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 
       14.50        17.98         4.01        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
       45.40         4.80         4.77        51.72        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        55.50        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22         6.35        31.07        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
        0.79         9.99        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       35.57        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 
        6.71        35.44        20.91         6.21        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
        2.73        12.39        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.18        11.54        38.01       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       58.65       118.42       107.28        63.09        20.35        69.73 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 
       45.99        43.86        35.28        35.31        13.61       111.39 
TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 
      153.37        95.15       145.45       102.84        71.74        66.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      134.04       127.79        50.37       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 
       44.55        37.64        58.68        84.53        83.74        85.94 

  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                         0.79                          0.26 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                       127.27                        180.20 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                       33.470                        31.975 
[1] "0.8 - 127.3 (33.5)" "0.3 - 180.2 (32.0)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  7(4P16.3) MUTATED         1   156                1
  AMP PEAK  7(4P16.3) WILD-TYPE       2   402                1
D7V3, multiclass
                  clus
vv                 AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  OMENTUM                                    1                             2
  OVARY                                    156                           402
  PERITONEUM OVARY                           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"
D7V4, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED   153   2
  AMP PEAK  7(4P16.3) WILD-TYPE 388   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED    153    2
  AMP PEAK  7(4P16.3) WILD-TYPE  388    3
     clus
vv    AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  NO                          153                           388
  YES                           2                             3
[1] 2 2
[1] FALSE
D7V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  7(4P16.3) MUTATED    4  9  2  0
  AMP PEAK  7(4P16.3) WILD-TYPE 11 17  3  3
D7V6, multiclass
    clus
vv   AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  R0                           4                            11
  R1                           9                            17
  R2                           2                             3
  RX                           0                             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"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED     4  87
  AMP PEAK  7(4P16.3) WILD-TYPE   6 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED      4   87
  AMP PEAK  7(4P16.3) WILD-TYPE    6  240
                        clus
vv                       AMP PEAK  7(4P16.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       AMP PEAK  7(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           240
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(4Q13.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(4Q13.3) MUTATED    42  69
  AMP PEAK  8(4Q13.3) WILD-TYPE 186 262
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                          111                           448 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           69                           262 
$`AMP PEAK  8(4Q13.3) MUTATED`
TCGA-59-A5PD TCGA-04-1332 TCGA-04-1338 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 
       20.52        41.00        46.62        63.09        21.57        65.46 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1525 TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 
       49.28        44.32        38.37        55.43        27.88        31.86 
TCGA-09-1665 TCGA-09-1674 TCGA-13-1408 TCGA-13-1410 TCGA-13-1483 TCGA-13-1495 
       41.62         8.55        55.23        81.01        29.42        90.38 
TCGA-13-1499 TCGA-13-1504 TCGA-13-2060 TCGA-13-A5FU TCGA-20-1685 TCGA-20-1686 
      115.07        34.82        77.88         8.42        16.70         2.93 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 
       68.68        19.46        33.30        86.01         4.27         6.38 
TCGA-23-1123 TCGA-23-2645 TCGA-24-0979 TCGA-24-1416 TCGA-24-1419 TCGA-24-1427 
       33.47         4.50        41.56         6.38         7.86         4.83 
TCGA-24-1428 TCGA-24-1466 TCGA-24-1470 TCGA-24-1551 TCGA-24-1555 TCGA-24-1614 
       17.39        45.14         3.45        51.91        88.50        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1924 TCGA-24-1928 
       38.24         8.32         3.72        11.28        30.21        11.05 
TCGA-24-2026 TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2295 
       34.82        28.18        36.16         0.79        47.54        33.11 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1632 TCGA-25-1635 TCGA-25-2042 TCGA-25-2396 
       53.26        26.96        59.15        52.04        13.02         3.02 
TCGA-25-2400 TCGA-29-1691 TCGA-29-1701 TCGA-29-1702 TCGA-29-1761 TCGA-29-1764 
       42.02        48.33        16.93        23.93        17.36        62.93 
TCGA-29-1770 TCGA-29-1775 TCGA-29-1778 TCGA-29-1784 TCGA-29-2432 TCGA-29-A5NZ 
       24.36        12.36        14.93         5.36        21.47        35.77 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1866 TCGA-30-1891 TCGA-31-1959 TCGA-36-1578 
       51.91         2.47        36.62        30.05         2.20        27.85 
TCGA-36-2529 TCGA-36-2551 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1994 
       35.05        16.18        24.03        11.38         1.74        25.02 
TCGA-61-1722 TCGA-61-1728 TCGA-61-1743 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
        8.09        27.88        43.69        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-2000 TCGA-61-2008 TCGA-61-2012 TCGA-61-2101 TCGA-61-2104 
       15.75        14.50        30.64        30.64        55.50        76.87 
TCGA-61-2614 TCGA-VG-A8LO TCGA-10-0936 TCGA-10-0938 TCGA-13-0764 TCGA-13-0791 
        8.61         0.79        36.92        20.91        61.84        40.24 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0802 TCGA-13-0883 
      118.42        63.09        69.73        83.34        51.02        68.94 
TCGA-13-0904 TCGA-13-0920 TCGA-13-2071 
       50.37        48.79        25.41 

$`AMP PEAK  8(4Q13.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        11.87        43.92         1.81        49.15         2.01 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 
        1.08        18.51        11.87        65.52        48.76        63.98 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
        0.53        32.52        33.67        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 
       56.55        41.59        19.99         0.79       119.08        29.10 
TCGA-04-1542 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       84.20        48.89        28.64        64.64        36.23        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       45.37         9.99        38.43        89.33        74.93        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       61.87        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1411 
       77.10        81.17        28.54        83.31        57.27        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 
       32.35        54.64        87.06        61.71       124.44        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
        4.24       127.27        66.15        13.97        43.20        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       34.16        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 
       80.02        78.48        76.90        65.52        70.45        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       25.94        26.20        72.20        27.52        25.38        19.10 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        49.68        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1119 TCGA-23-1122 
       51.35        54.51         3.22        31.20       129.96        39.09 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       58.13         0.53        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 
       77.00        49.84         2.76         4.70         7.63        11.64 
TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       21.80         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.31         7.82         7.99         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.95         5.36        28.37        18.64        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 
        8.55        72.92        12.46       105.99         9.11         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.06        41.39        58.09        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 
       90.15        88.37         3.48         3.81         4.37         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        5.52         9.80        22.68        16.44        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
      152.02        44.84        58.16       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 
       18.48        64.01        44.52        57.07         0.36        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       55.86         1.02        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       15.02        18.58        27.62        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       38.20         0.30        62.17        35.87        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 
       24.00        85.05        49.05         1.02        38.04        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        47.61       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20        68.32        36.36        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 
       31.27        34.62        86.60        66.81        39.42        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       22.98        22.55        17.33        11.84        12.30         8.38 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        7.23        36.30        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 
       13.84        42.25        11.47         9.76        38.07        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       15.68         0.26        48.10        44.91        34.78         6.12 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
        1.22        57.57        24.26        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       18.77        22.49         6.71        42.51        44.12        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        24.23        24.69        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 
       18.31        20.52        14.17         6.05        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 
       21.14        22.32        29.00        25.08       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
       44.81        11.11        20.94        31.43        18.54         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       33.67         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
        9.07        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 
       38.17         2.01         5.52        17.98         4.01        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
       71.74        61.64        58.39        60.62        65.52         6.48 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       20.68        44.52       125.75        22.22         6.35        31.07 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       39.68        18.94         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       17.98        35.57        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       34.19        32.88        14.66         6.71        35.44        19.99 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.20        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 
       11.38        11.54        38.01       111.78        56.71        58.65 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
      107.28        20.35        87.48        45.99        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.31        13.61       107.18       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       92.42        95.15       145.45       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       66.15       134.04        19.36       127.79       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       60.59       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       84.53        48.76        83.74        85.94 

  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                         0.79                          0.26 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                       118.42                        180.20 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                        33.11                         32.70 
[1] "0.8 - 118.4 (33.1)" "0.3 - 180.2 (32.7)"
[1] "hr=" "1.2"
D8V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  8(4Q13.3) MUTATED         1   110                1
  AMP PEAK  8(4Q13.3) WILD-TYPE       2   448                1
D8V3, multiclass
                  clus
vv                 AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  OMENTUM                                    1                             2
  OVARY                                    110                           448
  PERITONEUM OVARY                           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"
D8V4, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED   108   2
  AMP PEAK  8(4Q13.3) WILD-TYPE 433   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED    108    2
  AMP PEAK  8(4Q13.3) WILD-TYPE  433    3
     clus
vv    AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  NO                          108                           433
  YES                           2                             3
[1] 2 2
[1] FALSE
D8V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  8(4Q13.3) MUTATED    0  4  2  0
  AMP PEAK  8(4Q13.3) WILD-TYPE 15 22  3  3
D8V6, multiclass
    clus
vv   AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  R0                           0                            15
  R1                           4                            22
  R2                           2                             3
  RX                           0                             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"
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED     1  59
  AMP PEAK  8(4Q13.3) WILD-TYPE   9 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED      1   59
  AMP PEAK  8(4Q13.3) WILD-TYPE    9  268
                        clus
vv                       AMP PEAK  8(4Q13.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          59
                        clus
vv                       AMP PEAK  8(4Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           268
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(5P15.33) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(5P15.33) MUTATED   124 173
  AMP PEAK  9(5P15.33) WILD-TYPE 104 158
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           297                            262 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           173                            158 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 
       20.52        11.87        43.92         2.01         1.08        18.51 
TCGA-04-1346 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       65.52        21.57        63.98        49.28        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 
       76.57       103.40        56.55        19.99         0.79       119.08 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1654 TCGA-09-1659 TCGA-09-1661 
       84.20        27.88        64.64        47.70         9.99        38.43 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 
       89.33        41.62        57.60        17.98         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
       97.55         6.18         6.12        35.15       112.41        71.11 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 
       39.75        20.94        12.46        77.10        81.17        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1488 
       55.23        57.27        17.46        87.06       124.44        70.82 
TCGA-13-1489 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1501 
       83.93       125.56        90.38         4.24       127.27        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       34.82        65.69        34.16        65.52        80.15        44.68 
TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       14.53        77.88        76.90        65.52        70.45         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 
       23.05        25.94        26.20        27.52        25.38        16.70 
TCGA-20-1686 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
        2.93        15.39        26.83        32.09        49.41         8.81 
TCGA-23-1032 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
        2.76         3.22        68.68        19.46        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 
        4.27         6.38        39.09        58.13         0.53        91.66 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 
       49.84         2.76         4.70         4.50        21.80        41.56 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       22.32        54.12         6.31         7.82         7.99         7.86 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        6.25         6.02         5.95         4.83        17.39        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 
       18.67        43.53         8.55        72.92        45.14       105.99 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 TCGA-24-1552 
        9.11         1.18        26.96        57.40        56.58        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1603 TCGA-24-1604 
       58.09        88.50        70.62        39.88        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 
       48.33        38.24         3.72         3.81        11.28         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        9.80        22.68        30.21        11.05        81.11         4.87 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 
      152.02        34.82        55.92        18.48        28.18        57.07 
TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       36.16        47.54        70.45        44.61         0.82        67.36 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1318 TCGA-25-1319 
       16.64        33.11        55.86        53.26        34.98        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 TCGA-25-1630 
       33.96         2.99        15.02        18.58        12.95        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-2392 
        0.30        59.15        35.87        14.96        24.00         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 
       38.04         3.02        45.01        29.03        78.90        48.33 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1761 TCGA-29-1763 
      101.79        40.41        33.93        31.20        17.36        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 
       62.93        39.42        31.30        22.98        24.36        17.33 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 
       12.30         8.38         5.36        65.00        45.11        21.47 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1860 TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 
       51.91         2.47        44.91        36.62        24.26        30.05 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 
       18.77        22.49         2.20        28.77        29.10        30.08 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       27.85        24.69        35.05        25.08        21.60         2.24 
TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       20.98        20.52        14.17        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       23.74        28.93        10.42         1.48        24.03        11.38 
TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 
        1.74        29.00        25.08        25.02       180.20       116.12 
TCGA-59-2354 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1733 TCGA-61-1738 
       34.39        20.94        31.43        27.88        31.79        35.80 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1914 TCGA-61-1917 
        8.42        11.41        13.02        34.13        56.61        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       15.75        38.17         4.01        30.64        39.85        30.64 
TCGA-61-2087 TCGA-61-2098 TCGA-61-2101 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 
        4.80        65.52        55.50       125.75         6.35         8.61 
TCGA-OY-A56P TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0927 TCGA-10-0930 
       39.68        57.76        17.98        35.57        81.86        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0936 TCGA-10-0937 TCGA-13-0723 TCGA-13-0725 
       32.88        14.66        36.92        19.99        39.58        12.39 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0766 
       15.19        17.82        55.17        11.18        11.54        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       58.65        40.24       118.42       107.28        63.09        20.35 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0883 TCGA-13-0884 
       45.99        51.02        43.86        35.28        68.94       107.18 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0899 
      153.37        66.67        95.15       145.45        43.36        66.15 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0911 
       19.36       127.79        50.37       123.16       118.98        44.55 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       48.79        83.74        85.94 

$`AMP PEAK  9(5P15.33) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 
       13.81        41.00         1.81        49.15        46.62        11.87 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1371 
       63.09        48.76        65.46         0.53        32.52        82.39 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       41.59        38.37        29.10        55.43        48.89        28.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1664 TCGA-09-1667 TCGA-09-1668 
       36.23        31.86        45.37        74.93        61.87        55.36 
TCGA-09-1669 TCGA-09-1672 TCGA-09-2048 TCGA-09-2051 TCGA-09-2055 TCGA-13-1405 
       30.51         5.85         4.54        63.09        26.93        28.54 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
       81.01        32.35        54.64        61.71        29.42        20.68 
TCGA-13-1487 TCGA-13-1491 TCGA-13-1494 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       22.39        52.44        93.90        66.15       115.07        13.97 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-20-0996 TCGA-20-1684 TCGA-20-1687 
       54.25        80.02        78.48        72.20        19.10         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 
       47.54        49.68        40.54        29.13        18.90        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1117 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 
       54.51        31.20        33.30        33.47        24.95       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 TCGA-24-1104 
       87.48        77.00         7.63        11.64         7.66        63.55 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1422 TCGA-24-1426 TCGA-24-1430 TCGA-24-1464 
       47.41         6.38         0.76         5.36        28.37        12.46 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
        3.45        22.22        64.27        16.21        41.06        51.91 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 TCGA-24-1927 
       17.23         8.32         3.48         4.37         5.79        16.44 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2036 TCGA-24-2038 
       44.84        58.16       109.71        14.43        64.01        44.52 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2290 TCGA-25-1312 TCGA-25-1313 
        0.79         0.36        31.63        36.23         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 
       33.01        52.04        42.05         2.01        37.97        12.99 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 
       27.62        17.03        20.61        62.17        52.04        24.99 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 
       85.05        13.02        49.05        12.00        19.99        42.02 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 TCGA-29-1698 
        2.96        31.00        26.99        47.61        39.02        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       36.36        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       31.27        34.62        86.60        22.55        12.36        11.84 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 
       14.93         7.23        36.30        86.17        62.47        13.84 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 
       42.25        11.47         9.76        35.77        38.07        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 
       15.68         0.26        48.10        34.78         6.12         1.22 
TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 
       57.57        48.79        45.57        30.18         6.71        42.51 
TCGA-31-1956 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       44.12        21.53        22.85        22.55         8.55        25.74 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 
       24.23        33.01        29.49        29.82        25.91        23.80 
TCGA-36-2545 TCGA-36-2549 TCGA-42-2589 TCGA-42-2591 TCGA-57-1584 TCGA-57-1586 
       18.31         6.05        42.02        40.77        21.14        22.32 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       80.12        22.32         9.40         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 
       11.11         8.09        18.54         4.34        28.47        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 
       44.84         2.43        33.67        43.69         1.45         5.79 
TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 
        9.07        31.30        37.05        42.51        48.92        67.76 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 
        2.01         5.52        14.50        17.98         1.18        45.96 
TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.40         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 
       60.62         6.48        76.87        20.68        44.52        22.22 
TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       31.07        18.94         0.79         9.99        29.16         9.47 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0934 TCGA-10-0935 TCGA-10-0938 
       54.31        25.91        18.51         6.71        35.44        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 TCGA-13-0755 
        6.21        24.59        44.55         2.73        31.20         2.50 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0797 TCGA-13-0799 
       11.38        38.01       111.78        61.84        69.73        83.34 
TCGA-13-0800 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0888 TCGA-13-0891 
       87.48        35.31        13.61       111.39        92.42       102.84 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
       71.74       134.04        60.59       116.65        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-2071 
       58.68        84.53        48.76        25.41 

  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                          0.30                           0.26 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                        180.20                         134.04 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                        33.960                         31.465 
[1] "0.3 - 180.2 (34.0)" "0.3 - 134.0 (31.5)"
[1] "hr=" "1.2"
D9V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  9(5P15.33) MUTATED         1   298                2
  AMP PEAK  9(5P15.33) WILD-TYPE       2   260                0
D9V3, multiclass
                  clus
vv                 AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     298                            260
  PERITONEUM OVARY                            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"
D9V4, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED   293   1
  AMP PEAK  9(5P15.33) WILD-TYPE 248   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED    293    1
  AMP PEAK  9(5P15.33) WILD-TYPE  248    4
     clus
vv    AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  NO                           293                            248
  YES                            1                              4
[1] 2 2
[1] FALSE
D9V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  9(5P15.33) MUTATED    5 16  4  1
  AMP PEAK  9(5P15.33) WILD-TYPE 10 10  1  2
D9V6, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  R0                            5                             10
  R1                           16                             10
  R2                            4                              1
  RX                            1                              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"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED     6 169
  AMP PEAK  9(5P15.33) WILD-TYPE   4 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED      6  169
  AMP PEAK  9(5P15.33) WILD-TYPE    4  158
                        clus
vv                       AMP PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          169
                        clus
vv                       AMP PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            158
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6P22.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(6P22.3) MUTATED   133 158
  AMP PEAK 10(6P22.3) WILD-TYPE  95 173
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          291                           268 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          158                           173 
$`AMP PEAK 10(6P22.3) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1341 TCGA-04-1342 
       20.52        11.87        43.92         1.81         1.08        18.51 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 
       65.52        63.09        48.76        21.57        65.46         0.53 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       44.32        33.67        82.39        41.59        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1651 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       29.10        84.20        36.23         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 
       41.62        57.60        61.87        55.36        30.51         3.02 
TCGA-09-2043 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.18         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       20.94        26.93        81.17        83.31        55.23        57.27 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 
       17.46        32.35        54.64        87.06        29.42       124.44 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 
       22.39        70.82        83.93        93.90         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1505 TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 
       66.15       115.07        65.69        44.68        80.02        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0991 
       77.88        76.90        65.52        70.45        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       27.52        25.38        16.70         2.93         2.66        49.68 
TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       40.54        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 
       51.35        54.51        68.68        19.46        33.30       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        4.27         6.38        39.09        58.13         0.53       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2641 TCGA-23-2643 TCGA-24-0982 TCGA-24-1413 
       87.48        91.66         2.76         4.70        22.32         6.31 
TCGA-24-1417 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1428 TCGA-24-1430 
        7.82         6.25         6.02         5.95        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 
       18.64        43.53        12.46         9.11         3.45        22.22 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 
       51.91        58.09        88.50        70.62        19.53        47.70 
TCGA-24-1564 TCGA-24-1604 TCGA-24-1843 TCGA-24-1845 TCGA-24-1847 TCGA-24-1920 
       25.87        88.37         3.48         3.81        11.28         9.80 
TCGA-24-1927 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 
       16.44       152.02        34.82        55.92        18.48        64.01 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 
       57.07        36.16         0.79        47.54        44.61         0.82 
TCGA-24-2293 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 
       16.64         1.02        26.96        33.01         2.01        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1627 TCGA-25-1630 
       65.00        33.96         2.99        12.99        12.95        38.20 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 
       35.87        14.96        24.99        24.00        85.05         1.02 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       38.04        12.00        45.01        42.02         2.96        29.03 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1710 
       48.33        40.41        68.32        16.93        23.93        31.27 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       66.81        62.93        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1777 TCGA-29-1778 TCGA-29-2414 TCGA-29-2425 TCGA-29-2429 
       17.33        12.30        14.93        86.17        65.00        13.84 
TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       21.47        35.77        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1891 TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 
       15.68        48.10        30.05        30.18         6.71        42.51 
TCGA-31-1959 TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 
        2.20        21.53        22.85        30.08        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2542 TCGA-36-2543 
       24.69        35.05        33.01        29.49        21.60         2.24 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       18.31        20.52        11.47        47.57        23.74        28.93 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 
        1.48        24.03         1.74        22.32        25.08        25.02 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-61-1722 TCGA-61-1730 
      116.12         9.40         2.14        44.81         8.09         4.34 
TCGA-61-1734 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       28.47        44.84         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        8.42         5.79         9.07        34.13        31.30        37.05 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       48.92        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
        5.52        14.50         4.01        30.64        39.85        30.64 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 
        4.77        71.74        60.62        65.52         6.48        76.87 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q 
      125.75        22.22         6.35        31.07         8.61        18.94 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0928 
        9.99        29.16        57.76        17.98        54.31        18.51 
TCGA-10-0933 TCGA-10-0936 TCGA-13-0717 TCGA-13-0724 TCGA-13-0751 TCGA-13-0755 
       14.66        36.92        24.59         2.73        55.17         2.50 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 
       11.18        11.54       111.78        61.84        56.71       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
      107.28        63.09        20.35        83.34        87.48        45.99 
TCGA-13-0803 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 
       43.86        68.94       111.39       153.37        92.42       145.45 
TCGA-13-0891 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0920 
      102.84       134.04        19.36       127.79       123.16        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

$`AMP PEAK 10(6P22.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       13.81        41.00        49.15         2.01        46.62        11.87 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       63.98        49.28        32.52        76.57       103.40        56.55 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       19.99         0.79        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1664 TCGA-09-1670 
       64.64        31.86        47.70        45.37        74.93        17.98 
TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2056 
        5.85         8.55        97.55         6.12        35.15        12.46 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1410 TCGA-13-1482 TCGA-13-1485 TCGA-13-1491 
       77.10        28.54        81.01        61.71        20.68        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 
      125.56        90.38        13.97        43.20        34.82        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-A5FU TCGA-20-0987 
       65.52        80.15        54.25        14.53         8.42        23.05 
TCGA-20-0996 TCGA-20-1684 TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1032 
       72.20        19.10        47.54        15.39        26.83         2.76 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1118 TCGA-23-1123 TCGA-23-2072 TCGA-23-2081 
        3.22        31.20        86.01        33.47        24.95        77.00 
TCGA-23-2084 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       49.84         4.50         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1418 
        7.66        54.12        63.55        47.41         6.38         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 
        7.86         0.76         5.36         4.83        18.67         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
       72.92        45.14       105.99         1.18        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1557 
       64.27        16.21        56.58        41.06        41.39        39.88 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 
       44.09        45.50        10.26        17.23        90.15        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 
       38.24         8.32         3.72         4.37         5.79         5.52 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
       22.68        30.21        11.05        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2038 TCGA-24-2262 
       58.16       109.71        14.43        28.18        44.52         0.36 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 
       31.63        70.45        67.36        36.23        33.11        55.86 
TCGA-24-2298 TCGA-25-1315 TCGA-25-1316 TCGA-25-1320 TCGA-25-1329 TCGA-25-1623 
       53.26        52.04        42.05        37.97        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       27.62        17.03        20.61         0.30        59.15        62.17 
TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2399 TCGA-25-2408 
       52.04        13.02        49.05         3.02        19.99        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       26.99        78.90        47.61       101.79        39.02        33.93 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       31.20        36.36        59.67        18.25        41.98        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 TCGA-29-1775 TCGA-29-1776 TCGA-29-1781 
       17.36        86.60        39.42        12.36        11.84         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 
        7.23         5.36        36.30        62.47        45.11        42.25 
TCGA-29-2434 TCGA-29-2436 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       11.47         9.76         0.26        44.91        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
       36.62         1.22        57.57        24.26        48.79        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 
       18.77        22.49        44.12        28.77        29.10        22.55 
TCGA-36-1575 TCGA-36-1577 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
        8.55        25.74        29.82        25.91        25.08        23.80 
TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2589 TCGA-42-2590 
       20.98        14.17         6.05        16.18        42.02        10.42 
TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 
       40.77        11.38        21.14        29.00       180.20        80.12 
TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
       22.32        34.39         5.42        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1901 
       18.54        27.88        31.79        48.79        35.80        11.41 
TCGA-61-1903 TCGA-61-1911 TCGA-61-1995 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 
       13.02        42.51         2.01        17.98         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 
       45.40         4.80        51.72        61.64        58.39        55.50 
TCGA-61-2109 TCGA-61-2110 TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0365 TCGA-09-0369 
       20.68        44.52        39.68         0.79         9.47        35.57 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 
       25.91        81.86        34.19        32.88         6.71        35.44 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       19.99        20.91         6.21        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0758 TCGA-13-0761 TCGA-13-0768 
       31.20        15.19        17.82        11.38        38.01        58.65 
TCGA-13-0791 TCGA-13-0797 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       40.24        69.73        51.02        35.28        35.31        13.61 
TCGA-13-0884 TCGA-13-0887 TCGA-13-0889 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
      107.18        66.67        95.15        43.36        71.74        66.15 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
      109.32        58.68        84.53        48.76 

  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                         0.53                          0.26 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                       153.37                        180.20 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                       31.300                        34.045 
[1] "0.5 - 153.4 (31.3)" "0.3 - 180.2 (34.0)"
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 10(6P22.3) MUTATED         2   292                1
  AMP PEAK 10(6P22.3) WILD-TYPE       1   266                1
D10V3, multiclass
                  clus
vv                 AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    292                           266
  PERITONEUM OVARY                           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"
D10V4, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED   285   3
  AMP PEAK 10(6P22.3) WILD-TYPE 256   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED    285    3
  AMP PEAK 10(6P22.3) WILD-TYPE  256    2
     clus
vv    AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  NO                          285                           256
  YES                           3                             2
[1] 2 2
[1] FALSE
D10V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 10(6P22.3) MUTATED    9 13  2  2
  AMP PEAK 10(6P22.3) WILD-TYPE  6 13  3  1
D10V6, multiclass
    clus
vv   AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  R0                           9                             6
  R1                          13                            13
  R2                           2                             3
  RX                           2                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED     4 186
  AMP PEAK 10(6P22.3) WILD-TYPE   6 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED      4  186
  AMP PEAK 10(6P22.3) WILD-TYPE    6  141
                        clus
vv                       AMP PEAK 10(6P22.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         186
                        clus
vv                       AMP PEAK 10(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           141
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7Q36.3) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7Q36.3) MUTATED   140 168
  AMP PEAK 11(7Q36.3) WILD-TYPE  88 163
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                          308                           251 
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                          168                           163 
$`AMP PEAK 11(7Q36.3) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 
       20.52        11.87         2.01        46.62         1.08        18.51 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 
       63.09        21.57        65.46         0.53        32.52        44.32 
TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       33.67       103.40        82.39        56.55        41.59        19.99 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 
       29.10        84.20        48.89        27.88        64.64        36.23 
TCGA-04-1652 TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       31.86        45.37        38.43        89.33        41.62        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       61.87        30.51        17.98         5.85         3.02         8.55 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        6.18        35.15       112.41        63.09        39.75        20.94 
TCGA-09-2055 TCGA-13-1404 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       26.93        81.17        83.31        81.01        17.46        32.35 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1492 
       87.06        29.42       124.44        20.68        83.93       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 
       93.90        90.38         4.24       127.27       115.07        43.20 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2057 
       65.69        34.16        65.52        80.15        44.68        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       78.48        77.88        76.90        65.52        70.45         8.42 
TCGA-20-0987 TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       23.05        26.20        27.52        16.70         2.93         2.66 
TCGA-23-1022 TCGA-23-1026 TCGA-23-1027 TCGA-23-1031 TCGA-23-1032 TCGA-23-1111 
       49.68        26.83        32.09        18.90         2.76         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       31.20        68.68        86.01       129.96         4.27         6.38 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0979 
       49.84         2.76         4.70         4.50         7.63        41.56 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1424 
       54.12        63.55         6.31         7.82         7.99         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        5.95         5.36        28.37        18.64        18.67         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 
       12.46        45.14         1.18        22.22        26.96        64.27 
TCGA-24-1548 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
       16.21        39.88        19.53        48.33         8.32         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
        3.81         4.37        11.28         5.52         9.80        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2033 TCGA-24-2038 
       11.05        81.11         4.87       152.02        18.48        44.52 
TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 
       57.07         0.79         0.36        47.54        70.45         0.82 
TCGA-24-2290 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       36.23        53.26         1.02        26.96        33.01        52.04 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
        2.01        34.98        33.96         2.99        12.99        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
       17.03        12.95        20.61        14.96        24.99        85.05 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-29-1691 
       38.04         3.02        45.01        42.02         2.96        48.33 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 
       40.41        31.20        68.32        36.36        18.25        41.98 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 
       34.62        17.36        66.81        62.93        22.98        24.36 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        12.30        14.93         8.38         7.23         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 
       86.17        65.00        45.11        13.84        21.47        11.47 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 
       35.77        51.91        36.26         0.26        44.91        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1891 TCGA-31-1944 TCGA-31-1950 
        6.12        36.62         1.22        30.05        45.57        18.77 
TCGA-31-1953 TCGA-31-1955 TCGA-36-1568 TCGA-36-1577 TCGA-36-2529 TCGA-36-2537 
        6.71        42.51        28.77        25.74        35.05        25.91 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       21.60         2.24        18.31        20.52        14.17         6.05 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       11.47        47.57        23.74        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 
       24.03        22.32        25.08       180.20        80.12       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
        9.40         2.14        44.81        31.43        27.88         4.34 
TCGA-61-1733 TCGA-61-1737 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       31.79        44.84        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02         9.07        34.13        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1998 TCGA-61-2003 
       48.92        56.61        67.76        15.75         5.52         4.01 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2101 
       45.40         4.80         4.77        71.74        60.62        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2614 
        6.48        76.87        20.68        44.52        22.22         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0365 TCGA-09-0367 
       39.68        18.94         0.79         9.99         9.47        17.98 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-13-0717 
       25.91        81.86        18.51        34.19        32.88        24.59 
TCGA-13-0724 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0762 TCGA-13-0766 
        2.73        55.17        11.18        11.38       111.78        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 
       58.65        40.24       118.42        20.35        69.73        45.99 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0887 
       43.86        35.31        13.61        68.94       111.39        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 
       92.42       145.45       102.84        43.36        66.15        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0908 TCGA-13-0912 TCGA-13-0920 TCGA-13-0923 
      127.79        50.37        60.59        37.64        48.79        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

$`AMP PEAK 11(7Q36.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1343 
       13.81        43.92        41.00         1.81        49.15        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 TCGA-04-1365 TCGA-04-1519 
       65.52        48.76        63.98        49.28        76.57         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1648 TCGA-04-1654 TCGA-09-1659 
       38.37       119.08        55.43        28.64        47.70         9.99 
TCGA-09-1664 TCGA-09-1668 TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 TCGA-09-2050 
       74.93        55.36        97.55         6.12         4.54        71.11 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1477 
       12.46        77.10        28.54        55.23        57.27        54.64 
TCGA-13-1482 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1498 TCGA-13-1500 
       61.71        22.39        70.82        52.44        66.15        13.97 
TCGA-13-1504 TCGA-13-1511 TCGA-13-1512 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 
       34.82        54.25        14.53        25.94        72.20        25.38 
TCGA-20-1684 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1028 TCGA-23-1029 
       19.10        47.54        40.54        15.39        49.41         8.81 
TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1122 
       29.13        51.35        54.51        19.46        33.30        39.09 
TCGA-23-1123 TCGA-23-1809 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
       33.47         0.53        11.64        21.80         7.66        22.32 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1427 
       47.41         6.38         7.86         0.76         6.25         4.83 
TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       17.39        43.53        72.92       105.99         9.11         3.45 
TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       57.40        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       88.50        70.62        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 
       10.26        17.23        90.15        88.37        38.24         3.48 
TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
        5.79        22.68        16.44        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 
      109.71        14.43        55.92        28.18        64.01        36.16 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       31.63        44.61        67.36        16.64        33.11        55.86 
TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1329 TCGA-25-1625 TCGA-25-1630 
       42.05        65.00        37.97        15.02        27.62        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1877 
        0.30        59.15        62.17        35.87        52.04        24.00 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2399 TCGA-25-2404 
       13.02        49.05         1.02        12.00        19.99        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 
       31.00        26.99        78.90        47.61       101.79        39.02 
TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1762 
       33.93        16.93        23.93        59.67        31.27        86.60 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1785 
       39.42        31.30        22.55        17.33        11.84        36.30 
TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 
       62.47        42.25         9.76        38.07         2.47        15.68 
TCGA-30-1859 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1946 TCGA-31-1951 
       48.10        57.57        24.26        48.79        30.18        22.49 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12         2.20        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 
        8.55        30.08        27.85        24.23        24.69        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2551 
       29.49        29.82        25.08        23.80        20.98        16.18 
TCGA-42-2588 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 
       28.93         1.48        11.38        21.14         1.74        29.00 
TCGA-57-1994 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 
       25.02        22.32        34.39         5.42        11.11         8.09 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       20.94        18.54        28.47        48.79        35.80         2.43 
TCGA-61-1741 TCGA-61-1907 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 
       33.67        31.30        43.43        38.17         2.01        14.50 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98        30.64        39.85        30.64         1.18        45.96 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2111 TCGA-61-2612 
       51.72        61.64        58.39        65.52       125.75         6.35 
TCGA-61-2613 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0933 
       31.07        29.16        57.76        35.57        54.31        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        6.71        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58        12.39        31.20        15.19        17.82 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0793 TCGA-13-0794 
        2.50        11.54        38.01        61.84       107.28        63.09 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 TCGA-13-0886 
       83.34        87.48        51.02        35.28       107.18       153.37 
TCGA-13-0889 TCGA-13-0897 TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       95.15        71.74       134.04       123.16       118.98       116.65 
TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       44.55       109.32        58.68        84.53        48.76 

  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                         0.26                          0.30 
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                       180.20                        153.37 
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                        31.61                         33.93 
[1] "0.3 - 180.2 (31.6)" "0.3 - 153.4 (33.9)"
[1] "hr=" "1.2"
D11V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 11(7Q36.3) MUTATED         2   309                1
  AMP PEAK 11(7Q36.3) WILD-TYPE       1   249                1
D11V3, multiclass
                  clus
vv                 AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    309                           249
  PERITONEUM OVARY                           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"
D11V4, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q36.3) MUTATED   297   3
  AMP PEAK 11(7Q36.3) WILD-TYPE 244   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q36.3) MUTATED    297    3
  AMP PEAK 11(7Q36.3) WILD-TYPE  244    2
     clus
vv    AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE
  NO                          297                           244
  YES                           3                             2
[1] 2 2
[1] FALSE
D11V5, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 11(7Q36.3) MUTATED   11 16  3  2
  AMP PEAK 11(7Q36.3) WILD-TYPE  4 10  2  1
D11V6, multiclass
    clus
vv   AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE
  R0                          11                             4
  R1                          16                            10
  R2                           3                             2
  RX                           2                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q36.3) MUTATED     4 186
  AMP PEAK 11(7Q36.3) WILD-TYPE   6 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q36.3) MUTATED      4  186
  AMP PEAK 11(7Q36.3) WILD-TYPE    6  141
                        clus
vv                       AMP PEAK 11(7Q36.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         186
                        clus
vv                       AMP PEAK 11(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           141
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8P11.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8P11.21) MUTATED    72 129
  AMP PEAK 12(8P11.21) WILD-TYPE 156 202
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           201                            358 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           129                            202 
$`AMP PEAK 12(8P11.21) MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 
       11.87        41.00        18.51        11.87        63.09        21.57 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1542 TCGA-04-1638 
       49.28        44.32        33.67       103.40        84.20        55.43 
TCGA-04-1646 TCGA-04-1652 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       27.88        31.86        61.87        55.36        17.98         5.85 
TCGA-09-2043 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-13-1408 
        6.18       112.41        63.09        39.75        20.94        55.23 
TCGA-13-1409 TCGA-13-1481 TCGA-13-1485 TCGA-13-1489 TCGA-13-1497 TCGA-13-1504 
       57.27        87.06        20.68        83.93       127.27        34.82 
TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0991 
       34.16        54.25        80.02        76.90         8.42        26.20 
TCGA-20-1683 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 
       25.38        18.90        51.35        54.51         3.22        19.46 
TCGA-23-1118 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
       86.01         6.38        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2084 TCGA-23-2645 TCGA-24-0979 TCGA-24-1418 TCGA-24-1423 
      115.89        49.84         4.50        41.56         7.99         6.25 
TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
        4.83        18.67         8.55        12.46        45.14       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1552 
        3.45         1.18        22.22        26.96        64.27        41.39 
TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 
       58.09        70.62        39.88        19.53        25.87        17.23 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
       88.37        48.33         3.72         3.81        11.28         5.79 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-2019 TCGA-24-2023 TCGA-24-2030 
        5.52        22.68        30.21         4.87        44.84        55.92 
TCGA-24-2260 TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 TCGA-25-1317 
       36.16        47.54         0.82        67.36        33.11         2.01 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 
       34.98        37.97        33.96        15.02        18.58        12.95 
TCGA-25-1628 TCGA-25-1632 TCGA-25-1633 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       20.61        59.15        62.17        24.99        24.00        85.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-29-1691 TCGA-29-1693 TCGA-29-1697 
        1.02        38.04        45.01        48.33       101.79        31.20 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 
       68.32        16.93        23.93        17.36        66.81        62.93 
TCGA-29-1766 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-2414 TCGA-29-2428 
       39.42        12.36        12.30        14.93        86.17        45.11 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       42.25        21.47        11.47        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 TCGA-30-1892 TCGA-31-1951 TCGA-31-1953 
        2.47        48.10        34.78        48.79        22.49         6.71 
TCGA-31-1955 TCGA-36-1570 TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 
       42.51        21.53        30.08        24.69        35.05         2.24 
TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2593 TCGA-57-1582 
       14.17        16.18        47.57        28.93         1.48        24.03 
TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2352 TCGA-59-2355 
       11.38         1.74        22.32        25.02         9.40         2.14 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 TCGA-61-1740 TCGA-61-1743 
       44.81         8.09        18.54        27.88         2.43        43.69 
TCGA-61-1899 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1914 TCGA-61-2009 
        8.42        34.13        31.30        42.51        56.61        39.85 
TCGA-61-2012 TCGA-61-2088 TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 
       30.64         4.77         6.48       125.75         6.35         8.61 
TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-10-0930 
       18.94         9.99        29.16         9.47        35.57        34.19 
TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0726 TCGA-13-0730 
       35.44        36.92        24.59        39.58        31.20        17.82 
TCGA-13-0751 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 
       55.17        38.01        61.84        58.65       118.42        63.09 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       87.48        51.02        43.86        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0908 
      107.18       111.39        43.36        66.15        19.36        60.59 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0920 
       44.55        84.53        48.79 

$`AMP PEAK 12(8P11.21) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 
       46.62         1.08        65.52        48.76        63.98        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
        0.53        32.52        76.57        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1644 
       19.99         0.79        38.37       119.08        29.10        48.89 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       28.64        64.64        36.23        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       38.43        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        3.02         8.55        97.55         6.12        35.15         4.54 
TCGA-09-2050 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       71.11        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
       83.31        81.01        17.46        32.35        54.64        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       29.42       124.44        22.39        70.82        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       93.90        90.38         4.24        66.15       115.07        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       43.20        65.69        65.52        80.15        44.68        14.53 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 
       78.48        77.88        65.52        70.45        23.05        25.94 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       72.20        27.52        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 
       49.41         8.81        29.13         2.76        31.20        68.68 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-2078 TCGA-23-2079 
       33.30       129.96         4.27        39.09        87.48        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       77.00         2.76         4.70         7.63        11.64        21.80 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1425 
        6.38         7.82         7.86         0.76         6.02         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 
        5.36        17.39        28.37        18.64        43.53        72.92 
TCGA-24-1469 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
        9.11        57.40        16.21        56.58        41.06        51.91 
TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 
       88.50        44.09        45.50        47.70        10.26        90.15 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1920 TCGA-24-1927 
       38.24         8.32         3.48         4.37         9.80        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       11.05        81.11       152.02        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       14.43        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 
        0.79         0.36        31.63        70.45        44.61        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        55.86        53.26         1.02        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 
       52.04        42.05        65.00         2.99        12.99        27.62 
TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       17.03        38.20         0.30        35.87        52.04        14.96 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 
       13.02        49.05         3.02        12.00        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 
       39.02        40.41        33.93        36.36        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1768 TCGA-29-1769 
       41.98        31.27        34.62        86.60        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1781 TCGA-29-1783 
       24.36        22.55        17.33        11.84         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2436 
        5.36        36.30        65.00        62.47        13.84         9.76 
TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
       35.77        15.68         0.26        44.91         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 
        1.22        57.57        24.26        30.05        45.57        30.18 
TCGA-31-1950 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 
       18.77        44.12         2.20        28.77        29.10        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 
       22.55         8.55        25.74        27.85        24.23        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 
       20.98        18.31        20.52         6.05        11.47        23.74 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 
       42.02        10.42        40.77        21.14        29.00        25.08 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2363 
      180.20        80.12        22.32       116.12        34.39         5.42 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       11.11        20.94        31.43         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 
       48.79        44.84        35.80        33.67         1.45         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 
       11.41        13.02         9.07        37.05        48.92        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98         4.01        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.80        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 
       65.52        55.50        76.87        20.68        44.52        22.22 
TCGA-61-2613 TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 
       31.07        39.68         0.79        57.76        17.98        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.86        18.51        32.88        14.66         6.71 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 
       19.99        20.91         6.21        44.55         2.73        12.39 
TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       15.19         2.50        11.18        11.38        11.54       111.78 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       56.71        40.24       107.28        20.35        69.73        83.34 
TCGA-13-0801 TCGA-13-0804 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       45.99        35.28       153.37        66.67        92.42        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
      145.45       102.84        71.74       134.04       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      123.16       118.98       116.65        37.64       109.32        58.68 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.76        83.74        85.94        25.41 

  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                          0.53                           0.26 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                        127.27                         180.20 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                         33.67                          32.22 
[1] "0.5 - 127.3 (33.7)" "0.3 - 180.2 (32.2)"
[1] "hr=" "1.2"
D12V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 12(8P11.21) MUTATED         0   202                2
  AMP PEAK 12(8P11.21) WILD-TYPE       3   356                0
D12V3, multiclass
                  clus
vv                 AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  OMENTUM                                     0                              3
  OVARY                                     202                            356
  PERITONEUM OVARY                            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"
D12V4, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED   195   2
  AMP PEAK 12(8P11.21) WILD-TYPE 346   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED    195    2
  AMP PEAK 12(8P11.21) WILD-TYPE  346    3
     clus
vv    AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  NO                           195                            346
  YES                            2                              3
[1] 2 2
[1] FALSE
D12V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 12(8P11.21) MUTATED    5 11  3  1
  AMP PEAK 12(8P11.21) WILD-TYPE 10 15  2  2
D12V6, multiclass
    clus
vv   AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  R0                            5                             10
  R1                           11                             15
  R2                            3                              2
  RX                            1                              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"
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED     3 115
  AMP PEAK 12(8P11.21) WILD-TYPE   7 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED      3  115
  AMP PEAK 12(8P11.21) WILD-TYPE    7  212
                        clus
vv                       AMP PEAK 12(8P11.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          115
                        clus
vv                       AMP PEAK 12(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            212
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8Q24.21) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(8Q24.21) MUTATED   185 259
  AMP PEAK 13(8Q24.21) WILD-TYPE  43  72
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           444                            115 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           259                             72 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        41.00         1.81        49.15 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1349 
       46.62         1.08        18.51        11.87        65.52        21.57 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       65.46         0.53        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       76.57        41.59        19.99        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-1659 
       84.20        27.88        36.23        31.86        47.70         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       38.43        89.33        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.18         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1410 
       26.93        12.46        77.10        81.17        55.23        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       17.46        32.35        87.06        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       20.68        70.82        93.90         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
      115.07        13.97        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
       65.52        80.15        44.68        54.25        14.53        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       77.88        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       25.94        26.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
        2.93         2.66        47.54        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       51.35        54.51         3.22        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       24.95       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        2.76         4.70         4.50        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 
       22.32        54.12        63.55        47.41         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 
        7.99         7.86         0.76         6.25         5.95         4.83 
TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       17.39        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 
       45.14       105.99         3.45         1.18        22.22        57.40 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       64.27        56.58        41.06        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 
       70.62        39.88        19.53        47.70        25.87        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       90.15        88.37        48.33         8.32         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        4.37        11.28         5.79         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2030 
       16.44        11.05         4.87       152.02        44.84        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       18.48        28.18        64.01        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       67.36        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
        1.02        26.96        33.01         2.01        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       37.97        33.96         2.99        15.02        18.58        27.62 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1635 
       17.03        12.95        20.61        38.20        59.15        52.04 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
       24.00        85.05        13.02         1.02         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
       45.01        19.99        42.02         2.96        29.03        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        47.61       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32        36.36        16.93        23.93        59.67 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 
       18.25        31.27        34.62        17.36        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 
       39.42        31.30        22.98        24.36        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       86.17        65.00        62.47        45.11        13.84        42.25 
TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       21.47         9.76        35.77        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1862 
        2.47        15.68         0.26        48.10        34.78         6.12 
TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       36.62        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       30.08        25.74        27.85        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       33.01        29.82        25.91        25.08        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-42-2582 
       20.98        18.31        20.52        14.17         6.05        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       28.93        42.02        10.42        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       21.14         1.74        22.32        25.08        25.02       180.20 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 
       20.94        31.43        18.54        27.88        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
       44.84        35.80         2.43        33.67        43.69         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        5.79        11.41         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       42.51        48.92        56.61        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
       38.17         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2096 TCGA-61-2097 
       39.85         1.18         4.77        51.72        58.39        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2113 TCGA-61-2612 
       55.50         6.48        76.87        20.68        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 
       29.16         9.47        17.98        54.31        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       34.19        32.88        14.66         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       19.99        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 
        2.73        12.39        31.20        55.17         2.50        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        38.01       111.78        61.84        56.71        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0800 
       40.24       118.42       107.28        63.09        69.73        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       45.99        51.02        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0893 
       68.94       107.18       111.39        66.67       145.45        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       71.74        66.15       134.04        19.36       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 
      123.16       118.98        60.59        44.55       109.32        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.79        48.76        83.74        85.94        25.41 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1367 
       43.92         2.01        63.09        48.76        63.98       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1519 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       82.39        56.55         0.79        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1655 TCGA-09-1664 TCGA-09-2048 TCGA-09-2053 TCGA-09-2054 
       64.64        45.37        74.93         4.54        39.75        20.94 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1487 TCGA-13-1489 
       28.54        83.31        57.27        54.64        22.39        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-2057 TCGA-20-0996 TCGA-23-1032 
       52.44       125.56        90.38        80.02        72.20         2.76 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1809 TCGA-24-0966 TCGA-24-0970 TCGA-24-1413 
       31.20        68.68         0.53         7.63        11.64         6.31 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1469 TCGA-24-1544 
        6.02         5.36        28.37        18.64         9.11        26.96 
TCGA-24-1548 TCGA-24-1551 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1616 
       16.21        51.91        44.09        45.50        10.26        38.24 
TCGA-24-1843 TCGA-24-1850 TCGA-24-1930 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        3.48         5.52        81.11        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2038 TCGA-25-1315 TCGA-25-1316 TCGA-25-1323 TCGA-25-1631 
       14.43        44.52        52.04        42.05        12.99         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2391 TCGA-25-2393 
       62.17        35.87        14.96        24.99        49.05        38.04 
TCGA-25-2408 TCGA-29-1691 TCGA-29-1707 TCGA-29-1762 TCGA-29-1771 TCGA-29-1774 
       31.00        48.33        41.98        86.60        22.55        17.33 
TCGA-29-2434 TCGA-30-1860 TCGA-30-1867 TCGA-30-1880 TCGA-36-2532 TCGA-36-2540 
       11.47        44.91         1.22        57.57        29.49        23.80 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2593 TCGA-57-1992 TCGA-59-2349 
       16.18        11.47        23.74         1.48        29.00        80.12 
TCGA-59-2350 TCGA-61-1721 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1895 
       22.32        11.11         8.09         4.34        31.79         1.45 
TCGA-61-1903 TCGA-61-1995 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       13.02         2.01        30.64        45.96        45.40         4.80 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2098 TCGA-61-2110 TCGA-61-2111 TCGA-09-0366 
       71.74        61.64        65.52        44.52       125.75        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0795 
       35.57        25.91        15.19        17.82        11.18        20.35 
TCGA-13-0799 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0910 
       83.34       153.37        92.42        95.15       102.84       116.65 
TCGA-13-0912 
       37.64 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          0.26                           0.30 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        180.20                         153.37 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                         32.22                          35.87 
[1] "0.3 - 180.2 (32.2)" "0.3 - 153.4 (35.9)"
[1] "hr=" "1.1"
D13V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 13(8Q24.21) MUTATED         3   442                2
  AMP PEAK 13(8Q24.21) WILD-TYPE       0   116                0
D13V3, multiclass
                  clus
vv                 AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  OMENTUM                                     3                              0
  OVARY                                     442                            116
  PERITONEUM OVARY                            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"
D13V4, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED   431   3
  AMP PEAK 13(8Q24.21) WILD-TYPE 110   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED    431    3
  AMP PEAK 13(8Q24.21) WILD-TYPE  110    2
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                           431                            110
  YES                            3                              2
[1] 2 2
[1] FALSE
D13V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 13(8Q24.21) MUTATED   12 22  4  3
  AMP PEAK 13(8Q24.21) WILD-TYPE  3  4  1  0
D13V6, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  R0                           12                              3
  R1                           22                              4
  R2                            4                              1
  RX                            3                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED     7 262
  AMP PEAK 13(8Q24.21) WILD-TYPE   3  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      7  262
  AMP PEAK 13(8Q24.21) WILD-TYPE    3   65
                        clus
vv                       AMP PEAK 13(8Q24.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          262
                        clus
vv                       AMP PEAK 13(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             65
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(10P15.3) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(10P15.3) MUTATED    92 155
  AMP PEAK 14(10P15.3) WILD-TYPE 136 176
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                           247                            312 
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                           155                            176 
$`AMP PEAK 14(10P15.3) MUTATED`
TCGA-59-A5PD TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       20.52        41.00        46.62        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 TCGA-04-1517 TCGA-04-1530 TCGA-04-1542 
       48.76        21.57        49.28        19.99       119.08        84.20 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       27.88        64.64        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       38.43        41.62        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        5.85         3.02         8.55         6.12        35.15       112.41 
TCGA-09-2050 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 
       71.11        83.31        57.27        81.01        54.64        87.06 
TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1495 TCGA-13-1496 
      124.44        70.82        83.93        52.44        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1509 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 
      127.27        66.15        80.15        14.53        78.48        77.88 
TCGA-13-2061 TCGA-20-0987 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       76.90        23.05        25.38        16.70         2.93        47.54 
TCGA-23-1022 TCGA-23-1024 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1110 
       49.68        15.39        49.41         8.81        18.90        54.51 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       33.30        86.01         6.38        39.09        33.47        58.13 
TCGA-23-2077 TCGA-24-0970 TCGA-24-0982 TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 
      115.89        11.64        22.32        47.41         7.82         7.99 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 
        6.02         4.83        17.39        18.67         8.55        45.14 
TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 
        9.11        26.96        16.21        70.62        39.88        25.87 
TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1924 
       10.26        88.37        48.33        38.24         3.48        30.21 
TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 TCGA-24-2030 TCGA-24-2260 TCGA-24-2261 
       11.05       152.02        44.84        55.92        36.16         0.79 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        0.82        67.36        33.11        55.86        53.26         1.02 
TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 
        2.01        37.97        33.96        15.02        18.58        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 
       12.95        20.61         0.30        35.87        24.99        24.00 
TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 
       85.05        49.05         1.02        12.00        45.01         2.96 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1701 TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 
       48.33        40.41        16.93        23.93        41.98        31.27 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       66.81        39.42        22.98        17.33        12.36        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       14.93         8.38         7.23        36.30        86.17        65.00 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11        13.84        21.47        11.47         9.76        35.77 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
       51.91        36.26        15.68        44.91        34.78        36.62 
TCGA-30-1867 TCGA-30-1887 TCGA-31-1944 TCGA-31-1950 TCGA-31-1953 TCGA-36-1569 
        1.22        24.26        45.57        18.77         6.71        29.10 
TCGA-36-1571 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       22.85        25.74        27.85        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2542 TCGA-36-2543 TCGA-36-2548 TCGA-36-2549 
       33.01        29.49        21.60         2.24        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2593 
       16.18        11.47        23.74        28.93        42.02         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       24.03        11.38        22.32        25.08        25.02       180.20 
TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1728 TCGA-61-1730 
        9.40        44.81         8.09        20.94        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 TCGA-61-1904 TCGA-61-1906 
       31.79        28.47         2.43        33.67         9.07        34.13 
TCGA-61-1911 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 
       42.51        43.43        15.75        38.17         4.01        30.64 
TCGA-61-2018 TCGA-61-2088 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 
       45.40         4.77        65.52        55.50         6.48        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P 
       44.52       125.75        22.22         6.35        31.07        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 
       18.94         0.79         9.99         9.47        17.98        35.57 
TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
       34.19        14.66        35.44        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0764 
       15.19        17.82        55.17        11.18        11.54        61.84 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 
       58.65        40.24       118.42        63.09        87.48        51.02 
TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 
       13.61       107.18       111.39        66.67        92.42       102.84 
TCGA-13-0893 TCGA-13-0900 TCGA-13-0904 TCGA-13-0911 TCGA-13-0919 TCGA-13-0920 
       43.36       134.04        50.37        44.55        84.53        48.79 
TCGA-13-2071 
       25.41 

$`AMP PEAK 14(10P15.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        11.87        43.92         1.81        49.15         2.01 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 
        1.08        18.51        63.98        65.46         0.53        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       44.32        33.67        76.57       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 
       41.59         0.79        38.37        29.10        55.43        48.89 
TCGA-04-1648 TCGA-04-1651 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1675 
       28.64        36.23        89.33        74.93        57.60        97.55 
TCGA-09-2043 TCGA-09-2048 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        6.18         4.54        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 
       12.46        77.10        81.17        28.54        55.23        17.46 
TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1492 
       32.35        61.71        29.42        20.68        22.39       125.56 
TCGA-13-1494 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       93.90       115.07        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2065 
       34.16        65.52        44.68        54.25        80.02        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       70.45         8.42        25.94        26.20        72.20        27.52 
TCGA-20-1684 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1030 
       19.10         2.66        40.54        26.83        32.09        29.13 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.76        51.35         3.22        31.20        68.68        19.46 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 
      129.96         4.27         0.53        24.95        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 
       21.80        41.56         7.66        54.12        63.55         6.31 
TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        6.38         7.86         0.76         6.25         5.95         5.36 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 
       28.37        18.64        43.53        72.92        12.46       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
        3.45         1.18        22.22        57.40        64.27        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 
       41.06        51.91        41.39        58.09        88.50        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1842 
       44.09        45.50        47.70        17.23        90.15         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.72         3.81         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2024 
        9.80        22.68        16.44        81.11         4.87        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       34.82       109.71        14.43        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       44.52        57.07         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2290 TCGA-24-2293 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       44.61        36.23        16.64        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 
       42.05        34.98        65.00         2.99        12.99        27.62 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 
       38.20        59.15        62.17        52.04        14.96        13.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 
       38.04         3.02        19.99        42.02        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       26.99        78.90        47.61       101.79        39.02        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 
       31.20        68.32        36.36        59.67        18.25        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 
       17.36        86.60        62.93        31.30        24.36        22.55 
TCGA-29-1776 TCGA-29-1784 TCGA-29-2427 TCGA-29-2431 TCGA-30-1714 TCGA-30-1855 
       11.84         5.36        62.47        42.25        38.07         2.47 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
        0.26        48.10         6.12        57.57        30.05        48.79 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       30.18        22.49        42.51        44.12         2.20        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-2534 TCGA-36-2537 
       21.53        22.55         8.55        30.08        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-42-2582 
       25.08        23.80        20.98        18.31        20.52        47.57 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2349 
       10.42        40.77        21.14         1.74        29.00        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 
       22.32       116.12        34.39         2.14         5.42        11.11 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1743 
       31.43        18.54        48.79        44.84        35.80        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 
        1.45         8.42         5.79        11.41        13.02        31.30 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1995 TCGA-61-1998 
       37.05        48.92        56.61        67.76         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 
       14.50        17.98        30.64        39.85         1.18        45.96 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.80        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2104 TCGA-61-2614 TCGA-09-0364 TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 
       76.87         8.61        29.16        57.76        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       81.86        18.51        32.88         6.71        36.92        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0755 
       20.91         6.21        24.59        44.55        12.39         2.50 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 TCGA-13-0795 
       11.38        38.01       111.78        56.71       107.28        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       69.73        83.34        45.99        43.86        35.28        35.31 
TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 
       68.94       153.37        95.15       145.45        71.74        66.15 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36       127.79       123.16       118.98        60.59       116.65 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       37.64       109.32        58.68        48.76        83.74        85.94 

  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                          0.30                           0.26 
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                        180.20                         153.37 
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                        31.200                         34.045 
[1] "0.3 - 180.2 (31.2)" "0.3 - 153.4 (34.0)"
[1] "hr=" "1.2"
D14V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 14(10P15.3) MUTATED         1   245                2
  AMP PEAK 14(10P15.3) WILD-TYPE       2   313                0
D14V3, multiclass
                  clus
vv                 AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     245                            313
  PERITONEUM OVARY                            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"
D14V4, binary
                                cls
clus                               0   1
  AMP PEAK 14(10P15.3) MUTATED   239   3
  AMP PEAK 14(10P15.3) WILD-TYPE 302   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(10P15.3) MUTATED    239    3
  AMP PEAK 14(10P15.3) WILD-TYPE  302    2
     clus
vv    AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE
  NO                           239                            302
  YES                            3                              2
[1] 2 2
[1] FALSE
D14V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 14(10P15.3) MUTATED    8 16  4  1
  AMP PEAK 14(10P15.3) WILD-TYPE  7 10  1  2
D14V6, multiclass
    clus
vv   AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE
  R0                            8                              7
  R1                           16                             10
  R2                            4                              1
  RX                            1                              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"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(10P15.3) MUTATED     7 149
  AMP PEAK 14(10P15.3) WILD-TYPE   3 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(10P15.3) MUTATED      7  149
  AMP PEAK 14(10P15.3) WILD-TYPE    3  178
                        clus
vv                       AMP PEAK 14(10P15.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       AMP PEAK 14(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            178
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(10Q22.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(10Q22.3) MUTATED    80  99
  AMP PEAK 15(10Q22.3) WILD-TYPE 148 232
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                           179                            380 
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                            99                            232 
$`AMP PEAK 15(10Q22.3) MUTATED`
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
       46.62         1.08        18.51        63.09        21.57        63.98 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1365 TCGA-04-1517 TCGA-04-1530 
        0.53        49.28        44.32        76.57        19.99       119.08 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       84.20        27.88        31.86        45.37         9.99        38.43 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2044 
       57.60        61.87        17.98         5.85         8.55         6.12 
TCGA-09-2048 TCGA-09-2055 TCGA-13-1405 TCGA-13-1477 TCGA-13-1484 TCGA-13-1495 
        4.54        26.93        28.54        54.64       124.44        90.38 
TCGA-13-1496 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.24        34.82        65.52        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1682 TCGA-20-1685 TCGA-20-1687 
       14.53        70.45        25.94        27.52        16.70         2.66 
TCGA-23-1021 TCGA-23-1032 TCGA-23-1110 TCGA-23-1117 TCGA-23-1118 TCGA-23-1123 
       47.54         2.76        54.51        33.30        86.01        33.47 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0982 
      115.89        91.66         4.70         4.50        11.64        22.32 
TCGA-24-1104 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 
       63.55         6.25         6.02         4.83        17.39        18.67 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1563 
       16.21        56.58        51.91        58.09        70.62        47.70 
TCGA-24-1564 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1849 TCGA-24-1927 
       25.87         8.32         3.72        11.28         5.79        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2261 TCGA-24-2288 TCGA-24-2293 
       11.05        81.11         4.87         0.79         0.82        16.64 
TCGA-24-2297 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1323 
       55.86        33.01         2.01        34.98        33.96        12.99 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1634 TCGA-25-1877 TCGA-25-2042 TCGA-25-2392 
       18.58        17.03        35.87        24.00        13.02         1.02 
TCGA-25-2397 TCGA-25-2404 TCGA-29-1693 TCGA-29-1710 TCGA-29-1763 TCGA-29-1764 
       12.00        29.03       101.79        31.27        66.81        62.93 
TCGA-29-1766 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 
       39.42        12.36        12.30         7.23        65.00        45.11 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1855 TCGA-30-1860 TCGA-30-1861 
        9.76        35.77        36.26         2.47        44.91        34.78 
TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 
       36.62         1.22        18.77        27.85        24.23        35.05 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 TCGA-36-2552 
       29.49        29.82         2.24        20.52        14.17        11.47 
TCGA-42-2588 TCGA-57-1583 TCGA-57-1585 TCGA-59-2348 TCGA-59-2351 TCGA-59-2363 
       28.93        11.38         1.74       180.20       116.12         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        20.94        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1901 TCGA-61-1904 TCGA-61-1910 
       31.79        48.79        44.84        11.41         9.07        37.05 
TCGA-61-1915 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2096 
       67.76        14.50         4.01        30.64        30.64        58.39 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       65.52        55.50         6.48        20.68        44.52       125.75 
TCGA-61-2612 TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0365 TCGA-10-0928 TCGA-10-0930 
        6.35        18.94         9.99         9.47        18.51        34.19 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
        6.21        44.55        15.19        17.82        55.17        11.18 
TCGA-13-0762 TCGA-13-0791 TCGA-13-0792 TCGA-13-0802 TCGA-13-0884 TCGA-13-0885 
      111.78        40.24       118.42        51.02       107.18       111.39 
TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 
       66.67       145.45       102.84        43.36       134.04        19.36 
TCGA-13-0905 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
      123.16       109.32        84.53        48.79        83.74 

$`AMP PEAK 15(10Q22.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 
       49.15         2.01        11.87        65.52        48.76        65.46 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       32.52        33.67       103.40        82.39        56.55        41.59 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
        0.79        38.37        29.10        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       64.64        36.23        47.70        89.33        74.93        41.62 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 
       55.36        30.51         3.02        97.55         6.18        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 
      112.41        71.11        63.09        39.75        20.94        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       77.10        81.17        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
       17.46        32.35        87.06        61.71        29.42        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
      127.27        66.15       115.07        13.97        43.20        65.69 
TCGA-13-1506 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       34.16        80.02        78.48        77.88        76.90        65.52 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
        8.42        23.05        26.20        72.20        25.38        19.10 
TCGA-20-1686 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.93        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 
       49.41         8.81        29.13        18.90        51.35         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       31.20        68.68        19.46       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2081 
       39.09        58.13         0.53        24.95        87.48        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
       49.84         2.76         7.63        21.80        41.56         7.66 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       54.12        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 
        7.86         0.76         5.95         5.36        28.37        18.64 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       43.53         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 
       64.27        41.06        41.39        88.50        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       44.09        45.50        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 
       48.33        38.24         3.48         3.81         4.37         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
        9.80        22.68        30.21       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 
       64.01        44.52        57.07        36.16         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 
       31.63        70.45        44.61        67.36        36.23        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 
       53.26         1.02        26.96        52.04        42.05        65.00 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 
       37.97         2.99        15.02        27.62        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 
       38.20         0.30        59.15        62.17        52.04        14.96 
TCGA-25-1871 TCGA-25-1878 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       24.99        85.05        49.05        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       19.99        42.02         2.96        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       47.61        48.33        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1768 TCGA-29-1769 
       41.98        34.62        17.36        86.60        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 
       24.36        22.55        17.33        11.84        14.93         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        5.36        36.30        86.17        62.47        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1856 TCGA-30-1857 
       21.47        11.47        38.07        51.91        15.68         0.26 
TCGA-30-1859 TCGA-30-1862 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       48.10         6.12        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       45.57        30.18        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1581 TCGA-36-2530 TCGA-36-2537 
        8.55        30.08        25.74        24.69        33.01        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 
       25.08        23.80        21.60        20.98        18.31         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       16.18        47.57        23.74        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
        1.48        24.03        21.14        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       25.02        80.12        22.32         9.40        34.39         2.14 
TCGA-61-1721 TCGA-61-1725 TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       11.11        31.43        28.47        35.80         2.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1906 
       43.69         1.45         8.42         5.79        13.02        34.13 
TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 
       31.30        42.51        48.92        56.61        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 
       38.17         2.01         5.52        17.98        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2104 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 
       61.64        60.62        76.87        22.22        31.07         8.61 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       39.68         0.79        29.16        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       54.31        25.91        81.86        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 
       35.44        36.92        19.99        20.91        24.59        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 
        2.73        12.39        31.20         2.50        11.38        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0793 TCGA-13-0794 
       38.01        61.84        56.71        58.65       107.28        63.09 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 
       20.35        69.73        83.34        87.48        45.99        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0888 
       35.28        35.31        13.61        68.94       153.37        92.42 
TCGA-13-0889 TCGA-13-0897 TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       95.15        71.74        66.15       127.79        50.37       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0921 
       60.59       116.65        44.55        37.64        58.68        48.76 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                          0.53                           0.26 
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                        180.20                         153.37 
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                        29.490                         34.145 
[1] "0.5 - 180.2 (29.5)" "0.3 - 153.4 (34.1)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 15(10Q22.3) MUTATED         2   177                2
  AMP PEAK 15(10Q22.3) WILD-TYPE       1   381                0
D15V3, multiclass
                  clus
vv                 AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     177                            381
  PERITONEUM OVARY                            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"
D15V4, binary
                                cls
clus                               0   1
  AMP PEAK 15(10Q22.3) MUTATED   174   2
  AMP PEAK 15(10Q22.3) WILD-TYPE 367   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(10Q22.3) MUTATED    174    2
  AMP PEAK 15(10Q22.3) WILD-TYPE  367    3
     clus
vv    AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE
  NO                           174                            367
  YES                            2                              3
[1] 2 2
[1] FALSE
D15V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 15(10Q22.3) MUTATED    6  7  1  2
  AMP PEAK 15(10Q22.3) WILD-TYPE  9 19  4  1
D15V6, multiclass
    clus
vv   AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE
  R0                            6                              9
  R1                            7                             19
  R2                            1                              4
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(10Q22.3) MUTATED     3 106
  AMP PEAK 15(10Q22.3) WILD-TYPE   7 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(10Q22.3) MUTATED      3  106
  AMP PEAK 15(10Q22.3) WILD-TYPE    7  221
                        clus
vv                       AMP PEAK 15(10Q22.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       AMP PEAK 15(10Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            221
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(11Q14.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(11Q14.1) MUTATED   101 143
  AMP PEAK 16(11Q14.1) WILD-TYPE 127 188
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                           244                            315 
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                           143                            188 
$`AMP PEAK 16(11Q14.1) MUTATED`
TCGA-3P-A9WA TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 TCGA-04-1350 TCGA-04-1356 
       13.81         1.08        11.87        65.52        63.98        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        76.57       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 
       41.59        29.10        84.20        27.88        64.64        31.86 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 
        9.99        38.43        89.33        41.62        61.87        55.36 
TCGA-09-1673 TCGA-09-2044 TCGA-09-2048 TCGA-09-2051 TCGA-09-2055 TCGA-13-1403 
        3.02         6.12         4.54        63.09        26.93        77.10 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       81.17        83.31        55.23        81.01        17.46        32.35 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1497 TCGA-13-1499 
       87.06        29.42        22.39        83.93       127.27       115.07 
TCGA-13-1501 TCGA-13-1506 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 
       43.20        34.16        80.02        78.48        77.88        65.52 
TCGA-13-A5FU TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
        8.42        25.38        19.10        16.70         2.93        47.54 
TCGA-23-1022 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       49.68        32.09         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1116 TCGA-23-1119 TCGA-23-1120 TCGA-23-1124 
       51.35         3.22        19.46       129.96         4.27        58.13 
TCGA-23-2072 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 
       24.95        91.66        49.84         4.70         4.50        21.80 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 
       54.12        63.55        47.41         7.82         7.99         0.76 
TCGA-24-1423 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        6.25         4.83        17.39        18.64        18.67         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 TCGA-24-1549 
       72.92        45.14         9.11         1.18        57.40        56.58 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 
       51.91        58.09        70.62        39.88        19.53        47.70 
TCGA-24-1564 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       25.87        88.37        38.24         8.32         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-2026 
        4.37        11.28         9.80        30.21        16.44        34.82 
TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2262 
      109.71        55.92        18.48        28.18        57.07         0.36 
TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2298 TCGA-25-1312 
       47.54        44.61         0.82        67.36        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1623 
       26.96        33.01        65.00        33.96         2.99        18.58 
TCGA-25-1627 TCGA-25-1631 TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 
       12.95         0.30        52.04        24.00        85.05         1.02 
TCGA-25-2400 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1701 
       42.02        48.33       101.79        40.41        31.20        16.93 
TCGA-29-1702 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 
       23.93        66.81        62.93        31.30        22.98        17.33 
TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 TCGA-29-2425 TCGA-29-2429 TCGA-29-2434 
       11.84        14.93         7.23        65.00        13.84        11.47 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       35.77        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1891 TCGA-31-1946 
       44.91        34.78         6.12        36.62        30.05        30.18 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 
        2.20        28.77        21.53        22.55        30.08        27.85 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2534 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 
       24.23        33.01        29.82        20.52         6.05        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       11.47        23.74         1.48        11.38        21.14         1.74 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-61-1722 
       25.02       180.20       116.12         9.40         2.14         8.09 
TCGA-61-1728 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1906 
       27.88        35.80         2.43        43.69         1.45        34.13 
TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       31.30        42.51        48.92        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2018 TCGA-61-2087 
       38.17        17.98        30.64        30.64        45.40         4.80 
TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2109 TCGA-61-2612 
       71.74        60.62        65.52        76.87        20.68         6.35 
TCGA-VG-A8LO TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0931 TCGA-10-0935 
        0.79        57.76        17.98        35.57        32.88        35.44 
TCGA-10-0936 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0726 TCGA-13-0751 
       36.92         6.21        44.55        39.58        31.20        55.17 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0791 TCGA-13-0792 
        2.50        11.54        38.01       111.78        40.24       118.42 
TCGA-13-0802 TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       51.02       111.39        66.67       145.45       102.84        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0919 
       71.74        66.15        50.37       123.16        60.59        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-2071 
       48.79        48.76        83.74        25.41 

$`AMP PEAK 16(11Q14.1) WILD-TYPE`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       20.52        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
        2.01        46.62        18.51        63.09        48.76        21.57 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1364 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       65.46         0.53        33.67        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 
      119.08        55.43        48.89        28.64        36.23        47.70 
TCGA-04-1655 TCGA-09-1664 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       45.37        74.93        57.60        30.51        17.98         5.85 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.18        35.15       112.41        71.11 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-13-1405 TCGA-13-1409 TCGA-13-1477 
       39.75        20.94        12.46        28.54        57.27        54.64 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       61.71       124.44        20.68        70.82        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 
       93.90        90.38         4.24        66.15        13.97        34.82 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       65.69        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2061 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       76.90        70.45        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 
       27.52         2.66        40.54        15.39        26.83        49.41 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 
       54.51        31.20        68.68        33.30        86.01         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 
       39.09        33.47         0.53       115.89        87.48        77.00 
TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        2.76         7.63        11.64        41.56         7.66        22.32 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        6.31         6.38         7.86         6.02         5.95         5.36 
TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 
       28.37        43.53        12.46       105.99         3.45        22.22 
TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 
       26.96        64.27        16.21        41.06        41.39        88.50 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 
       44.09        45.50        10.26        17.23        90.15        48.33 
TCGA-24-1843 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1928 TCGA-24-1930 
        3.48         5.79         5.52        22.68        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2036 
        4.87       152.02        44.84        58.16        14.43        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 
       44.52        36.16         0.79        31.63        70.45        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       16.64        33.11        55.86        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 
       34.98        37.97        12.99        15.02        27.62        17.03 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 
       20.61        38.20        59.15        62.17        35.87        14.96 
TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       24.99        13.02        49.05        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 
       78.90        47.61        39.02        33.93        68.32        36.36 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 
       86.60        39.42        24.36        22.55        12.36        12.30 
TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
        8.38         5.36        36.30        86.17        62.47        45.11 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1859 TCGA-30-1867 
       42.25        21.47         9.76        38.07        48.10         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 
       57.57        24.26        48.79        45.57        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 
        6.71        42.51        44.12        29.10        22.85         8.55 
TCGA-36-1577 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
       25.74        24.69        35.05        29.49        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 
       23.80        21.60         2.24        20.98        18.31        14.17 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 
       47.57        28.93        42.02        10.42        40.77        24.03 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       22.32        29.00        25.08        80.12        22.32        34.39 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        5.42        44.81        11.11        20.94        31.43        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 
        4.34        31.79        28.47        48.79        44.84        33.67 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 
        8.42         5.79        11.41        13.02         9.07        37.05 
TCGA-61-1914 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 
       56.61         2.01         5.52        14.50         4.01        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
        1.18        45.96         4.77        51.72        61.64        58.39 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 
       55.50         6.48        44.52       125.75        22.22        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
        8.61        39.68        18.94         9.99        29.16         9.47 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 
       54.31        25.91        81.86        18.51        34.19        14.66 
TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0724 TCGA-13-0725 
        6.71        19.99        20.91        24.59         2.73        12.39 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0758 TCGA-13-0764 TCGA-13-0766 
       15.19        17.82        11.18        11.38        61.84        56.71 
TCGA-13-0768 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       58.65       107.28        63.09        20.35        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       87.48        45.99        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0900 
       68.94       107.18       153.37        92.42        95.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       19.36       127.79       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0924 
      109.32        58.68        85.94 

  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                          0.26                           0.53 
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                        180.20                         153.37 
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                         32.70                          33.11 
[1] "0.3 - 180.2 (32.7)" "0.5 - 153.4 (33.1)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 16(11Q14.1) MUTATED         1   247                0
  AMP PEAK 16(11Q14.1) WILD-TYPE       2   311                2
D16V3, multiclass
                  clus
vv                 AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     247                            311
  PERITONEUM OVARY                            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"
D16V4, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q14.1) MUTATED   239   1
  AMP PEAK 16(11Q14.1) WILD-TYPE 302   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q14.1) MUTATED    239    1
  AMP PEAK 16(11Q14.1) WILD-TYPE  302    4
     clus
vv    AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE
  NO                           239                            302
  YES                            1                              4
[1] 2 2
[1] FALSE
D16V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 16(11Q14.1) MUTATED    5  8  3  1
  AMP PEAK 16(11Q14.1) WILD-TYPE 10 18  2  2
D16V6, multiclass
    clus
vv   AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE
  R0                            5                             10
  R1                            8                             18
  R2                            3                              2
  RX                            1                              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"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q14.1) MUTATED     3 141
  AMP PEAK 16(11Q14.1) WILD-TYPE   7 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q14.1) MUTATED      3  141
  AMP PEAK 16(11Q14.1) WILD-TYPE    7  186
                        clus
vv                       AMP PEAK 16(11Q14.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       AMP PEAK 16(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            186
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(12P13.33) MUTATION ANALYSIS
D17V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 17(12P13.33) MUTATED   132 186
  AMP PEAK 17(12P13.33) WILD-TYPE  96 145
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                            318                             241 
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                            186                             145 
$`AMP PEAK 17(12P13.33) MUTATED`
TCGA-3P-A9WA TCGA-04-1332 TCGA-04-1338 TCGA-04-1341 TCGA-04-1346 TCGA-04-1347 
       13.81        41.00        46.62         1.08        65.52        63.09 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       21.57        65.46         0.53        49.28        32.52        44.32 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        41.59        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 
       29.10        84.20        27.88        36.23        31.86        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
        9.99        38.43        89.33        57.60        61.87        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2048 
       17.98         5.85         8.55         6.18         6.12         4.54 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1407 TCGA-13-1411 
       71.11        63.09        39.75        12.46        83.31        17.46 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 
      124.44        20.68        22.39        83.93        90.38         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15       115.07        43.20        34.82        65.69        34.16 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       80.15        44.68        54.25        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-1682 
       76.90        65.52        70.45         8.42        25.94        27.52 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 
       16.70         2.93         2.66        47.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1031 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       32.09        18.90         3.22        68.68        19.46        33.30 
TCGA-23-1119 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2643 
      129.96         6.38        58.13         0.53       115.89         4.70 
TCGA-23-2645 TCGA-24-0970 TCGA-24-0982 TCGA-24-1104 TCGA-24-1418 TCGA-24-1424 
        4.50        11.64        22.32        63.55         7.99         6.02 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 
        4.83        28.37        18.64        18.67         8.55        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       45.14         9.11         3.45        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 
       64.27        16.21        51.91        41.39        58.09        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       39.88        19.53        44.09        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       17.23        88.37        48.33        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 
        3.72         3.81        11.28         5.52         9.80        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 
       81.11         4.87       152.02        58.16        34.82        55.92 
TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       18.48        44.52        36.16        47.54        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
        0.82        67.36        36.23        16.64        33.11        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1318 TCGA-25-1321 TCGA-25-1323 
        1.02        26.96        33.01        34.98        33.96        12.99 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1634 TCGA-25-1635 
       27.62        17.03        12.95        38.20        35.87        52.04 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 
       24.99        24.00        85.05        13.02         1.02         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 
       12.00        45.01        42.02        26.99        47.61        48.33 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       40.41        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       59.67        31.27        17.36        66.81        62.93        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 
       31.30        22.98        17.33        12.36        12.30        14.93 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 
        7.23         5.36        86.17        65.00        45.11        42.25 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       11.47        35.77        36.26         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1950 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 
       24.26        30.05        18.77        42.51         2.20        29.10 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85         8.55        30.08        25.74        27.85        24.23 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       21.60        20.98        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 
       11.47        23.74        28.93        40.77         1.48        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 
       21.14        22.32        25.08        25.02       180.20       116.12 
TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 
        9.40         5.42        44.81         8.09        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       31.79        28.47        35.80        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42         5.79        13.02         9.07        34.13        31.30 
TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-2002 TCGA-61-2009 
       48.92        67.76        43.43        38.17        17.98        39.85 
TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 TCGA-61-2097 TCGA-61-2104 TCGA-61-2110 
       30.64        45.40         4.77        60.62        76.87        44.52 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75         6.35        31.07         8.61        39.68        18.94 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        9.99        29.16         9.47        57.76        17.98        35.57 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0937 
       25.91        81.86        18.51        34.19        14.66        19.99 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       20.91        24.59        39.58        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
        2.50        11.18        11.38        11.54        38.01       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       61.84        56.71       118.42        63.09        20.35        69.73 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 
       87.48        51.02        43.86        68.94       111.39       153.37 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0906 
       66.67        92.42        66.15        19.36        50.37       118.98 
TCGA-13-0908 TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-2071 
       60.59        37.64        58.68        48.79        83.74        25.41 

$`AMP PEAK 17(12P13.33) WILD-TYPE`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       20.52        11.87        43.92         1.81        49.15         2.01 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 TCGA-04-1364 TCGA-04-1365 
       18.51        11.87        48.76        63.98        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
      103.40        56.55        55.43        48.89        28.64        64.64 
TCGA-04-1654 TCGA-09-1664 TCGA-09-1665 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 
       47.70        74.93        41.62        30.51         3.02        97.55 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 
       35.15       112.41        20.94        26.93        77.10        81.17 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       28.54        55.23        57.27        81.01        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       87.06        61.71        29.42        70.82        52.44       125.56 
TCGA-13-1494 TCGA-13-1497 TCGA-13-1500 TCGA-13-1507 TCGA-13-1512 TCGA-20-0987 
       93.90       127.27        13.97        65.52        14.53        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-23-1022 TCGA-23-1023 
       26.20        72.20        25.38        19.10        49.68        40.54 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        29.13         2.76        51.35        54.51 
TCGA-23-1113 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 
       31.20        86.01         4.27        39.09        33.47        24.95 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 
       87.48        91.66        77.00        49.84         2.76         7.63 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 
       21.80        41.56         7.66        54.12        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        6.38         7.82         7.86         0.76         6.25         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1471 
        5.36        17.39        43.53        72.92       105.99         1.18 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1555 TCGA-24-1562 TCGA-24-1603 TCGA-24-1846 
       56.58        41.06        88.50        45.50        90.15         4.37 
TCGA-24-1849 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2023 TCGA-24-2027 
        5.79        22.68        30.21        16.44        44.84       109.71 
TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 
       14.43        28.18        64.01        57.07         0.79         0.36 
TCGA-24-2271 TCGA-24-2297 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 
       31.63        55.86        52.04        42.05         2.01        65.00 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 TCGA-25-1631 
       37.97         2.99        15.02        18.58        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 TCGA-25-2391 TCGA-25-2393 TCGA-25-2399 
       59.15        62.17        14.96        49.05        38.04        19.99 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 
        2.96        29.03        31.00        78.90       101.79        39.02 
TCGA-29-1696 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 TCGA-29-1770 
       33.93        18.25        41.98        34.62        86.60        24.36 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
       22.55        11.84         8.38        36.30        62.47        13.84 
TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1857 TCGA-30-1892 
       21.47         9.76        38.07        51.91         0.26        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 
       45.57        30.18        22.49         6.71        44.12        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       21.53        22.55        24.69        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2545 
       29.82        25.91        25.08        23.80         2.24        18.31 
TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 TCGA-57-1582 TCGA-57-1585 TCGA-57-1992 
       47.57        42.02        10.42        24.03         1.74        29.00 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 TCGA-61-1724 
       80.12        22.32        34.39         2.14        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1901 
       31.43        18.54        48.79        44.84         2.43        11.41 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       37.05        42.51        56.61        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
       14.50         4.01        30.64         1.18        45.96         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 
       51.72        71.74        61.64        58.39        65.52        55.50 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2113 TCGA-VG-A8LO TCGA-10-0925 TCGA-10-0931 
        6.48        20.68        22.22         0.79        54.31        32.88 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 
        6.71        35.44        36.92         6.21        44.55         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0799 
       12.39        31.20        58.65        40.24       107.28        83.34 
TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0889 
       45.99        35.28        35.31        13.61       107.18        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 
      145.45       102.84        43.36        71.74       134.04       127.79 
TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 
      123.16       116.65        44.55       109.32        84.53        48.76 
TCGA-13-0924 
       85.94 

  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                           0.53                            0.26 
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                         180.20                          145.45 
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                         31.285                          34.620 
[1] "0.5 - 180.2 (31.3)" "0.3 - 145.4 (34.6)"
[1] "hr=" "1.1"
D17V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 17(12P13.33) MUTATED         3   317                1
  AMP PEAK 17(12P13.33) WILD-TYPE       0   241                1
D17V3, multiclass
                  clus
vv                 AMP PEAK 17(12P13.33) MUTATED
  OMENTUM                                      3
  OVARY                                      317
  PERITONEUM OVARY                             1
                  clus
vv                 AMP PEAK 17(12P13.33) WILD-TYPE
  OMENTUM                                        0
  OVARY                                        241
  PERITONEUM OVARY                               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"
D17V4, binary
                                 cls
clus                                0   1
  AMP PEAK 17(12P13.33) MUTATED   305   5
  AMP PEAK 17(12P13.33) WILD-TYPE 236   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 17(12P13.33) MUTATED    305    5
  AMP PEAK 17(12P13.33) WILD-TYPE  236    0
     clus
vv    AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE
  NO                            305                             236
  YES                             5                               0
[1] 2 2
[1] FALSE
D17V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 17(12P13.33) MUTATED    9 12  4  3
  AMP PEAK 17(12P13.33) WILD-TYPE  6 14  1  0
D17V6, multiclass
    clus
vv   AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE
  R0                             9                               6
  R1                            12                              14
  R2                             4                               1
  RX                             3                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                 cls
clus                                0   1
  AMP PEAK 17(12P13.33) MUTATED     5 176
  AMP PEAK 17(12P13.33) WILD-TYPE   5 151
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 17(12P13.33) MUTATED      5  176
  AMP PEAK 17(12P13.33) WILD-TYPE    5  151
                        clus
vv                       AMP PEAK 17(12P13.33) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           176
                        clus
vv                       AMP PEAK 17(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             151
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(12P12.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(12P12.1) MUTATED   118 182
  AMP PEAK 18(12P12.1) WILD-TYPE 110 149
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                           300                            259 
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                           182                            149 
$`AMP PEAK 18(12P12.1) MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 
       11.87        41.00        46.62         1.08        18.51        65.52 
TCGA-04-1347 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1371 TCGA-04-1516 
       63.09        65.46        49.28        44.32        82.39        41.59 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 
       19.99        38.37       119.08        29.10        84.20        27.88 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 
       36.23        31.86        45.37         9.99        38.43        41.62 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       61.87        55.36        17.98         5.85         8.55         6.18 
TCGA-09-2044 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1411 
        6.12       112.41        63.09        39.75        12.46        17.46 
TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1494 
       87.06       124.44        20.68        70.82        83.93        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 
       90.38         4.24       127.27       115.07        34.82        65.69 
TCGA-13-1506 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       34.16        54.25        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-1682 TCGA-20-1684 
       76.90        65.52        70.45         8.42        27.52        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 
       16.70         2.93         2.66        47.54        49.68        15.39 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 
       29.13         2.76         3.22        68.68        19.46        86.01 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 
        6.38        39.09        33.47        58.13         0.53        91.66 
TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 TCGA-24-0982 TCGA-24-1105 TCGA-24-1418 
       77.00         4.70         4.50        22.32        47.41         7.99 
TCGA-24-1422 TCGA-24-1424 TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 
        0.76         6.02         4.83        18.67         8.55        45.14 
TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        9.11        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 
       58.09        39.88        19.53        44.09        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       10.26        17.23        88.37        48.33        38.24         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
        3.72         3.81        11.28         5.52         9.80        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2033 TCGA-24-2038 
       11.05        81.11         4.87       152.02        18.48        44.52 
TCGA-24-2260 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       36.16        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 
       16.64        33.11         1.02        26.96        52.04        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 
       37.97        33.96        12.99        15.02        27.62        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       12.95        20.61        38.20        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 
       24.99        24.00        85.05        13.02         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-25-2409 TCGA-29-1690 
        3.02        45.01        42.02        29.03        26.99        47.61 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 
       40.41        31.20        68.32        36.36        23.93        31.27 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 
       17.36        66.81        39.42        31.30        22.98        17.33 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        12.30        14.93         8.38         7.23         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ 
       86.17        65.00        45.11        21.47        11.47        35.77 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91        36.26         2.47         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1950 
       34.78        36.62         1.22        24.26        30.05        18.77 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 
        6.71        42.51         2.20        29.10        22.85         8.55 
TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2542 TCGA-36-2543 TCGA-36-2548 
       30.08        24.23        35.05        21.60         2.24        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
        6.05        16.18        11.47         1.48        24.03        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 
        1.74        22.32        25.08        25.02       180.20       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 
        9.40        34.39         5.42        44.81         8.09        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
        4.34        31.79        28.47         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        1.45         8.42         5.79        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-2002 TCGA-61-2009 
       31.30        67.76        43.43        38.17        17.98        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2088 TCGA-61-2097 TCGA-61-2102 
       30.64         1.18        45.40         4.77        60.62         6.48 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       39.68        18.94         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       17.98        35.57        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 
       32.88        14.66        20.91        24.59        39.58        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 
      111.78        61.84       118.42        63.09        20.35        87.48 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       51.02        43.86        13.61        68.94       107.18       111.39 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
       66.67        92.42       145.45        66.15        19.36        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-2071 
      123.16       118.98        58.68        48.79        83.74        25.41 

$`AMP PEAK 18(12P12.1) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92         1.81        49.15         2.01 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1361 
       11.87        48.76        21.57        63.98         0.53        32.52 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1519 TCGA-04-1638 
       33.67        76.57       103.40        56.55         0.79        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 
       48.89        28.64        64.64        47.70        89.33        74.93 
TCGA-09-1666 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 
       57.60        30.51         3.02        97.55        35.15         4.54 
TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       71.11        20.94        26.93        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       83.31        55.23        57.27        81.01        32.35        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 TCGA-13-1498 
       61.71        29.42        22.39        52.44       125.56        66.15 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-20-0987 
       13.97        43.20        65.52        80.15        44.68        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-23-1023 TCGA-23-1026 
       25.94        26.20        72.20        25.38        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       32.09        49.41         8.81        18.90        51.35        54.51 
TCGA-23-1113 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-2072 TCGA-23-2077 
       31.20        33.30       129.96         4.27        24.95       115.89 
TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       87.48        49.84         2.76         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 
       41.56         7.66        54.12        63.55         6.31         6.38 
TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 
        7.82         7.86         6.25         5.95         5.36        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 
       28.37        18.64        43.53        72.92        12.46       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
        3.45         1.18        56.58        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 TCGA-24-1603 TCGA-24-1843 TCGA-24-1846 
       88.50        70.62        45.50        90.15         3.48         4.37 
TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
        5.79        22.68        16.44        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 
      109.71        14.43        55.92        28.18        64.01        57.07 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2297 TCGA-24-2298 
        0.79         0.36        47.54        31.63        55.86        53.26 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1322 TCGA-25-1623 
       33.01        42.05         2.01        65.00         2.99        18.58 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-2391 TCGA-25-2397 TCGA-25-2399 
        0.30        59.15        62.17        49.05        12.00        19.99 
TCGA-25-2401 TCGA-25-2408 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
        2.96        31.00        78.90        48.33       101.79        39.02 
TCGA-29-1696 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       33.93        16.93        59.67        18.25        41.98        34.62 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 TCGA-29-1785 
       86.60        62.93        24.36        22.55        11.84        36.30 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-30-1714 TCGA-30-1856 
       62.47        13.84        42.25         9.76        38.07        15.68 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
        6.12        57.57        48.79        45.57        30.18        22.49 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 
       44.12        28.77        21.53        22.55        25.74        27.85 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.69        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-42-2582 TCGA-42-2587 
       23.80        20.98        18.31        20.52        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1584 TCGA-57-1992 
       28.93        42.02        10.42        40.77        21.14        29.00 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2355 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
       80.12        22.32         2.14        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1901 TCGA-61-1910 
       18.54        48.79        44.84        35.80        11.41        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       42.51        48.92        56.61        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 
       14.50         4.01        30.64        45.96         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 
       71.74        61.64        58.39        65.52        55.50        76.87 
TCGA-61-2109 TCGA-VG-A8LO TCGA-10-0925 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       20.68         0.79        54.31         6.71        35.44        36.92 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       19.99         6.21        44.55         2.73        12.39        31.20 
TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0797 
       38.01        56.71        58.65        40.24       107.28        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 TCGA-13-0886 TCGA-13-0889 
       83.34        45.99        35.28        35.31       153.37        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0908 
      102.84        43.36        71.74       134.04       127.79        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 
      116.65        44.55        37.64       109.32        84.53        48.76 
TCGA-13-0924 
       85.94 

  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                          0.26                           0.30 
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                        180.20                         153.37 
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                        30.065                         35.440 
[1] "0.3 - 180.2 (30.1)" "0.3 - 153.4 (35.4)"
[1] "hr=" "1.2"
D18V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 18(12P12.1) MUTATED         3   299                2
  AMP PEAK 18(12P12.1) WILD-TYPE       0   259                0
D18V3, multiclass
                  clus
vv                 AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE
  OMENTUM                                     3                              0
  OVARY                                     299                            259
  PERITONEUM OVARY                            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"
D18V4, binary
                                cls
clus                               0   1
  AMP PEAK 18(12P12.1) MUTATED   290   3
  AMP PEAK 18(12P12.1) WILD-TYPE 251   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(12P12.1) MUTATED    290    3
  AMP PEAK 18(12P12.1) WILD-TYPE  251    2
     clus
vv    AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE
  NO                           290                            251
  YES                            3                              2
[1] 2 2
[1] FALSE
D18V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 18(12P12.1) MUTATED    8 14  3  2
  AMP PEAK 18(12P12.1) WILD-TYPE  7 12  2  1
D18V6, multiclass
    clus
vv   AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE
  R0                            8                              7
  R1                           14                             12
  R2                            3                              2
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(12P12.1) MUTATED     5 174
  AMP PEAK 18(12P12.1) WILD-TYPE   5 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(12P12.1) MUTATED      5  174
  AMP PEAK 18(12P12.1) WILD-TYPE    5  153
                        clus
vv                       AMP PEAK 18(12P12.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          174
                        clus
vv                       AMP PEAK 18(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            153
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(12Q15) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(12Q15) MUTATED    84 127
  AMP PEAK 19(12Q15) WILD-TYPE 144 204
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         211                          348 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         127                          204 
$`AMP PEAK 19(12Q15) MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 
       11.87        41.00         2.01        46.62         1.08        18.51 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 TCGA-04-1362 TCGA-04-1517 
       65.52        63.09        48.76        65.46        44.32        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1646 TCGA-04-1655 TCGA-09-1668 
       38.37       119.08        29.10        27.88        45.37        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 
       17.98         5.85         3.02         4.54       112.41        39.75 
TCGA-13-1407 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1496 
       83.31        87.06       124.44        20.68        70.82         4.24 
TCGA-13-1499 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-2057 
      115.07        65.69        34.16        80.15        54.25        80.02 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-1682 TCGA-20-1685 
       77.88        76.90        65.52         8.42        27.52        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 TCGA-23-1116 
        2.93        47.54        29.13         2.76         3.22        19.46 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2643 TCGA-23-2645 
        6.38        39.09        58.13         0.53         4.70         4.50 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1427 TCGA-24-1434 
        7.99         7.86         0.76         6.02         4.83        18.67 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 
        8.55        12.46        45.14         9.11        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       57.40        16.21        58.09        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1616 TCGA-24-1845 
       45.50        47.70        25.87        10.26        38.24         3.81 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 
       11.28         5.52         9.80        30.21        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2027 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 
        4.87       152.02       109.71        18.48        44.52        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 
        0.79         0.36        70.45        44.61         0.82        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1315 TCGA-25-1321 TCGA-25-1323 
       16.64        33.11         1.02        52.04        33.96        12.99 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       17.03        12.95        20.61        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 
       24.99         1.02        38.04        45.01        42.02        29.03 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1761 
       78.90        47.61        68.32        36.36        23.93        17.36 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1784 
       66.81        39.42        17.33        12.36        14.93         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 TCGA-29-A5NZ 
       86.17        65.00        45.11        42.25        11.47        35.77 
TCGA-30-1859 TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 TCGA-31-1955 TCGA-31-1959 
       48.10        36.62         1.22        18.77        42.51         2.20 
TCGA-36-1571 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 TCGA-36-2548 TCGA-36-2551 
       22.85        27.85        35.05        33.01        14.17        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 
       11.47        23.74        28.93        10.42        24.03        11.38 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
       22.32        29.00        25.08        25.02       180.20        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 
      116.12         9.40        44.81         8.09         4.34        31.79 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1906 TCGA-61-1907 TCGA-61-2000 
        2.43        33.67        43.69        34.13        31.30        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 
       17.98        39.85        30.64         4.77        71.74        60.62 
TCGA-61-2098 TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       65.52         6.48       125.75         6.35        31.07         8.61 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 
        9.99        29.16         9.47        57.76        35.57        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 
       81.86        18.51        34.19        36.92         6.21        24.59 
TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 
        2.73        15.19        17.82        56.71       118.42        63.09 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 
       20.35        87.48        35.28       107.18        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0901 TCGA-13-0910 TCGA-13-0911 
       95.15       145.45        43.36        19.36       116.65        44.55 
TCGA-13-0920 
       48.79 

$`AMP PEAK 19(12Q15) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1343 
       13.81        20.52        43.92         1.81        49.15        11.87 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 
       21.57        63.98         0.53        49.28        32.52        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 
       76.57       103.40        82.39        56.55        41.59         0.79 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       84.20        55.43        48.89        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       31.86        47.70         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1674 TCGA-09-1675 
       41.62        57.60        61.87        30.51         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 
        6.18         6.12        35.15        71.11        63.09        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
       26.93        12.46        77.10        81.17        28.54        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
       57.27        81.01        17.46        32.35        54.64        61.71 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       29.42        22.39        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       90.38       127.27        66.15        13.97        43.20        34.82 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 TCGA-13-A5FT TCGA-20-0987 
       65.52        44.68        14.53        78.48        70.45        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 
       25.94        26.20        72.20        25.38        19.10         2.66 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       49.68        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
        8.81        18.90        51.35        54.51        31.20        68.68 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 TCGA-23-2072 
       33.30        86.01       129.96         4.27        33.47        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        6.25         5.95         5.36        17.39        28.37        18.64 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 
       43.53        72.92       105.99         3.45         1.18        64.27 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 
       56.58        41.06        51.91        41.39        88.50        70.62 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 
       17.23        90.15        88.37        48.33         8.32         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2023 
        3.72         4.37         5.79        22.68        16.44        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       58.16        34.82        14.43        55.92        28.18        64.01 
TCGA-24-2254 TCGA-24-2267 TCGA-24-2271 TCGA-24-2289 TCGA-24-2297 TCGA-24-2298 
       57.07        47.54        31.63        67.36        55.86        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       26.96        33.01        42.05         2.01        34.98        65.00 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1630 
       37.97         2.99        15.02        18.58        27.62        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
        0.30        59.15        62.17        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 
       49.05         3.02        12.00        19.99         2.96        31.00 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       26.99        48.33       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       31.20        16.93        59.67        18.25        41.98        31.27 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       34.62        86.60        62.93        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 
       22.55        11.84        12.30         8.38         7.23        36.30 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       62.47        13.84        21.47         9.76        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 
       36.26         2.47        15.68         0.26        44.91        34.78 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        6.12        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       30.18        22.49         6.71        44.12        28.77        29.10 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
       21.53        22.55         8.55        30.08        25.74        24.23 
TCGA-36-1581 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       24.69        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       21.60         2.24        20.98        18.31        20.52         6.05 
TCGA-42-2582 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 
       47.57        42.02        40.77         1.48        21.14         1.74 
TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 
       80.12        34.39         2.14         5.42        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       31.43        18.54        27.88        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
        9.07        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 
       43.43        15.75        38.17         2.01         5.52         4.01 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       61.64        58.39        55.50        76.87        20.68        44.52 
TCGA-61-2113 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0367 TCGA-10-0925 
       22.22        39.68        18.94         0.79        17.98        54.31 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 
       44.55        39.58        12.39        31.20        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        38.01       111.78        61.84 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       58.65        40.24       107.28        69.73        83.34        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 
       51.02        43.86        35.31        13.61        68.94       111.39 
TCGA-13-0886 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
      153.37       102.84        71.74        66.15       134.04       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 
       50.37       123.16       118.98        60.59        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        84.53        48.76        83.74        85.94        25.41 

  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                        0.36                         0.26 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                      180.20                       153.37 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                      29.130                       34.505 
[1] "0.4 - 180.2 (29.1)" "0.3 - 153.4 (34.5)"
[1] "hr=" "1.1"
D19V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 19(12Q15) MUTATED         3   209                2
  AMP PEAK 19(12Q15) WILD-TYPE       0   349                0
D19V3, multiclass
                  clus
vv                 AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  OMENTUM                                   3                            0
  OVARY                                   209                          349
  PERITONEUM OVARY                          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"
D19V4, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED   204   3
  AMP PEAK 19(12Q15) WILD-TYPE 337   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED    204    3
  AMP PEAK 19(12Q15) WILD-TYPE  337    2
     clus
vv    AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  NO                         204                          337
  YES                          3                            2
[1] 2 2
[1] FALSE
D19V5, continuous
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 19(12Q15) MUTATED    6 14  2  0
  AMP PEAK 19(12Q15) WILD-TYPE  9 12  3  3
D19V6, multiclass
    clus
vv   AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  R0                          6                            9
  R1                         14                           12
  R2                          2                            3
  RX                          0                            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"
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED     4 110
  AMP PEAK 19(12Q15) WILD-TYPE   6 217
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED      4  110
  AMP PEAK 19(12Q15) WILD-TYPE    6  217
                        clus
vv                       AMP PEAK 19(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        110
                        clus
vv                       AMP PEAK 19(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          217
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(14Q11.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(14Q11.2) MUTATED    51  89
  AMP PEAK 20(14Q11.2) WILD-TYPE 177 242
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                           140                            419 
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                            89                            242 
$`AMP PEAK 20(14Q11.2) MUTATED`
TCGA-04-1332 TCGA-04-1341 TCGA-04-1347 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 
       41.00         1.08        63.09         0.53        49.28        44.32 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 TCGA-04-1646 
       56.55        41.59         0.79       119.08        29.10        27.88 
TCGA-04-1652 TCGA-09-1659 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       31.86         9.99        41.62        61.87        55.36        30.51 
TCGA-09-1674 TCGA-09-2053 TCGA-13-1408 TCGA-13-1489 TCGA-13-1497 TCGA-13-1499 
        8.55        39.75        55.23        83.93       127.27       115.07 
TCGA-13-1501 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-20-0990 TCGA-20-0991 
       43.20        54.25        80.02        78.48        25.94        26.20 
TCGA-23-1021 TCGA-23-1029 TCGA-23-1031 TCGA-23-1110 TCGA-23-1114 TCGA-23-1123 
       47.54         8.81        18.90        54.51        68.68        33.47 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 TCGA-23-2645 TCGA-24-0966 
        0.53        24.95        87.48        49.84         4.50         7.63 
TCGA-24-0979 TCGA-24-1417 TCGA-24-1424 TCGA-24-1464 TCGA-24-1466 TCGA-24-1474 
       41.56         7.82         6.02        12.46        45.14        22.22 
TCGA-24-1545 TCGA-24-1555 TCGA-24-1557 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 
       57.40        88.50        39.88        88.37        38.24         8.32 
TCGA-24-1844 TCGA-24-1850 TCGA-24-1923 TCGA-24-2019 TCGA-24-2020 TCGA-24-2030 
        3.72         5.52        22.68         4.87       152.02        55.92 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 
       44.61        67.36        53.26        26.96        33.01         2.01 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1627 TCGA-25-1628 
       34.98        33.96         2.99        12.99        12.95        20.61 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2400 TCGA-25-2408 
       24.99        24.00        85.05         1.02        42.02        31.00 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1766 TCGA-29-1775 TCGA-29-1784 
       68.32        16.93        23.93        39.42        12.36         5.36 
TCGA-29-2414 TCGA-29-2428 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       86.17        45.11        11.47        35.77        38.07        51.91 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-31-1959 TCGA-36-1571 TCGA-36-1576 
       48.10        44.91        36.62         2.20        22.85        30.08 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 
       27.85        24.69        35.05        18.31        14.17         6.05 
TCGA-57-1582 TCGA-57-1583 TCGA-59-2352 TCGA-59-2355 TCGA-61-1724 TCGA-61-1728 
       24.03        11.38         9.40         2.14        20.94        27.88 
TCGA-61-1730 TCGA-61-1904 TCGA-61-1907 TCGA-61-1917 TCGA-61-1918 TCGA-61-2009 
        4.34         9.07        31.30        43.43        15.75        39.85 
TCGA-61-2012 TCGA-61-2097 TCGA-61-2612 TCGA-WR-A838 TCGA-09-0364 TCGA-09-0367 
       30.64        60.62         6.35         9.99        29.16        17.98 
TCGA-10-0928 TCGA-10-0933 TCGA-13-0714 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 
       18.51        14.66         6.21         2.73        17.82        55.17 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0794 
       11.54       111.78        56.71        58.65        40.24        63.09 
TCGA-13-0795 TCGA-13-0888 TCGA-13-0891 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
       20.35        92.42       102.84        66.15        19.36        50.37 
TCGA-13-0911 TCGA-13-0919 
       44.55        84.53 

$`AMP PEAK 20(14Q11.2) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        43.92         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 
        2.01        46.62        18.51        11.87        65.52        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       21.57        63.98        65.46        32.52        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 
      103.40        82.39        19.99        38.37        84.20        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       48.89        28.64        64.64        36.23        47.70        45.37 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1670 TCGA-09-1672 
       38.43        89.33        74.93        57.60        17.98         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        3.02        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
      112.41        71.11        63.09        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
       77.10        81.17        28.54        83.31        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
      124.44        20.68        22.39        70.82        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 
       93.90        90.38         4.24        66.15        13.97        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       65.69        34.16        65.52        80.15        44.68        14.53 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       77.88        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       72.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.66        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 
       49.41        29.13         2.76        51.35         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       19.46        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 
       39.09        58.13       115.89        91.66        77.00         2.76 
TCGA-23-2643 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
        4.70        11.64        21.80         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.31         6.38         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       28.37        18.64        18.67        43.53         8.55        72.92 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1546 
      105.99         9.11         3.45         1.18        26.96        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       16.21        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       70.62        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 TCGA-24-1845 
       10.26        17.23        90.15        48.33         3.48         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 
        4.37        11.28         5.79         9.80        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       11.05        81.11        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       14.43        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
        0.82        36.23        16.64        33.11        55.86         1.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1329 TCGA-25-1623 
       52.04        42.05        65.00        37.97        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       27.62        17.03        38.20         0.30        59.15        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       35.87        52.04        14.96        13.02        49.05        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 
        3.02        12.00        45.01        19.99         2.96        29.03 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        47.61        48.33       101.79        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 
       40.41        33.93        31.20        36.36        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 
       11.84        12.30        14.93         8.38         7.23        36.30 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
       65.00        62.47        13.84        42.25        21.47         9.76 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 
       36.26         2.47        15.68         0.26        34.78         6.12 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       28.77        29.10        21.53        22.55         8.55        25.74 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.23        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 TCGA-36-2551 
       23.80        21.60         2.24        20.98        20.52        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       40.77         1.48        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       25.08        25.02       180.20        80.12        22.32       116.12 
TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 
       34.39         5.42        44.81        11.11         8.09        31.43 
TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       11.41        13.02        34.13        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        67.76        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98         4.01        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
        0.79         9.47        57.76        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       81.86        34.19        32.88         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       19.99        20.91        24.59        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 
       31.20        15.19         2.50        11.18        11.38        38.01 
TCGA-13-0764 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       61.84       118.42       107.28        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       45.99        51.02        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18       111.39       153.37        66.67        95.15 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 
      145.45        43.36        71.74       134.04       127.79       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      118.98        60.59       116.65        37.64       109.32        58.68 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.79        48.76        83.74        85.94        25.41 

  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                          0.53                           0.26 
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                        152.02                         180.20 
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                         31.15                          33.11 
[1] "0.5 - 152.0 (31.1)" "0.3 - 180.2 (33.1)"
[1] "hr=" "1.2"
D20V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 20(14Q11.2) MUTATED         1   141                2
  AMP PEAK 20(14Q11.2) WILD-TYPE       2   417                0
D20V3, multiclass
                  clus
vv                 AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     141                            417
  PERITONEUM OVARY                            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"
D20V4, binary
                                cls
clus                               0   1
  AMP PEAK 20(14Q11.2) MUTATED   136   1
  AMP PEAK 20(14Q11.2) WILD-TYPE 405   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(14Q11.2) MUTATED    136    1
  AMP PEAK 20(14Q11.2) WILD-TYPE  405    4
     clus
vv    AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE
  NO                           136                            405
  YES                            1                              4
[1] 2 2
[1] FALSE
D20V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 20(14Q11.2) MUTATED    4  6  0  0
  AMP PEAK 20(14Q11.2) WILD-TYPE 11 20  5  3
D20V6, multiclass
    clus
vv   AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE
  R0                            4                             11
  R1                            6                             20
  R2                            0                              5
  RX                            0                              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"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(14Q11.2) MUTATED     5  85
  AMP PEAK 20(14Q11.2) WILD-TYPE   5 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(14Q11.2) MUTATED      5   85
  AMP PEAK 20(14Q11.2) WILD-TYPE    5  242
                        clus
vv                       AMP PEAK 20(14Q11.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       AMP PEAK 20(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            242
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(14Q32.33) MUTATION ANALYSIS
D21V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 21(14Q32.33) MUTATED    66  85
  AMP PEAK 21(14Q32.33) WILD-TYPE 162 246
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                            151                             408 
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                             85                             246 
$`AMP PEAK 21(14Q32.33) MUTATED`
TCGA-04-1338 TCGA-04-1341 TCGA-04-1350 TCGA-04-1353 TCGA-04-1365 TCGA-04-1367 
       46.62         1.08        63.98         0.53        76.57       103.40 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1644 TCGA-04-1646 TCGA-09-1662 
       56.55        19.99         0.79        48.89        27.88        89.33 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1675 TCGA-09-2044 
       41.62        61.87        55.36        30.51        97.55         6.12 
TCGA-09-2045 TCGA-13-1408 TCGA-13-1412 TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 
       35.15        55.23        32.35       127.27        43.20        65.69 
TCGA-13-1509 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU 
       80.15        80.02        77.88        76.90        70.45         8.42 
TCGA-20-0991 TCGA-23-1021 TCGA-23-1028 TCGA-23-1029 TCGA-23-1116 TCGA-23-1117 
       26.20        47.54        49.41         8.81        19.46        33.30 
TCGA-23-1118 TCGA-23-1124 TCGA-23-1809 TCGA-23-2078 TCGA-23-2081 TCGA-24-0975 
       86.01        58.13         0.53        87.48        77.00        21.80 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1419 TCGA-24-1422 TCGA-24-1427 TCGA-24-1435 
       54.12        47.41         7.86         0.76         4.83        43.53 
TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1555 TCGA-24-1557 TCGA-24-1842 
       22.22        57.40        64.27        88.50        39.88         8.32 
TCGA-24-1844 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        3.72        22.68        30.21        16.44        81.11         4.87 
TCGA-24-2023 TCGA-24-2030 TCGA-24-2035 TCGA-24-2261 TCGA-24-2280 TCGA-24-2281 
       44.84        55.92        28.18         0.79        70.45        44.61 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1322 TCGA-25-2392 TCGA-25-2400 
       26.96        33.01         2.01         2.99         1.02        42.02 
TCGA-25-2401 TCGA-25-2408 TCGA-29-1688 TCGA-29-1691 TCGA-29-1697 TCGA-29-1701 
        2.96        31.00        78.90        48.33        31.20        16.93 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1762 TCGA-29-1770 TCGA-29-1775 
       23.93        18.25        41.98        86.60        24.36        12.36 
TCGA-29-1776 TCGA-29-1784 TCGA-29-2428 TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 
       11.84         5.36        45.11        11.47        38.07        36.26 
TCGA-30-1860 TCGA-30-1866 TCGA-31-1951 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 
       44.91        36.62        22.49         2.20        29.10        21.53 
TCGA-36-1577 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2543 TCGA-36-2545 
       25.74        24.69        35.05        33.01         2.24        18.31 
TCGA-36-2547 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-57-1582 
       20.52        16.18        47.57        28.93        10.42        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-59-2348 TCGA-59-2355 TCGA-61-1725 TCGA-61-1730 
       11.38        21.14       180.20         2.14        31.43         4.34 
TCGA-61-1740 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 TCGA-61-1915 TCGA-61-1918 
        2.43         5.79        13.02        31.30        67.76        15.75 
TCGA-61-1919 TCGA-61-2012 TCGA-61-2097 TCGA-61-2109 TCGA-61-2612 TCGA-WR-A838 
       38.17        30.64        60.62        20.68         6.35         9.99 
TCGA-09-0369 TCGA-10-0931 TCGA-10-0933 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 
       35.57        32.88        14.66        19.99         6.21        24.59 
TCGA-13-0723 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0801 
       39.58       111.78        56.71        58.65        40.24        45.99 
TCGA-13-0803 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0899 
       43.86       153.37        92.42       145.45        43.36        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0905 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 
      134.04        19.36       123.16        37.64        58.68        84.53 
TCGA-13-0920 
       48.79 

$`AMP PEAK 21(14Q32.33) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       49.15         2.01        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       48.76        21.57        65.46        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       33.67        82.39        41.59        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       84.20        55.43        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 TCGA-09-1666 
       47.70        45.37         9.99        38.43        74.93        57.60 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 
       17.98         5.85         3.02         8.55         6.18         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 
       12.46        77.10        81.17        28.54        83.31        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       81.01        17.46        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
      124.44        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
      125.56        93.90        90.38         4.24        66.15       115.07 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 
       13.97        34.82        34.16        65.52        44.68        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2065 TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 
       14.53        78.48        65.52        23.05        25.94        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1030 
       49.68        40.54        15.39        26.83        32.09        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.76        51.35        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       68.68       129.96         4.27         6.38        39.09        33.47 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       24.95       115.89        91.66        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.50         7.63        11.64        41.56         7.66        22.32 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 
       63.55         6.31         6.38         7.82         7.99         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        6.02         5.95         5.36        17.39        28.37        18.64 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       18.67         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 
        9.11         3.45         1.18        26.96        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1558 
       41.06        51.91        41.39        58.09        70.62        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 
       90.15        88.37        48.33        38.24         3.48         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 
        4.37        11.28         5.79         5.52         9.80        11.05 
TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
      152.02        58.16        34.82       109.71        14.43        18.48 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 
       64.01        44.52        57.07        36.16         0.36        47.54 
TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       31.63         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 
       55.86        53.26         1.02        52.04        42.05        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        37.97        33.96        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       24.00        85.05        13.02        49.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2404 TCGA-25-2409 TCGA-29-1690 
       12.00        45.01        19.99        29.03        26.99        47.61 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 
      101.79        39.02        40.41        33.93        68.32        36.36 
TCGA-29-1703 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 
       59.67        31.27        34.62        17.36        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1777 
       39.42        31.30        22.98        22.55        17.33        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       14.93         8.38         7.23        36.30        86.17        65.00 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ 
       62.47        13.84        42.25        21.47         9.76        35.77 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       51.91         2.47        15.68         0.26        48.10        34.78 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
        6.12         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       45.57        30.18        18.77         6.71        42.51        44.12 
TCGA-36-1568 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 
       28.77        22.85        22.55         8.55        30.08        27.85 
TCGA-36-1580 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       24.23        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 
       21.60        20.98        14.17         6.05        11.47        23.74 
TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       42.02        40.77         1.48         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       34.39         5.42        44.81        11.11         8.09        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       18.54        27.88        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 
       35.80        33.67        43.69         1.45         8.42        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        37.05        42.51        48.92        56.61 
TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       43.43         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
        4.77        51.72        71.74        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 
       31.07         8.61        39.68        18.94         0.79        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        9.47        57.76        17.98        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 
       18.51        34.19         6.71        35.44        36.92        20.91 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55         2.73        12.39        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       55.17         2.50        11.18        11.38        11.54        38.01 
TCGA-13-0764 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       61.84       118.42       107.28        63.09        20.35        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       83.34        87.48        51.02        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       68.94       107.18       111.39        66.67        95.15       102.84 
TCGA-13-0897 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       71.74       127.79        50.37       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0913 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       44.55       109.32        48.76        83.74        85.94        25.41 

  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                           0.53                            0.26 
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                         180.20                          152.02 
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                         33.010                          31.975 
[1] "0.5 - 180.2 (33.0)" "0.3 - 152.0 (32.0)"
[1] "hr=" "1.2"
D21V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 21(14Q32.33) MUTATED         0   152                1
  AMP PEAK 21(14Q32.33) WILD-TYPE       3   406                1
D21V3, multiclass
                  clus
vv                 AMP PEAK 21(14Q32.33) MUTATED
  OMENTUM                                      0
  OVARY                                      152
  PERITONEUM OVARY                             1
                  clus
vv                 AMP PEAK 21(14Q32.33) WILD-TYPE
  OMENTUM                                        3
  OVARY                                        406
  PERITONEUM OVARY                               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"
D21V4, binary
                                 cls
clus                                0   1
  AMP PEAK 21(14Q32.33) MUTATED   143   3
  AMP PEAK 21(14Q32.33) WILD-TYPE 398   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(14Q32.33) MUTATED    143    3
  AMP PEAK 21(14Q32.33) WILD-TYPE  398    2
     clus
vv    AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE
  NO                            143                             398
  YES                             3                               2
[1] 2 2
[1] FALSE
D21V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 21(14Q32.33) MUTATED    4  8  2  1
  AMP PEAK 21(14Q32.33) WILD-TYPE 11 18  3  2
D21V6, multiclass
    clus
vv   AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE
  R0                             4                              11
  R1                             8                              18
  R2                             2                               3
  RX                             1                               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"
D21V7, binary
                                 cls
clus                                0   1
  AMP PEAK 21(14Q32.33) MUTATED     3  83
  AMP PEAK 21(14Q32.33) WILD-TYPE   7 244
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(14Q32.33) MUTATED      3   83
  AMP PEAK 21(14Q32.33) WILD-TYPE    7  244
                        clus
vv                       AMP PEAK 21(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            83
                        clus
vv                       AMP PEAK 21(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             244
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(15Q26.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(15Q26.3) MUTATED    72  85
  AMP PEAK 22(15Q26.3) WILD-TYPE 156 246
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           157                            402 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            85                            246 
$`AMP PEAK 22(15Q26.3) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1347 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       43.92        49.15        63.09        65.46         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1516 TCGA-04-1644 TCGA-09-1662 TCGA-09-1665 
       32.52        44.32        41.59        48.89        89.33        41.62 
TCGA-09-1669 TCGA-09-1674 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-13-1404 
       30.51         8.55       112.41        63.09        39.75        81.17 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1481 TCGA-13-1483 TCGA-13-1489 TCGA-13-1495 
       83.31        55.23        87.06        29.42        83.93        90.38 
TCGA-13-1501 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       43.20        14.53        78.48        77.88        76.90        65.52 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
        2.93        47.54        49.68        32.09        49.41         8.81 
TCGA-23-1031 TCGA-23-1110 TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 TCGA-23-1124 
       18.90        54.51        68.68        86.01        39.09        58.13 
TCGA-23-2072 TCGA-23-2079 TCGA-24-0966 TCGA-24-0975 TCGA-24-1103 TCGA-24-1413 
       24.95        91.66         7.63        21.80        54.12         6.31 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1428 TCGA-24-1436 TCGA-24-1466 TCGA-24-1470 
        7.86         6.25        17.39         8.55        45.14         3.45 
TCGA-24-1546 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 
       64.27        51.91        58.09        70.62        19.53        47.70 
TCGA-24-1847 TCGA-24-1849 TCGA-24-2027 TCGA-24-2033 TCGA-24-2267 TCGA-24-2288 
       11.28         5.79       109.71        18.48        47.54         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-25-1313 TCGA-25-1319 
       67.36        36.23        33.11        55.86        26.96        65.00 
TCGA-25-1321 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 TCGA-25-2391 
       33.96        27.62        12.95        38.20        59.15        49.05 
TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1707 
       78.90        48.33       101.79        39.02        33.93        41.98 
TCGA-29-1761 TCGA-29-1768 TCGA-29-1769 TCGA-29-1775 TCGA-29-1776 TCGA-29-1781 
       17.36        31.30        22.98        12.36        11.84         8.38 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1861 TCGA-31-1944 TCGA-31-1955 TCGA-31-1956 
       51.91        36.26        34.78        45.57        42.51        44.12 
TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-1580 TCGA-36-2534 TCGA-36-2538 
        2.20        22.85         8.55        24.23        29.82        25.08 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-42-2587 TCGA-57-1582 
       21.60        20.98        18.31        20.52        23.74        24.03 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1727 
       29.00        25.02         9.40         5.42        44.81        18.54 
TCGA-61-1730 TCGA-61-1738 TCGA-61-1740 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 
        4.34        35.80         2.43        11.41        13.02        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-2009 
       37.05        42.51        67.76        15.75        38.17        39.85 
TCGA-61-2018 TCGA-61-2096 TCGA-61-2097 TCGA-61-2109 TCGA-61-2613 TCGA-VG-A8LO 
       45.40        58.39        60.62        20.68        31.07         0.79 
TCGA-WR-A838 TCGA-09-0367 TCGA-09-0369 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
        9.99        17.98        35.57        18.51        34.19        32.88 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-13-0761 TCGA-13-0764 TCGA-13-0792 
        6.71        35.44        19.99        38.01        61.84       118.42 
TCGA-13-0797 TCGA-13-0802 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 
       69.73        51.02       107.18       111.39        66.67       145.45 
TCGA-13-0897 TCGA-13-0903 TCGA-13-0906 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 
       71.74       127.79       118.98        58.68        84.53        83.74 
TCGA-13-2071 
       25.41 

$`AMP PEAK 22(15Q26.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 
       13.81        20.52        11.87        41.00         1.81         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 
       46.62         1.08        18.51        11.87        65.52        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       21.57        63.98        33.67        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       56.55        19.99         0.79        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       84.20        55.43        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 
       31.86        47.70        45.37         9.99        38.43        74.93 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        61.87        55.36        17.98         5.85         3.02 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
       97.55         6.18         6.12        35.15         4.54        71.11 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1405 TCGA-13-1409 
       20.94        26.93        12.46        77.10        28.54        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1484 
       81.01        17.46        32.35        54.64        61.71       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       20.68        22.39        70.82        52.44       125.56        93.90 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 
        4.24       127.27        66.15       115.07        13.97        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       65.69        34.16        65.52        80.15        44.68        54.25 
TCGA-13-2057 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       80.02        70.45         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 
       72.20        27.52        25.38        19.10        16.70         2.66 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 
       40.54        15.39        26.83        29.13         2.76        51.35 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 
        3.22        31.20        19.46        33.30       129.96         4.27 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 
        6.38        33.47         0.53       115.89        87.48        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0979 
       49.84         2.76         4.70         4.50        11.64        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 
        7.66        22.32        63.55        47.41         6.38         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.99         0.76         6.02         5.95         5.36         4.83 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 
       28.37        18.64        18.67        43.53        72.92        12.46 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
      105.99         9.11         1.18        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 
       16.21        56.58        41.06        41.39        88.50        39.88 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       44.09        45.50        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       88.37        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        3.81         4.37         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       16.44        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       58.16        34.82        14.43        55.92        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 
       44.52        57.07        36.16         0.79         0.36        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2293 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 
       70.45        44.61        16.64        53.26         1.02        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 
       52.04        42.05         2.01        34.98        37.97         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 
       12.99        15.02        18.58        17.03        20.61         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       62.17        35.87        52.04        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       85.05        13.02         1.02        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       26.99        47.61        40.41        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       16.93        23.93        59.67        18.25        31.27        34.62 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 
       86.60        66.81        62.93        39.42        24.36        22.55 
TCGA-29-1774 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       17.33        12.30        14.93         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       86.17        65.00        62.47        45.11        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 
       21.47        11.47         9.76        35.77        38.07         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
       15.68         0.26        48.10        44.91         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 
        1.22        57.57        24.26        30.05        48.79        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       18.77        22.49         6.71        28.77        29.10        21.53 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
       22.55        30.08        25.74        27.85        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2540 TCGA-36-2543 TCGA-36-2548 
       33.01        29.49        25.91        23.80         2.24        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
        6.05        16.18        11.47        47.57        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       10.42        40.77         1.48        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       22.32        25.08       180.20        80.12        22.32       116.12 
TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       34.39         2.14        11.11         8.09        20.94        31.43 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 
       27.88        31.79        28.47        48.79        44.84        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 
       43.69         1.45         8.42         5.79         9.07        34.13 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       48.92        56.61        43.43         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98         4.01        30.64        30.64         1.18        45.96 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2098 
        4.80         4.77        51.72        71.74        61.64        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 
        6.35         8.61        39.68        18.94        29.16         9.47 
TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0936 
       57.76        54.31        25.91        81.86        14.66        36.92 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       12.39        31.20        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 
       11.18        11.38        11.54       111.78        56.71        58.65 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 
       40.24       107.28        63.09        20.35        83.34        87.48 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       45.99        43.86        35.28        35.31        13.61        68.94 
TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
      153.37        92.42        95.15       102.84        43.36        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 
      134.04        19.36        50.37       123.16        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 
       44.55        37.64       109.32        48.79        48.76        85.94 

  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                          0.53                           0.26 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                        145.45                         180.20 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                        38.170                         30.195 
[1] "0.5 - 145.4 (38.2)" "0.3 - 180.2 (30.2)"
[1] "hr=" "1.3"
D22V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 22(15Q26.3) MUTATED         1   158                0
  AMP PEAK 22(15Q26.3) WILD-TYPE       2   400                2
D22V3, multiclass
                  clus
vv                 AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     158                            400
  PERITONEUM OVARY                            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"
D22V4, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED   152   1
  AMP PEAK 22(15Q26.3) WILD-TYPE 389   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED    152    1
  AMP PEAK 22(15Q26.3) WILD-TYPE  389    4
     clus
vv    AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  NO                           152                            389
  YES                            1                              4
[1] 2 2
[1] FALSE
D22V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 22(15Q26.3) MUTATED    5  8  1  0
  AMP PEAK 22(15Q26.3) WILD-TYPE 10 18  4  3
D22V6, multiclass
    clus
vv   AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  R0                            5                             10
  R1                            8                             18
  R2                            1                              4
  RX                            0                              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"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED     3  88
  AMP PEAK 22(15Q26.3) WILD-TYPE   7 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED      3   88
  AMP PEAK 22(15Q26.3) WILD-TYPE    7  239
                        clus
vv                       AMP PEAK 22(15Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       AMP PEAK 22(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            239
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(17Q25.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(17Q25.3) MUTATED    81 128
  AMP PEAK 23(17Q25.3) WILD-TYPE 147 203
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           209                            350 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           128                            203 
$`AMP PEAK 23(17Q25.3) MUTATED`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 
       20.52        43.92         2.01        46.62        18.51        63.09 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1525 
       49.28        44.32        76.57       103.40        56.55        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1652 TCGA-09-1662 TCGA-09-1665 
      119.08        29.10        55.43        31.86        89.33        41.62 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       57.60        55.36        30.51        97.55         6.12        35.15 
TCGA-09-2051 TCGA-09-2053 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1411 
       63.09        39.75        77.10        81.17        55.23        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 
       32.35        54.64        87.06        61.71        29.42        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 TCGA-13-1498 TCGA-13-1500 TCGA-13-1507 
       70.82        83.93        90.38        66.15        13.97        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 
       80.15        44.68        14.53        80.02        77.88        65.52 
TCGA-13-A5FU TCGA-20-1685 TCGA-23-1026 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 
        8.42        16.70        26.83         8.81        29.13        51.35 
TCGA-23-1110 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1124 
       54.51        33.30        86.01       129.96         6.38        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2643 TCGA-24-0966 
       24.95       115.89        87.48        77.00         4.70         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-1413 TCGA-24-1424 TCGA-24-1425 TCGA-24-1428 
       11.64        21.80         6.31         6.02         5.95        17.39 
TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1549 TCGA-24-1552 
       28.37        43.53        12.46       105.99        56.58        41.39 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1563 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 
       88.50        70.62        47.70        17.23        48.33         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1849 TCGA-24-1850 TCGA-24-1924 TCGA-24-2020 
        3.72         3.81         5.79         5.52        30.21       152.02 
TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2267 TCGA-24-2280 
       58.16        14.43        28.18        64.01        47.54        70.45 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 
       44.61        67.36        36.23        16.64        53.26        26.96 
TCGA-25-1315 TCGA-25-1319 TCGA-25-1320 TCGA-25-1630 TCGA-25-1632 TCGA-25-1877 
       52.04        65.00        37.97        38.20        59.15        24.00 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-29-1688 
        1.02         3.02        19.99        42.02        29.03        78.90 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 
      101.79        39.02        40.41        31.20        36.36        16.93 
TCGA-29-1705 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 
       18.25        66.81        62.93        22.98        24.36        11.84 
TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2429 TCGA-29-2432 
        8.38        36.30        86.17        65.00        13.84        21.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
       38.07        51.91         2.47        44.91         6.12        36.62 
TCGA-30-1887 TCGA-31-1944 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 
       24.26        45.57        28.77        29.10        21.53        22.55 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 
       27.85        24.69        35.05        25.91        25.08        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
        2.24        20.98        20.52        16.18        11.47        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1585 TCGA-57-1586 
       28.93        42.02        10.42         1.48         1.74        22.32 
TCGA-59-2348 TCGA-59-2354 TCGA-59-2355 TCGA-61-1722 TCGA-61-1725 TCGA-61-1737 
      180.20        34.39         2.14         8.09        31.43        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1900 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 
       35.80         2.43         5.79        37.05        48.92        56.61 
TCGA-61-1917 TCGA-61-1919 TCGA-61-2098 TCGA-61-2101 TCGA-61-2612 TCGA-VG-A8LO 
       43.43        38.17        65.52        55.50         6.35         0.79 
TCGA-09-0364 TCGA-09-0369 TCGA-10-0925 TCGA-10-0931 TCGA-10-0936 TCGA-13-0714 
       29.16        35.57        54.31        32.88        36.92         6.21 
TCGA-13-0717 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 TCGA-13-0760 TCGA-13-0761 
       24.59         2.73        17.82        55.17        11.54        38.01 
TCGA-13-0768 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0807 TCGA-13-0886 
       58.65        63.09        87.48        43.86        13.61       153.37 
TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
      145.45        71.74        19.36       127.79        50.37       123.16 
TCGA-13-0908 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 TCGA-13-2071 
       60.59       109.32        48.79        48.76        25.41 

$`AMP PEAK 23(17Q25.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1341 
       13.81        11.87        41.00         1.81        49.15         1.08 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       11.87        65.52        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 
        0.53        32.52        33.67        82.39        41.59        19.99 
TCGA-04-1519 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
        0.79        84.20        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 
       36.23        47.70        45.37         9.99        38.43        74.93 
TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 
       61.87        17.98         5.85         3.02         8.55         6.18 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
        4.54       112.41        71.11        20.94        26.93        12.46 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1484 TCGA-13-1485 
       28.54        83.31        57.27        81.01       124.44        20.68 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 
       52.44       125.56        93.90         4.24       127.27       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 TCGA-13-2059 
       43.20        34.82        65.69        34.16        54.25        78.48 
TCGA-13-2061 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       76.90        70.45        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       27.52        25.38        19.10         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1031 
       49.68        40.54        15.39        32.09        49.41        18.90 
TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 
        2.76         3.22        31.20        68.68        19.46         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 
       39.09        33.47         0.53        91.66        49.84         2.76 
TCGA-23-2645 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
        4.50        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       47.41         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1426 TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        6.25         5.36         4.83        18.64        18.67         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       72.92        45.14         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
       26.96        57.40        64.27        16.21        41.06        51.91 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 
       58.09        39.88        19.53        44.09        45.50        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1846 
       10.26        90.15        88.37        38.24         3.48         4.37 
TCGA-24-1847 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
       11.28         9.80        22.68        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 
        4.87        44.84        34.82       109.71        55.92        18.48 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 
       44.52        57.07        36.16         0.79         0.36        31.63 
TCGA-24-2288 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 
        0.82        33.11        55.86         1.02        33.01        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
        2.01        34.98        33.96         2.99        12.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       18.58        27.62        17.03        12.95        20.61         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
       62.17        35.87        52.04        14.96        24.99        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 
       13.02        49.05        38.04        12.00        45.01         2.96 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1696 TCGA-29-1698 
       31.00        26.99        47.61        48.33        33.93        68.32 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       23.93        59.67        41.98        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       86.60        39.42        31.30        22.55        17.33        12.36 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2427 TCGA-29-2428 
       12.30        14.93         7.23         5.36        62.47        45.11 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1856 
       42.25        11.47         9.76        35.77        36.26        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 
        0.26        48.10        34.78         1.22        57.57        30.05 
TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       48.79        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       44.12         2.20        22.85         8.55        30.08        25.74 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 TCGA-36-2545 
       24.23        33.01        29.49        29.82        23.80        18.31 
TCGA-36-2548 TCGA-36-2549 TCGA-42-2587 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       14.17         6.05        23.74        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 
       21.14        29.00        25.08        25.02        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 
      116.12         9.40         5.42        44.81        11.11        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 
       33.67        43.69         1.45         8.42        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1915 TCGA-61-1918 
        9.07        34.13        31.30        42.51        67.76        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       39.85        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.77        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0365 
       31.07         8.61        39.68        18.94         9.99         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       57.76        17.98        25.91        81.86        18.51        34.19 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0720 
       14.66         6.71        35.44        19.99        20.91        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 
       39.58        12.39        31.20        15.19         2.50        11.18 
TCGA-13-0758 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.38       111.78        61.84        56.71        40.24       118.42 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
      107.28        20.35        69.73        83.34        45.99        51.02 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 
       35.28        35.31        68.94       107.18       111.39        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       92.42        95.15       102.84        43.36        66.15       134.04 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 
      118.98       116.65        44.55        37.64        58.68        84.53 
TCGA-13-0923 TCGA-13-0924 
       83.74        85.94 

  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                          0.79                           0.26 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                        180.20                         134.04 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                         36.92                          30.82 
[1] "0.8 - 180.2 (36.9)" "0.3 - 134.0 (30.8)"
[1] "hr=" "1.2"
D23V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 23(17Q25.3) MUTATED         2   207                1
  AMP PEAK 23(17Q25.3) WILD-TYPE       1   351                1
D23V3, multiclass
                  clus
vv                 AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     207                            351
  PERITONEUM OVARY                            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"
D23V4, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED   202   1
  AMP PEAK 23(17Q25.3) WILD-TYPE 339   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED    202    1
  AMP PEAK 23(17Q25.3) WILD-TYPE  339    4
     clus
vv    AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  NO                           202                            339
  YES                            1                              4
[1] 2 2
[1] FALSE
D23V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 23(17Q25.3) MUTATED    4 14  4  0
  AMP PEAK 23(17Q25.3) WILD-TYPE 11 12  1  3
D23V6, multiclass
    clus
vv   AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  R0                            4                             11
  R1                           14                             12
  R2                            4                              1
  RX                            0                              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"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED     4 121
  AMP PEAK 23(17Q25.3) WILD-TYPE   6 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED      4  121
  AMP PEAK 23(17Q25.3) WILD-TYPE    6  206
                        clus
vv                       AMP PEAK 23(17Q25.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          121
                        clus
vv                       AMP PEAK 23(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            206
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(18Q11.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(18Q11.2) MUTATED    57  77
  AMP PEAK 24(18Q11.2) WILD-TYPE 171 254
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           134                            425 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            77                            254 
$`AMP PEAK 24(18Q11.2) MUTATED`
TCGA-04-1332 TCGA-04-1343 TCGA-04-1346 TCGA-04-1349 TCGA-04-1371 TCGA-04-1516 
       41.00        11.87        65.52        21.57        82.39        41.59 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 
       29.10        84.20        48.89        27.88        36.23        31.86 
TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 TCGA-09-2055 TCGA-13-1407 TCGA-13-1410 
       38.43        41.62        55.36        26.93        83.31        81.01 
TCGA-13-1411 TCGA-13-1489 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
       17.46        83.93         4.24       127.27       115.07        13.97 
TCGA-13-1504 TCGA-13-1507 TCGA-13-2059 TCGA-13-2060 TCGA-20-1682 TCGA-20-1684 
       34.82        65.52        78.48        77.88        27.52        19.10 
TCGA-20-1685 TCGA-23-1024 TCGA-23-1110 TCGA-23-1114 TCGA-23-1123 TCGA-23-1809 
       16.70        15.39        54.51        68.68        33.47         0.53 
TCGA-23-2078 TCGA-23-2645 TCGA-24-0966 TCGA-24-0979 TCGA-24-0982 TCGA-24-1422 
       87.48         4.50         7.63        41.56        22.32         0.76 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1466 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       45.14        88.37        48.33         8.32         3.72         3.81 
TCGA-24-1850 TCGA-24-1924 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2260 
        5.52        30.21         4.87       152.02        34.82        36.16 
TCGA-24-2261 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2298 TCGA-25-1314 
        0.79        44.61         0.82        67.36        53.26        33.01 
TCGA-25-1315 TCGA-25-1319 TCGA-25-1633 TCGA-25-1635 TCGA-25-1878 TCGA-25-2393 
       52.04        65.00        62.17        52.04        85.05        38.04 
TCGA-25-2397 TCGA-25-2400 TCGA-25-2404 TCGA-29-1695 TCGA-29-1698 TCGA-29-1705 
       12.00        42.02        29.03        40.41        68.32        18.25 
TCGA-29-1761 TCGA-29-1766 TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 TCGA-29-2434 
       17.36        39.42         5.36        65.00        21.47        11.47 
TCGA-30-1853 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-31-1953 TCGA-31-1959 
       36.26        44.91         6.12        36.62         6.71         2.20 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1581 TCGA-36-2529 TCGA-36-2547 TCGA-36-2552 
       22.85        22.55        24.69        35.05        20.52        11.47 
TCGA-57-1992 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-61-1722 
       29.00       180.20       116.12         9.40         2.14         8.09 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1740 TCGA-61-1899 TCGA-61-1907 TCGA-61-1917 
       27.88        31.79         2.43         8.42        31.30        43.43 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 TCGA-61-2101 
       38.17         5.52        30.64        30.64         4.77        55.50 
TCGA-61-2111 TCGA-61-2614 TCGA-VG-A8LO TCGA-09-0369 TCGA-10-0927 TCGA-10-0930 
      125.75         8.61         0.79        35.57        81.86        34.19 
TCGA-10-0937 TCGA-13-0717 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0795 
       19.99        24.59        11.54       111.78        61.84        20.35 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0890 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 
       13.61       111.39       145.45       134.04        19.36        50.37 
TCGA-13-0919 TCGA-13-0920 
       84.53        48.79 

$`AMP PEAK 24(18Q11.2) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        43.92         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 
        2.01        46.62         1.08        18.51        63.09        48.76 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       63.98        65.46         0.53        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 
       33.67        76.57       103.40        56.55        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1654 
       38.37       119.08        55.43        28.64        64.64        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 
       45.37         9.99        89.33        74.93        57.60        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        6.18         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       63.09        39.75        20.94        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
       28.54        55.23        57.27        32.35        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42       124.44        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1501 
       52.44       125.56        93.90        90.38        66.15        43.20 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       65.69        34.16        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       80.02        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 
       25.94        26.20        72.20        25.38         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        49.68        40.54        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 
        8.81        29.13        18.90         2.76        51.35         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        19.46        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 
        6.38        39.09        58.13        24.95       115.89        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0970 TCGA-24-0975 
       77.00        49.84         2.76         4.70        11.64        21.80 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.82         7.99         7.86         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 
        5.36         4.83        72.92        12.46       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        3.45         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       16.21        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 
       47.70        25.87        10.26        17.23        90.15        38.24 
TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.48         4.37        11.28         5.79         9.80        22.68 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
       16.44        11.05        81.11        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        55.92        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 
       57.07         0.36        47.54        31.63        70.45        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1316 
       16.64        33.11        55.86         1.02        26.96        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
        2.01        34.98        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       15.02        18.58        27.62        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       38.20         0.30        59.15        35.87        14.96        24.99 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2398 
       24.00        13.02        49.05         1.02         3.02        45.01 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
       19.99         2.96        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       48.33       101.79        39.02        33.93        31.20        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       16.93        23.93        59.67        41.98        31.27        34.62 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       86.60        66.81        62.93        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
        8.38         7.23        36.30        86.17        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       13.84        42.25         9.76        35.77        38.07        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1867 
        2.47        15.68         0.26        48.10        34.78         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       18.77        22.49        42.51        44.12        28.77        29.10 
TCGA-36-1570 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       21.53         8.55        30.08        25.74        27.85        24.23 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 
       21.60         2.24        20.98        18.31        14.17         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       16.18        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       22.32        25.08        25.02        80.12        22.32        34.39 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        5.42        44.81        11.11        20.94        31.43        18.54 
TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 
        4.34        28.47        48.79        44.84        35.80        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       43.69         1.45         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       34.13        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 
       15.75         2.01        14.50        17.98         4.01        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 
        1.18        45.96        45.40         4.80        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 
       61.64        58.39        60.62        65.52         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P 
       20.68        44.52        22.22         6.35        31.07        39.68 
TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       18.94         9.99        29.16         9.47        57.76        17.98 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       54.31        25.91        18.51        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 
       35.44        36.92        20.91         6.21        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
        2.73        12.39        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 
        2.50        11.18        11.38        38.01        56.71        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       40.24       118.42       107.28        63.09        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       87.48        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       68.94       107.18       153.37        66.67        92.42        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0903 TCGA-13-0905 
      102.84        43.36        71.74        66.15       127.79       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      118.98        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        48.76        83.74        85.94        25.41 

  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                          0.53                           0.26 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                        180.20                         153.37 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                        32.435                         32.880 
[1] "0.5 - 180.2 (32.4)" "0.3 - 153.4 (32.9)"
[1] "hr=" "1.1"
D24V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 24(18Q11.2) MUTATED         0   135                2
  AMP PEAK 24(18Q11.2) WILD-TYPE       3   423                0
D24V3, multiclass
                  clus
vv                 AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  OMENTUM                                     0                              3
  OVARY                                     135                            423
  PERITONEUM OVARY                            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"
D24V4, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED   131   1
  AMP PEAK 24(18Q11.2) WILD-TYPE 410   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED    131    1
  AMP PEAK 24(18Q11.2) WILD-TYPE  410    4
     clus
vv    AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  NO                           131                            410
  YES                            1                              4
[1] 2 2
[1] FALSE
D24V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 24(18Q11.2) MUTATED    4  6  1  0
  AMP PEAK 24(18Q11.2) WILD-TYPE 11 20  4  3
D24V6, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  R0                            4                             11
  R1                            6                             20
  R2                            1                              4
  RX                            0                              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"
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED     4  77
  AMP PEAK 24(18Q11.2) WILD-TYPE   6 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      4   77
  AMP PEAK 24(18Q11.2) WILD-TYPE    6  250
                        clus
vv                       AMP PEAK 24(18Q11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       AMP PEAK 24(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            250
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(19P13.12) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(19P13.12) MUTATED   126 181
  AMP PEAK 25(19P13.12) WILD-TYPE 102 150
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                            307                             252 
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                            181                             150 
$`AMP PEAK 25(19P13.12) MUTATED`
TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1342 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 
       11.87         1.81        18.51        65.52        48.76        21.57 
TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       63.98         0.53        49.28        44.32        33.67        76.57 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       82.39        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-09-1659 TCGA-09-1665 TCGA-09-1667 
       64.64        31.86        47.70         9.99        41.62        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       55.36        30.51        17.98         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 TCGA-13-1403 
        6.18         6.12       112.41        39.75        20.94        77.10 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 
       81.17        83.31        55.23        57.27        81.01        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1495 
       61.71       124.44        22.39        83.93        52.44        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1504 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
        4.24       127.27        34.82        34.16        80.15        44.68 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       80.02        78.48        76.90         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1030 TCGA-23-1031 
        2.66        47.54        15.39        26.83        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        2.76        51.35         3.22        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
        0.53       115.89        87.48         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       11.64        41.56        22.32        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 
        7.82         7.99         0.76         5.36        17.39        18.64 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 
       43.53         8.55        45.14       105.99         1.18        22.22 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1553 TCGA-24-1555 
       57.40        16.21        56.58        41.06        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 
       70.62        39.88        19.53        10.26        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       38.24         8.32         3.48         3.72         3.81        11.28 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 TCGA-24-2020 TCGA-24-2027 TCGA-24-2033 
        5.52         9.80        11.05       152.02       109.71        18.48 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2295 
       36.16         0.79        47.54        70.45        44.61        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 
       53.26         1.02        33.01        52.04         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       65.00        37.97        33.96         2.99        12.99        15.02 
TCGA-25-1623 TCGA-25-1628 TCGA-25-1870 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 
       18.58        20.61        14.96        85.05        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2409 TCGA-29-1691 
       45.01        19.99        42.02         2.96        26.99        48.33 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 
      101.79        40.41        31.20        68.32        36.36        23.93 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1770 
       59.67        41.98        31.27        34.62        17.36        24.36 
TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2429 
       12.36        14.93         7.23        36.30        86.17        13.84 
TCGA-29-2431 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 
       42.25        11.47        35.77        38.07        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
       15.68         0.26        48.10        44.91         6.12        36.62 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 
        1.22        24.26        48.79        45.57        18.77        22.49 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       42.51         2.20        28.77        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2543 
        8.55        35.05        33.01        29.82        25.91         2.24 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2552 TCGA-42-2582 TCGA-42-2589 TCGA-42-2593 
       20.52        14.17        11.47        47.57        42.02         1.48 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 
       11.38        21.14        22.32        25.08       180.20        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1724 TCGA-61-1725 
      116.12         9.40         2.14         5.42        20.94        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1904 
       27.88         4.34        35.80        33.67        43.69         9.07 
TCGA-61-1906 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       34.13        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2000 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 
       15.75        38.17        14.50        30.64        39.85        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       45.40         4.80         4.77        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
       22.22        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0367 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0936 TCGA-10-0938 
       17.98        25.91        81.86        14.66        36.92        20.91 
TCGA-13-0724 TCGA-13-0727 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 
        2.73        15.19        55.17        11.18        11.54        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 
      111.78        61.84        58.65        40.24        63.09        20.35 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       87.48        51.02        43.86        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0897 
      107.18       153.37        66.67        92.42       102.84        71.74 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0905 TCGA-13-0910 TCGA-13-0912 TCGA-13-0921 
       66.15        19.36       123.16       116.65        37.64        48.76 
TCGA-13-0923 
       83.74 

$`AMP PEAK 25(19P13.12) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92        41.00        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1347 TCGA-04-1351 TCGA-04-1361 
       46.62         1.08        11.87        63.09        65.46        32.52 
TCGA-04-1367 TCGA-04-1536 TCGA-04-1651 TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 
      103.40        29.10        36.23        45.37        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1672 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
       74.93        57.60         5.85        35.15         4.54        71.11 
TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 
       63.09        26.93        12.46        28.54        17.46        32.35 
TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1488 TCGA-13-1492 TCGA-13-1494 
       54.64        29.42        20.68        70.82       125.56        93.90 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 
       66.15       115.07        13.97        43.20        65.69        65.52 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0996 
       54.25        14.53        77.88        65.52        70.45        72.20 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1110 
       49.68        40.54        32.09        49.41         8.81        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-2072 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       31.20        68.68        24.95        91.66        77.00        49.84 
TCGA-23-2641 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1419 
        2.76        21.80         7.66        54.12        63.55         7.86 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 
        6.25         6.02         5.95         4.83        28.37        18.67 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1546 
       72.92        12.46         9.11         3.45        26.96        64.27 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       51.91        41.39        44.09        45.50        47.70        25.87 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1846 TCGA-24-1849 TCGA-24-1923 TCGA-24-1924 
       17.23        90.15         4.37         5.79        22.68        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       16.44        81.11         4.87        44.84        58.16        34.82 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       14.43        55.92        28.18        64.01        44.52        57.07 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
        0.36        31.63         0.82        67.36        36.23        16.64 
TCGA-24-2297 TCGA-25-1313 TCGA-25-1316 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       55.86        26.96        42.05        27.62        17.03        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       38.20         0.30        59.15        62.17        35.87        52.04 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 
       24.99        24.00        13.02        49.05         1.02        12.00 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 
       29.03        31.00        78.90        47.61        39.02        33.93 
TCGA-29-1701 TCGA-29-1705 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       16.93        18.25        86.60        66.81        62.93        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 
       31.30        22.98        22.55        17.33        11.84        12.30 
TCGA-29-1781 TCGA-29-1784 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2432 
        8.38         5.36        65.00        62.47        45.11        21.47 
TCGA-29-2436 TCGA-30-1718 TCGA-30-1861 TCGA-30-1880 TCGA-30-1891 TCGA-31-1946 
        9.76        51.91        34.78        57.57        30.05        30.18 
TCGA-31-1953 TCGA-31-1956 TCGA-36-1569 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
        6.71        44.12        29.10        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2532 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       24.23        24.69        29.49        25.08        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-36-2551 TCGA-42-2587 TCGA-42-2588 
       20.98        18.31         6.05        16.18        23.74        28.93 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 
       10.42        40.77        24.03         1.74        29.00        25.02 
TCGA-59-2349 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 
       80.12        34.39        44.81        11.11         8.09        18.54 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1895 
       31.79        28.47        48.79        44.84         2.43         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
        8.42         5.79        11.41        13.02        31.30        37.05 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 
        2.01         5.52        17.98         4.01        30.64         1.18 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       51.72        71.74        61.64         6.35        31.07         8.61 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0928 TCGA-10-0930 
        9.47        57.76        35.57        54.31        18.51        34.19 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 
       32.88         6.71        35.44        19.99         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 
       44.55        39.58        12.39        31.20        17.82         2.50 
TCGA-13-0758 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 
       11.38        56.71       118.42       107.28        69.73        83.34 
TCGA-13-0801 TCGA-13-0804 TCGA-13-0885 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 
       45.99        35.28       111.39        95.15       145.45        43.36 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0911 
      134.04       127.79        50.37       118.98        60.59        44.55 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
      109.32        58.68        84.53        48.79        85.94        25.41 

  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                           0.26                            0.30 
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                         180.20                          145.45 
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                         33.670                          31.465 
[1] "0.3 - 180.2 (33.7)" "0.3 - 145.4 (31.5)"
[1] "hr=" "1"  
D25V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 25(19P13.12) MUTATED         1   307                1
  AMP PEAK 25(19P13.12) WILD-TYPE       2   251                1
D25V3, multiclass
                  clus
vv                 AMP PEAK 25(19P13.12) MUTATED
  OMENTUM                                      1
  OVARY                                      307
  PERITONEUM OVARY                             1
                  clus
vv                 AMP PEAK 25(19P13.12) WILD-TYPE
  OMENTUM                                        2
  OVARY                                        251
  PERITONEUM OVARY                               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"
D25V4, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19P13.12) MUTATED   296   3
  AMP PEAK 25(19P13.12) WILD-TYPE 245   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19P13.12) MUTATED    296    3
  AMP PEAK 25(19P13.12) WILD-TYPE  245    2
     clus
vv    AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE
  NO                            296                             245
  YES                             3                               2
[1] 2 2
[1] FALSE
D25V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 25(19P13.12) MUTATED   10 11  4  1
  AMP PEAK 25(19P13.12) WILD-TYPE  5 15  1  2
D25V6, multiclass
    clus
vv   AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE
  R0                            10                               5
  R1                            11                              15
  R2                             4                               1
  RX                             1                               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"
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19P13.12) MUTATED     6 182
  AMP PEAK 25(19P13.12) WILD-TYPE   4 145
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19P13.12) MUTATED      6  182
  AMP PEAK 25(19P13.12) WILD-TYPE    4  145
                        clus
vv                       AMP PEAK 25(19P13.12) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           182
                        clus
vv                       AMP PEAK 25(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             145
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(19Q12) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 26(19Q12) MUTATED   124 188
  AMP PEAK 26(19Q12) WILD-TYPE 104 143
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         312                          247 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         188                          143 
$`AMP PEAK 26(19Q12) MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       11.87        41.00        46.62        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       63.09        48.76        21.57        49.28        44.32        33.67 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 
       64.64        31.86        47.70         9.99        38.43        41.62 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 
       61.87        55.36        30.51        17.98         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
       97.55         6.18        71.11        63.09        39.75        20.94 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 
       83.31        55.23        81.01        17.46        87.06        61.71 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
      124.44        22.39        83.93        52.44       125.56        90.38 
TCGA-13-1496 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 
        4.24        13.97        34.82        34.16        65.52        54.25 
TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       77.88        76.90         8.42        23.05        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       47.54        49.68        15.39        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       51.35        54.51         3.22        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 
      129.96         4.27         6.38        39.09        33.47         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2084 TCGA-23-2645 TCGA-24-0966 TCGA-24-0979 
       24.95       115.89        49.84         4.50         7.63        41.56 
TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1424 
       22.32        47.41         6.31         7.82         7.99         6.02 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 
        5.36        17.39        18.64        18.67         8.55        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
      105.99         9.11         1.18        26.96        57.40        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1557 
       56.58        41.06        51.91        41.39        58.09        39.88 
TCGA-24-1558 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       19.53        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-2019 
        3.81        11.28         5.52         9.80        22.68         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2261 
      152.02        44.84       109.71        55.92        18.48         0.79 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2295 TCGA-24-2298 
       47.54        70.45        44.61         0.82        33.11        53.26 
TCGA-25-1312 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
        1.02         2.01        34.98        65.00        37.97        33.96 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 
       12.99        15.02        18.58        17.03        20.61         0.30 
TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       52.04        24.99        24.00        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-29-1691 TCGA-29-1694 
       45.01        19.99         2.96        29.03        48.33        39.02 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 
       40.41        31.20        68.32        36.36        16.93        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 
       41.98        31.27        34.62        17.36        66.81        39.42 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       24.36        17.33        12.36        14.93         8.38         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       36.30        86.17        45.11        13.84        42.25        21.47 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       11.47        38.07        51.91         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 
       44.91         6.12        36.62         1.22        24.26        48.79 
TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 
       45.57        18.77        22.49         6.71         2.20        28.77 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 TCGA-36-2537 
       30.08        27.85        24.69        35.05        29.82        25.91 
TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
        2.24        20.52        14.17        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2589 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       23.74        42.02         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
        1.74        22.32        25.08        25.02       180.20        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-61-1722 TCGA-61-1724 TCGA-61-1728 
      116.12        34.39         2.14         8.09        20.94        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
        4.34        31.79        35.80         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1913 
        1.45         8.42         9.07        34.13        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2000 
       56.61        67.76        43.43        15.75        38.17        14.50 
TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
        4.01        30.64         1.18        45.96         4.80         4.77 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 
       58.39        60.62        65.52         6.48        76.87       125.75 
TCGA-61-2113 TCGA-61-2614 TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       22.22         8.61         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0933 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 
       17.98        35.57        14.66        36.92        20.91        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       39.58         2.73        15.19        17.82        55.17        11.18 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       11.54        38.01        61.84        58.65        40.24       118.42 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       63.09        20.35        69.73        45.99        51.02        43.86 
TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 
       35.28        13.61        68.94       111.39       153.37        92.42 
TCGA-13-0893 TCGA-13-0904 TCGA-13-0905 TCGA-13-0911 TCGA-13-0920 TCGA-13-0923 
       43.36        50.37       123.16        44.55        48.79        83.74 

$`AMP PEAK 26(19Q12) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92         1.81        49.15         2.01 
TCGA-04-1341 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 
        1.08        63.98        65.46         0.53        32.52        76.57 
TCGA-04-1367 TCGA-04-1519 TCGA-04-1651 TCGA-04-1655 TCGA-09-1662 TCGA-09-1664 
      103.40         0.79        36.23        45.37        89.33        74.93 
TCGA-09-1666 TCGA-09-1672 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       57.60         5.85         6.12        35.15         4.54       112.41 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 
       26.93        12.46        77.10        81.17        28.54        57.27 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1488 TCGA-13-1494 
       32.35        54.64        29.42        20.68        70.82        93.90 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1509 
      127.27        66.15       115.07        43.20        65.69        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FT 
       44.68        14.53        80.02        78.48        65.52        70.45 
TCGA-20-0996 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       72.20        40.54        26.83        32.09        49.41         8.81 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       31.20        68.68        58.13        87.48        91.66        77.00 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 
        2.76         4.70        11.64        21.80         7.66        54.12 
TCGA-24-1104 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
       63.55         6.38         7.86         0.76         6.25         5.95 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 
        4.83        28.37        43.53        72.92        12.46         3.45 
TCGA-24-1474 TCGA-24-1546 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 
       22.22        64.27        88.50        70.62        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1846 TCGA-24-1849 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        4.37         5.79        30.21        16.44        11.05        81.11 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       58.16        34.82        14.43        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2289 TCGA-24-2290 
       57.07        36.16         0.36        31.63        67.36        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       16.64        55.86        26.96        33.01        52.04        42.05 
TCGA-25-1322 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 
        2.99        27.62        12.95        38.20        59.15        62.17 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       35.87        14.96        85.05        13.02        49.05         1.02 
TCGA-25-2400 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       42.02        31.00        26.99        78.90        47.61       101.79 
TCGA-29-1696 TCGA-29-1702 TCGA-29-1705 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 
       33.93        23.93        18.25        86.60        62.93        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1784 TCGA-29-2425 
       22.98        22.55        11.84        12.30         5.36        65.00 
TCGA-29-2427 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 
       62.47         9.76        35.77        36.26         0.26        34.78 
TCGA-30-1880 TCGA-30-1891 TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 TCGA-36-1569 
       57.57        30.05        30.18        42.51        44.12        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 
       21.53        22.85        22.55         8.55        25.74        24.23 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       33.01        29.49        25.08        23.80        21.60        20.98 
TCGA-36-2545 TCGA-36-2549 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-57-1992 
       18.31         6.05        28.93        10.42        40.77        29.00 
TCGA-59-2349 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1725 
       80.12         9.40         5.42        44.81        11.11        31.43 
TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1900 TCGA-61-1901 
       18.54        28.47        48.79        44.84         5.79        11.41 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 
       13.02        31.30        37.05         2.01         5.52        17.98 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       30.64        39.85        45.40        51.72        71.74        61.64 
TCGA-61-2101 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P 
       55.50        20.68        44.52         6.35        31.07        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       18.94         0.79        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-13-0714 
       34.19        32.88         6.71        35.44        19.99         6.21 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0762 
       44.55        12.39        31.20         2.50        11.38       111.78 
TCGA-13-0766 TCGA-13-0793 TCGA-13-0799 TCGA-13-0800 TCGA-13-0805 TCGA-13-0884 
       56.71       107.28        83.34        87.48        35.31       107.18 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 
       66.67        95.15       145.45       102.84        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      134.04        19.36       127.79       118.98        60.59       116.65 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 
       37.64       109.32        58.68        84.53        48.76        85.94 
TCGA-13-2071 
       25.41 

  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                        0.30                         0.26 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                      180.20                       145.45 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                      30.575                       34.780 
[1] "0.3 - 180.2 (30.6)" "0.3 - 145.4 (34.8)"
[1] "hr=" "1.3"
D26V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 26(19Q12) MUTATED         0   312                2
  AMP PEAK 26(19Q12) WILD-TYPE       3   246                0
D26V3, multiclass
                  clus
vv                 AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  OMENTUM                                   0                            3
  OVARY                                   312                          246
  PERITONEUM OVARY                          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"
D26V4, binary
                              cls
clus                             0   1
  AMP PEAK 26(19Q12) MUTATED   303   2
  AMP PEAK 26(19Q12) WILD-TYPE 238   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED    303    2
  AMP PEAK 26(19Q12) WILD-TYPE  238    3
     clus
vv    AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  NO                         303                          238
  YES                          2                            3
[1] 2 2
[1] FALSE
D26V5, continuous
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 26(19Q12) MUTATED    9 16  2  0
  AMP PEAK 26(19Q12) WILD-TYPE  6 10  3  3
D26V6, multiclass
    clus
vv   AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  R0                          9                            6
  R1                         16                           10
  R2                          2                            3
  RX                          0                            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"
D26V7, binary
                              cls
clus                             0   1
  AMP PEAK 26(19Q12) MUTATED     6 181
  AMP PEAK 26(19Q12) WILD-TYPE   4 146
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED      6  181
  AMP PEAK 26(19Q12) WILD-TYPE    4  146
                        clus
vv                       AMP PEAK 26(19Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        181
                        clus
vv                       AMP PEAK 26(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          146
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(19Q13.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(19Q13.2) MUTATED    88 149
  AMP PEAK 27(19Q13.2) WILD-TYPE 140 182
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                           237                            322 
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                           149                            182 
$`AMP PEAK 27(19Q13.2) MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       11.87        41.00        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1361 TCGA-04-1362 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       48.76        32.52        44.32        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1649 TCGA-04-1652 
       19.99        38.37       119.08        29.10        64.64        31.86 
TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 
       41.62        55.36        30.51         8.55         6.18         4.54 
TCGA-09-2051 TCGA-09-2053 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
       63.09        39.75        83.31        55.23        81.01        17.46 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
       61.71       124.44        22.39       125.56        90.38         4.24 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-2061 
       13.97        43.20        34.82        34.16        65.52        76.90 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0991 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       70.45        23.05        26.20        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 
        2.66        49.68        15.39        29.13         2.76        54.51 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1121 TCGA-23-1809 TCGA-23-2072 
        3.22        19.46        33.30         6.38         0.53        24.95 
TCGA-23-2084 TCGA-23-2645 TCGA-24-0979 TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 
       49.84         4.50        41.56        47.41         7.82         7.99 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        6.02         5.36        17.39        18.64        18.67         8.55 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
       45.14         9.11         1.18        26.96        57.40        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 
       56.58        41.06        41.39        58.09        39.88        19.53 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 
       48.33         8.32         3.48         3.81        11.28         5.52 
TCGA-24-1923 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 
       22.68       152.02        44.84       109.71        55.92        18.48 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       36.16         0.79        47.54        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1317 TCGA-25-1318 
       67.36        33.11        53.26         1.02         2.01        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       37.97        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       17.03        12.95        20.61        38.20         0.30        59.15 
TCGA-25-1635 TCGA-25-1871 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       52.04        24.99         1.02         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 
       19.99         2.96        29.03        48.33        40.41        31.20 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       36.36        16.93        18.25        17.36        86.60        66.81 
TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1784 
       39.42        24.36        17.33        12.36        14.93         5.36 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-30-1714 
       36.30        62.47        45.11        13.84        21.47        38.07 
TCGA-30-1718 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-30-1867 
       51.91         0.26        48.10        44.91        36.62         1.22 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 
       24.26        48.79        45.57         2.20        28.77        22.85 
TCGA-36-1576 TCGA-36-1578 TCGA-36-2529 TCGA-36-2537 TCGA-36-2543 TCGA-36-2544 
       30.08        27.85        35.05        25.91         2.24        20.98 
TCGA-36-2548 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       14.17        11.47        47.57        23.74        28.93        42.02 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.48        24.03         1.74        25.08        25.02       180.20 
TCGA-59-2351 TCGA-59-2354 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1736 
      116.12        34.39         8.09        27.88         4.34        48.79 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1899 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 
        2.43        33.67         8.42        11.41         9.07        34.13 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-2003 TCGA-61-2012 TCGA-61-2087 
       42.51        48.92        56.61         4.01        30.64         4.80 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 
       60.62        65.52        76.87        22.22         6.35         8.61 
TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 
       18.94         9.99        29.16         9.47        17.98        35.57 
TCGA-10-0927 TCGA-10-0933 TCGA-13-0717 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 
       81.86        14.66        24.59         2.73        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0768 
       55.17         2.50        11.18        11.54        38.01        58.65 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0802 
       40.24        63.09        20.35        69.73        87.48        51.02 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 
       13.61        68.94       111.39       153.37        92.42       145.45 
TCGA-13-0905 TCGA-13-0916 TCGA-13-0920 
      123.16        58.68        48.79 

$`AMP PEAK 27(19Q13.2) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       46.62         1.08        21.57        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1519 TCGA-04-1542 
       49.28        33.67        76.57       103.40         0.79        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 
       55.43        48.89        27.88        28.64        36.23        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       45.37         9.99        38.43        89.33        74.93        57.60 
TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       61.87        17.98         5.85         3.02        97.55         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       35.15       112.41        71.11        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 
       77.10        81.17        28.54        57.27        32.35        54.64 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       87.06        29.42        20.68        70.82        83.93        52.44 
TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1505 TCGA-13-1509 
       93.90       127.27        66.15       115.07        65.69        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       44.68        54.25        14.53        80.02        78.48        77.88 
TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       65.52         8.42        25.94        72.20        27.52        25.38 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       47.54        40.54        26.83        32.09        49.41         8.81 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 
       18.90        51.35        31.20        68.68        86.01       129.96 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2078 
        4.27        39.09        33.47        58.13       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 
       91.66        77.00         2.76         4.70         7.63        11.64 
TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 
       21.80         7.66        22.32        54.12        63.55         6.31 
TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 
        6.38         7.86         0.76         6.25         5.95         4.83 
TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 
       28.37        43.53        72.92        12.46       105.99         3.45 
TCGA-24-1474 TCGA-24-1546 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 
       22.22        64.27        51.91        88.50        70.62        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 
       88.37        38.24         3.72         4.37         5.79         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2024 
       30.21        16.44        11.05        81.11         4.87        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       34.82        14.43        28.18        64.01        44.52        57.07 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1313 
        0.36        31.63        36.23        16.64        55.86        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1625 TCGA-25-1633 
       33.01        52.04        42.05        65.00        27.62        62.17 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       35.87        14.96        24.00        85.05        13.02        49.05 
TCGA-25-2393 TCGA-25-2400 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
       38.04        42.02        31.00        26.99        78.90        47.61 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1698 TCGA-29-1702 TCGA-29-1703 
      101.79        39.02        33.93        68.32        23.93        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 
       41.98        31.27        34.62        62.93        31.30        22.98 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-2414 
       22.55        11.84        12.30         8.38         7.23        86.17 
TCGA-29-2425 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 
       65.00        42.25        11.47         9.76        35.77        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1861 TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 
        2.47        15.68        34.78         6.12        57.57        30.05 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 
       29.10        21.53        22.55         8.55        25.74        24.23 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 
       24.69        33.01        29.49        29.82        25.08        23.80 
TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-42-2590 
       21.60        18.31        20.52         6.05        16.18        10.42 
TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-59-2349 
       40.77        11.38        21.14        22.32        29.00        80.12 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
       22.32         9.40         2.14         5.42        44.81        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 
       20.94        31.43        18.54        31.79        28.47        44.84 
TCGA-61-1738 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 
       35.80        43.69         1.45         5.79        13.02        31.30 
TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       37.05        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 
        5.52        14.50        17.98        30.64        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       58.39        55.50         6.48        20.68        44.52       125.75 
TCGA-61-2613 TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 
       31.07        39.68         0.79        57.76        54.31        25.91 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       18.51        34.19        32.88         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       19.99        20.91         6.21        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0758 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 
       31.20        11.38       111.78        61.84        56.71       118.42 
TCGA-13-0793 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
      107.28        83.34        45.99        43.86        35.28        35.31 
TCGA-13-0884 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
      107.18        66.67        95.15       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       66.15       134.04        19.36       127.79        50.37       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 
       60.59       116.65        44.55        37.64       109.32        84.53 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.76        83.74        85.94        25.41 

  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                          0.26                           0.36 
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                        180.20                         134.04 
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                        29.030                         34.985 
[1] "0.3 - 180.2 (29.0)" "0.4 - 134.0 (35.0)"
[1] "hr=" "1.4"
D27V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 27(19Q13.2) MUTATED         0   237                2
  AMP PEAK 27(19Q13.2) WILD-TYPE       3   321                0
D27V3, multiclass
                  clus
vv                 AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE
  OMENTUM                                     0                              3
  OVARY                                     237                            321
  PERITONEUM OVARY                            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"
D27V4, binary
                                cls
clus                               0   1
  AMP PEAK 27(19Q13.2) MUTATED   229   2
  AMP PEAK 27(19Q13.2) WILD-TYPE 312   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(19Q13.2) MUTATED    229    2
  AMP PEAK 27(19Q13.2) WILD-TYPE  312    3
     clus
vv    AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE
  NO                           229                            312
  YES                            2                              3
[1] 2 2
[1] FALSE
D27V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 27(19Q13.2) MUTATED    6 14  2  2
  AMP PEAK 27(19Q13.2) WILD-TYPE  9 12  3  1
D27V6, multiclass
    clus
vv   AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE
  R0                            6                              9
  R1                           14                             12
  R2                            2                              3
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(19Q13.2) MUTATED     5 136
  AMP PEAK 27(19Q13.2) WILD-TYPE   5 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(19Q13.2) MUTATED      5  136
  AMP PEAK 27(19Q13.2) WILD-TYPE    5  191
                        clus
vv                       AMP PEAK 27(19Q13.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       AMP PEAK 27(19Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            191
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(20P13) MUTATION ANALYSIS
D28V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 28(20P13) MUTATED   126 183
  AMP PEAK 28(20P13) WILD-TYPE 102 148
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                         309                          250 
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                         183                          148 
$`AMP PEAK 28(20P13) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1337 TCGA-04-1341 
       13.81        20.52        11.87        43.92         2.01         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
       18.51        11.87        65.52        63.09        21.57        63.98 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       49.28        44.32        33.67        76.57       103.40        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 
       41.59        19.99         0.79        84.20        27.88        64.64 
TCGA-04-1651 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 
       36.23        45.37         9.99        38.43        41.62        55.36 
TCGA-09-1670 TCGA-09-1674 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       17.98         8.55         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2055 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       39.75        26.93        28.54        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       81.01        87.06       124.44        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1492 TCGA-13-1497 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 
       83.93       125.56       127.27       115.07        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
       34.16        65.52        80.02        78.48        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 
       70.45         8.42        25.94        26.20        25.38        19.10 
TCGA-20-1685 TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1030 TCGA-23-1031 
       16.70        47.54        15.39        26.83        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 
        2.76        51.35         3.22        68.68        19.46        86.01 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 TCGA-24-0982 
       24.95        87.48        91.66        49.84         4.70        22.32 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
       47.41         6.31         7.99         0.76         6.25         6.02 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
       28.37        18.64        18.67         8.55        12.46        45.14 
TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1551 TCGA-24-1553 
        9.11        22.22        26.96        16.21        51.91        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 TCGA-24-1616 
       70.62        39.88        25.87        17.23        88.37        38.24 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
        3.48         3.72         3.81        11.28         5.52         9.80 
TCGA-24-1923 TCGA-24-1930 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 
       22.68        81.11       152.02        34.82        55.92        18.48 
TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       36.16        47.54        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 
       36.23        16.64        33.11         1.02        26.96        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       42.05         2.01        34.98        65.00        37.97        33.96 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       12.99        18.58        17.03        12.95        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2400 TCGA-25-2404 
       24.00        85.05        38.04         3.02        42.02        29.03 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       31.00        78.90        40.41        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1763 
       16.93        59.67        41.98        31.27        34.62        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 
       62.93        39.42        31.30        22.98        24.36        12.36 
TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       11.84        14.93         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ 
       65.00        45.11        13.84        42.25        21.47        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91         2.47        15.68         0.26        48.10 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 
        6.12         1.22        24.26        30.05        48.79        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 
       18.77        22.49         6.71        42.51         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 
       29.10        21.53        22.85         8.55        30.08        24.23 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       33.01        29.82         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 
       14.17         6.05        16.18        11.47        23.74        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 
       10.42         1.48        24.03        11.38         1.74        22.32 
TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 
       25.02       116.12         9.40         5.42        44.81         8.09 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        4.34        31.79        43.69         1.45         8.42         5.79 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 
       13.02         9.07        34.13        37.05        42.51        67.76 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
       15.75        38.17        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2018 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       30.64        45.40        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       76.87        22.22         6.35         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0927 TCGA-10-0931 
        0.79        57.76        17.98        35.57        81.86        32.88 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 
       14.66        35.44        36.92        20.91        24.59        44.55 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
        2.73        12.39        15.19        55.17        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0794 
       11.54        38.01        61.84        56.71        40.24        63.09 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 
       87.48        45.99        51.02        43.86       107.18       111.39 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0899 TCGA-13-0904 TCGA-13-0913 TCGA-13-0919 
       66.67        92.42        66.15        50.37       109.32        84.53 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       48.79        83.74        85.94 

$`AMP PEAK 28(20P13) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1348 TCGA-04-1351 
       41.00         1.81        49.15        46.62        48.76        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1371 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
        0.53        32.52        82.39        38.37       119.08        29.10 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-1662 
       55.43        48.89        28.64        31.86        47.70        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 
       74.93        57.60        61.87        30.51         5.85         3.02 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2054 TCGA-09-2056 
       97.55         6.18        35.15         4.54        20.94        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
       77.10        81.17        17.46        32.35        54.64        61.71 
TCGA-13-1483 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       29.42        52.44        93.90        90.38         4.24        66.15 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       13.97        43.20        80.15        44.68        54.25        14.53 
TCGA-13-2060 TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 
       77.88        23.05        72.20        27.52         2.93         2.66 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1110 
       49.68        40.54        32.09        49.41         8.81        54.51 
TCGA-23-1113 TCGA-23-1117 TCGA-23-1119 TCGA-23-2077 TCGA-23-2081 TCGA-23-2641 
       31.20        33.30       129.96       115.89        77.00         2.76 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1425 
       54.12        63.55         6.38         7.82         7.86         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 
        5.36         4.83        17.39        43.53        72.92       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
        3.45         1.18        57.40        64.27        56.58        41.06 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       41.39        88.50        19.53        44.09        45.50        47.70 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1614 TCGA-24-1842 TCGA-24-1846 TCGA-24-1849 
       10.26        90.15        48.33         8.32         4.37         5.79 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
       30.21        16.44        11.05         4.87        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
      109.71        14.43        28.18        64.01        44.52        57.07 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 
        0.79         0.36        31.63        55.86        53.26        33.01 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 TCGA-25-2391 
        2.99        15.02        27.62        38.20        13.02        49.05 
TCGA-25-2392 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 
        1.02        12.00        45.01        19.99         2.96        26.99 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1702 
       47.61        48.33       101.79        39.02        33.93        23.93 
TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1771 TCGA-29-1774 TCGA-29-1777 
       18.25        17.36        86.60        22.55        17.33        12.30 
TCGA-29-1781 TCGA-29-2427 TCGA-29-2434 TCGA-29-2436 TCGA-30-1853 TCGA-30-1860 
        8.38        62.47        11.47         9.76        36.26        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-31-1944 TCGA-31-1956 TCGA-36-1574 
       34.78        36.62        57.57        45.57        44.12        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 
       25.74        27.85        24.69        35.05        29.49        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-42-2582 TCGA-42-2588 TCGA-42-2591 
       25.08        23.80        21.60        47.57        28.93        40.77 
TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       21.14        29.00        25.08       180.20        80.12        22.32 
TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       34.39         2.14        11.11        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       27.88        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1901 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 
       33.67        11.41        31.30        48.92        56.61        43.43 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
        2.01         5.52        14.50         1.18        45.96         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 
        4.77        51.72        71.74        61.64        58.39        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       44.52       125.75        31.07         9.99        29.16         9.47 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0934 TCGA-10-0937 
       54.31        25.91        18.51        34.19         6.71        19.99 
TCGA-13-0714 TCGA-13-0723 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0762 
        6.21        39.58        31.20        17.82         2.50       111.78 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       58.65       118.42       107.28        20.35        69.73        83.34 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 
       35.28        35.31        13.61        68.94       153.37        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
      145.45       102.84        43.36        71.74       134.04        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
      127.79       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0921 TCGA-13-2071 
       37.64        58.68        48.76        25.41 

  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                        0.26                         0.36 
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                      152.02                       180.20 
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                       31.00                        34.29 
[1] "0.3 - 152.0 (31.0)" "0.4 - 180.2 (34.3)"
[1] "hr=" "1.1"
D28V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 28(20P13) MUTATED         3   306                1
  AMP PEAK 28(20P13) WILD-TYPE       0   252                1
D28V3, multiclass
                  clus
vv                 AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE
  OMENTUM                                   3                            0
  OVARY                                   306                          252
  PERITONEUM OVARY                          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"
D28V4, binary
                              cls
clus                             0   1
  AMP PEAK 28(20P13) MUTATED   302   2
  AMP PEAK 28(20P13) WILD-TYPE 239   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(20P13) MUTATED    302    2
  AMP PEAK 28(20P13) WILD-TYPE  239    3
     clus
vv    AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE
  NO                         302                          239
  YES                          2                            3
[1] 2 2
[1] FALSE
D28V5, continuous
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 28(20P13) MUTATED   10 16  4  3
  AMP PEAK 28(20P13) WILD-TYPE  5 10  1  0
D28V6, multiclass
    clus
vv   AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE
  R0                         10                            5
  R1                         16                           10
  R2                          4                            1
  RX                          3                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                              cls
clus                             0   1
  AMP PEAK 28(20P13) MUTATED     4 176
  AMP PEAK 28(20P13) WILD-TYPE   6 151
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(20P13) MUTATED      4  176
  AMP PEAK 28(20P13) WILD-TYPE    6  151
                        clus
vv                       AMP PEAK 28(20P13) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        176
                        clus
vv                       AMP PEAK 28(20P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          151
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(20Q11.21) MUTATION ANALYSIS
D29V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 29(20Q11.21) MUTATED   131 205
  AMP PEAK 29(20Q11.21) WILD-TYPE  97 126
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                            336                             223 
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                            205                             126 
$`AMP PEAK 29(20Q11.21) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       20.52        11.87        43.92        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
        1.08        18.51        11.87        65.52        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1364 
       21.57        63.98        65.46         0.53        49.28        33.67 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        19.99         0.79        38.37       119.08 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 
       84.20        27.88        64.64        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 TCGA-09-2043 
       38.43        41.62        55.36        17.98         8.55         6.18 
TCGA-09-2044 TCGA-09-2053 TCGA-09-2054 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 
        6.12        39.75        20.94        77.10        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       57.27        81.01        87.06       124.44        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
       70.82        83.93       125.56       115.07        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       65.69        34.16        65.52        54.25        14.53        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       78.48        77.88        76.90        65.52        70.45         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        26.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1030 TCGA-23-1031 
       16.70         2.93        47.54        49.68        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 
        2.76        51.35        54.51         3.22        68.68        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       86.01       129.96         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 
        0.53        24.95       115.89        91.66        49.84         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
        4.50         7.63        11.64        21.80        41.56        22.32 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 
       47.41         6.31         7.82         7.99         0.76         6.25 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        6.02         5.36         4.83        17.39        18.64        18.67 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 
        8.55        72.92        12.46        45.14         9.11        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       26.96        57.40        16.21        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1604 TCGA-24-1842 
       58.09        70.62        39.88        19.53        88.37         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
        3.48         3.72         3.81        11.28         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2260 
       44.84        34.82       109.71        55.92        18.48        36.16 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 
        0.79        47.54        70.45        44.61         0.82        16.64 
TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       33.11        53.26         1.02        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       65.00        37.97        33.96         2.99        12.99        15.02 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       18.58        17.03        12.95        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       62.17        35.87        52.04        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 
       85.05        38.04         3.02        45.01        42.02        29.03 
TCGA-25-2408 TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       31.00        48.33        40.41        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       16.93        23.93        59.67        18.25        41.98        31.27 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 
       17.36        66.81        39.42        22.98        24.36        17.33 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       36.30        86.17        65.00        45.11        13.84        42.25 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       11.47         9.76        35.77        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        2.47        15.68        48.10        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 TCGA-31-1951 
        1.22        57.57        24.26        48.79        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 
        6.71        42.51         2.20        29.10        22.85         8.55 
TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2534 TCGA-36-2543 TCGA-36-2547 
       30.08        24.23        24.69        29.82         2.24        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2593 
       14.17        16.18        11.47        23.74        28.93         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       24.03        11.38         1.74        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-61-1722 
      180.20       116.12         9.40         2.14        44.81         8.09 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1741 
       18.54        27.88         4.34        31.79        48.79        33.67 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 
       43.69         8.42         5.79         9.07        34.13        42.51 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 
       56.61        67.76        43.43        15.75        38.17         4.01 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       39.85        30.64         4.77        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
        6.48        76.87        22.22         6.35         8.61        39.68 
TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0930 
       18.94         9.99        57.76        17.98        35.57        34.19 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 
       14.66        35.44        36.92        20.91        24.59        39.58 
TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
        2.73        15.19        17.82        55.17        11.18        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 
       11.54       111.78        61.84        40.24        63.09        20.35 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       87.48        51.02        43.86       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
       66.67        92.42       145.45       102.84        43.36        66.15 
TCGA-13-0901 TCGA-13-0911 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       19.36        44.55        84.53        48.79        83.74        85.94 

$`AMP PEAK 29(20Q11.21) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1332 TCGA-04-1335 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       13.81        41.00         1.81        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1516 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
      103.40        41.59        29.10        55.43        48.89        28.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 
       36.23        47.70        89.33        74.93        57.60        61.87 
TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 
       30.51         5.85         3.02        97.55        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 TCGA-13-1404 
      112.41        71.11        63.09        26.93        12.46        81.17 
TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
       28.54        17.46        32.35        54.64        61.71        29.42 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1500 TCGA-13-1509 TCGA-13-1510 TCGA-20-0996 TCGA-20-1687 TCGA-23-1023 
       13.97        80.15        44.68        72.20         2.66        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1113 
       15.39        26.83        32.09        49.41         8.81        31.20 
TCGA-23-1116 TCGA-23-1120 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-24-0980 
       19.46         4.27        87.48        77.00         2.76         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1419 TCGA-24-1425 TCGA-24-1430 
       54.12        63.55         6.38         7.86         5.95        28.37 
TCGA-24-1435 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1549 
       43.53       105.99         3.45         1.18        64.27        56.58 
TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       88.50        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1846 TCGA-24-1849 
       17.23        90.15        48.33        38.24         4.37         5.79 
TCGA-24-1927 TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       16.44        58.16        14.43        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 
       57.07         0.36        31.63        67.36        36.23        55.86 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 
       26.96        33.01        52.04        27.62        38.20        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 
       49.05         1.02        12.00        19.99         2.96        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1711 
       78.90        47.61       101.79        39.02        33.93        34.62 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-2427 
       86.60        62.93        31.30        22.55        11.84        62.47 
TCGA-29-2432 TCGA-30-1857 TCGA-30-1860 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 
       21.47         0.26        44.91        30.05        45.57        30.18 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 
       44.12        28.77        21.53        22.55        25.74        27.85 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       35.05        33.01        29.49        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2589 
       21.60        20.98        18.31         6.05        47.57        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1584 TCGA-57-1586 TCGA-59-2349 TCGA-59-2350 
       10.42        40.77        21.14        22.32        80.12        22.32 
TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 
       34.39         5.42        11.11        20.94        31.43        28.47 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 
       44.84        35.80         2.43         1.45        11.41        13.02 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       31.30        37.05        48.92         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       17.98        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 
       51.72        71.74        61.64        58.39        20.68        44.52 
TCGA-61-2111 TCGA-61-2613 TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-10-0925 
      125.75        31.07         0.79        29.16         9.47        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 
       25.91        81.86        18.51        32.88         6.71        19.99 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0761 
        6.21        44.55        12.39        31.20         2.50        38.01 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 
       56.71        58.65       118.42       107.28        69.73        83.34 
TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0889 
       45.99        35.28        35.31        13.61        68.94        95.15 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       71.74       134.04       127.79        50.37       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 
       60.59       116.65        37.64       109.32        58.68        48.76 
TCGA-13-2071 
       25.41 

  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                           0.30                            0.26 
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                         180.20                          134.04 
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                          31.10                           34.39 
[1] "0.3 - 180.2 (31.1)" "0.3 - 134.0 (34.4)"
[1] "hr=" "1.2"
D29V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 29(20Q11.21) MUTATED         2   335                1
  AMP PEAK 29(20Q11.21) WILD-TYPE       1   223                1
D29V3, multiclass
                  clus
vv                 AMP PEAK 29(20Q11.21) MUTATED
  OMENTUM                                      2
  OVARY                                      335
  PERITONEUM OVARY                             1
                  clus
vv                 AMP PEAK 29(20Q11.21) WILD-TYPE
  OMENTUM                                        1
  OVARY                                        223
  PERITONEUM OVARY                               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"
D29V4, binary
                                 cls
clus                                0   1
  AMP PEAK 29(20Q11.21) MUTATED   324   3
  AMP PEAK 29(20Q11.21) WILD-TYPE 217   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(20Q11.21) MUTATED    324    3
  AMP PEAK 29(20Q11.21) WILD-TYPE  217    2
     clus
vv    AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE
  NO                            324                             217
  YES                             3                               2
[1] 2 2
[1] FALSE
D29V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 29(20Q11.21) MUTATED    8 13  4  2
  AMP PEAK 29(20Q11.21) WILD-TYPE  7 13  1  1
D29V6, multiclass
    clus
vv   AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE
  R0                             8                               7
  R1                            13                              13
  R2                             4                               1
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                 cls
clus                                0   1
  AMP PEAK 29(20Q11.21) MUTATED     5 190
  AMP PEAK 29(20Q11.21) WILD-TYPE   5 137
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(20Q11.21) MUTATED      5  190
  AMP PEAK 29(20Q11.21) WILD-TYPE    5  137
                        clus
vv                       AMP PEAK 29(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           190
                        clus
vv                       AMP PEAK 29(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             137
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(20Q13.33) MUTATION ANALYSIS
D30V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 30(20Q13.33) MUTATED   156 234
  AMP PEAK 30(20Q13.33) WILD-TYPE  72  97
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            390                             169 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            234                              97 
$`AMP PEAK 30(20Q13.33) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 
       13.81        20.52        11.87        43.92        41.00         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       46.62         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       48.76        21.57        63.98        65.46         0.53        49.28 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       44.32        33.67        82.39        56.55        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       38.37       119.08        29.10        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       36.23        31.86        45.37         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 
       41.62        55.36        30.51        17.98         3.02         8.55 
TCGA-09-2043 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.18         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       20.94        26.93        77.10        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 
       81.01        32.35        87.06        61.71       124.44        20.68 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1492 TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 
       22.39        83.93       125.56        90.38        66.15       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        43.20        34.82        65.69        34.16        65.52 
TCGA-13-1509 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       80.15        54.25        80.02        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 
       70.45         8.42        23.05        25.94        26.20        25.38 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 
       16.70         2.93         2.66        47.54        49.68        15.39 
TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       49.41        18.90         2.76        51.35        54.51         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       68.68        19.46        33.30       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 TCGA-23-2081 
       39.09        33.47        58.13         0.53        91.66        77.00 
TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 
       49.84         4.70         4.50         7.63        21.80        41.56 
TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 
       22.32        47.41         6.31         7.99         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        18.64 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       18.67         8.55        72.92        12.46        45.14         9.11 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 
       22.22        26.96        57.40        64.27        16.21        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       70.62        39.88        19.53        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 
       11.28         5.79         5.52         9.80        30.21        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87       152.02        58.16        34.82       109.71        14.43 
TCGA-24-2033 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2280 
       18.48        57.07        36.16         0.79         0.36        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       53.26         1.02        26.96        33.01        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 
       34.98        65.00        37.97        33.96        12.99        15.02 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       18.58        17.03        12.95        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       62.17        35.87        52.04        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       85.05        13.02         1.02        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       78.90        48.33       101.79        33.93        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       36.36        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 
       31.27        34.62        17.36        66.81        39.42        22.98 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 
       24.36        17.33        14.93         7.23         5.36        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       65.00        45.11        13.84        42.25        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       35.77        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       48.10        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 
       24.26        48.79        45.57        18.77        22.49        42.51 
TCGA-31-1959 TCGA-36-1569 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 
        2.20        29.10         8.55        30.08        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       24.69        35.05        29.82        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 
       16.18        11.47        28.93        42.02        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       24.03        11.38        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      180.20       116.12         9.40         2.14         5.42        44.81 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        8.09        20.94        18.54        27.88         4.34        31.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       31.30        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
       15.75        38.17        14.50         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       30.64         4.77        71.74        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        20.68       125.75        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 
        6.35         8.61        39.68        18.94         9.99        29.16 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0928 TCGA-10-0933 
       57.76        17.98        35.57        54.31        18.51        14.66 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        36.92        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        12.39        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 
       11.18        11.38        11.54        38.01       111.78        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 
       58.65        40.24       107.28        63.09        20.35        87.48 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       51.02        43.86        35.31       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       66.67        92.42       145.45        43.36        71.74        66.15 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       19.36       127.79       123.16       118.98       116.65        44.55 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
      109.32        84.53        48.79        48.76        83.74        85.94 

$`AMP PEAK 30(20Q13.33) WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1519 
        1.81        49.15        32.52        76.57       103.40         0.79 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1654 TCGA-09-1664 TCGA-09-1666 
       84.20        55.43        48.89        47.70        74.93        57.60 
TCGA-09-1667 TCGA-09-1672 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2056 
       61.87         5.85        97.55         6.12        35.15        12.46 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 TCGA-13-1477 TCGA-13-1483 TCGA-13-1488 
       81.17        28.54        17.46        54.64        29.42        70.82 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1510 TCGA-13-1512 
       52.44        93.90         4.24       127.27        44.68        14.53 
TCGA-13-2059 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-23-1023 TCGA-23-1026 
       78.48        72.20        27.52        19.10        40.54        26.83 
TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1113 TCGA-23-1118 TCGA-23-2072 
       32.09         8.81        29.13        31.20        86.01        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2641 TCGA-24-0970 TCGA-24-0980 TCGA-24-1103 
      115.89        87.48         2.76        11.64         7.66        54.12 
TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1430 TCGA-24-1435 
       63.55         6.38         7.82         7.86        28.37        43.53 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
      105.99         3.45         1.18        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       41.39        88.50        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1846 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 
       10.26         4.37        22.68        16.44        81.11        44.84 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2267 TCGA-24-2271 
       55.92        28.18        64.01        44.52        47.54        31.63 
TCGA-24-2297 TCGA-25-1315 TCGA-25-1322 TCGA-25-1625 TCGA-25-1630 TCGA-25-2391 
       55.86        52.04         2.99        27.62        38.20        49.05 
TCGA-25-2399 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1762 TCGA-29-1764 
       19.99        47.61        39.02        40.41        86.60        62.93 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       31.30        22.55        12.36        11.84        12.30         8.38 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2432 TCGA-30-1857 TCGA-30-1880 TCGA-30-1891 
       36.30        62.47        21.47         0.26        57.57        30.05 
TCGA-31-1946 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 
       30.18         6.71        44.12        28.77        21.53        22.85 
TCGA-36-1574 TCGA-36-1577 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
       22.55        25.74        33.01        29.49        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-42-2582 
       23.80        21.60         2.24        20.98        18.31        47.57 
TCGA-42-2587 TCGA-42-2590 TCGA-57-1584 TCGA-57-1585 TCGA-59-2349 TCGA-59-2350 
       23.74        10.42        21.14         1.74        80.12        22.32 
TCGA-59-2354 TCGA-61-1721 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 TCGA-61-1910 
       34.39        11.11        31.43        28.47        48.79        37.05 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        2.01         5.52        17.98         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2110 TCGA-61-2613 TCGA-VG-A8LO 
        4.80        51.72        61.64        44.52        31.07         0.79 
TCGA-09-0365 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
        9.47        25.91        81.86        34.19        32.88         6.71 
TCGA-10-0937 TCGA-13-0726 TCGA-13-0755 TCGA-13-0764 TCGA-13-0792 TCGA-13-0797 
       19.99        31.20         2.50        61.84       118.42        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0889 
       83.34        45.99        35.28        13.61        68.94        95.15 
TCGA-13-0891 TCGA-13-0900 TCGA-13-0904 TCGA-13-0908 TCGA-13-0912 TCGA-13-0916 
      102.84       134.04        50.37        60.59        37.64        58.68 
TCGA-13-2071 
       25.41 

  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                           0.30                            0.26 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                         180.20                          134.04 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                          33.06                           32.52 
[1] "0.3 - 180.2 (33.1)" "0.3 - 134.0 (32.5)"
[1] "hr=" "1.1"
D30V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 30(20Q13.33) MUTATED         3   389                2
  AMP PEAK 30(20Q13.33) WILD-TYPE       0   169                0
D30V3, multiclass
                  clus
vv                 AMP PEAK 30(20Q13.33) MUTATED
  OMENTUM                                      3
  OVARY                                      389
  PERITONEUM OVARY                             2
                  clus
vv                 AMP PEAK 30(20Q13.33) WILD-TYPE
  OMENTUM                                        0
  OVARY                                        169
  PERITONEUM OVARY                               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"
D30V4, binary
                                 cls
clus                                0   1
  AMP PEAK 30(20Q13.33) MUTATED   378   3
  AMP PEAK 30(20Q13.33) WILD-TYPE 163   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 30(20Q13.33) MUTATED    378    3
  AMP PEAK 30(20Q13.33) WILD-TYPE  163    2
     clus
vv    AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  NO                            378                             163
  YES                             3                               2
[1] 2 2
[1] FALSE
D30V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 30(20Q13.33) MUTATED   12 12  4  3
  AMP PEAK 30(20Q13.33) WILD-TYPE  3 14  1  0
D30V6, multiclass
    clus
vv   AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  R0                            12                               3
  R1                            12                              14
  R2                             4                               1
  RX                             3                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                                 cls
clus                                0   1
  AMP PEAK 30(20Q13.33) MUTATED     8 234
  AMP PEAK 30(20Q13.33) WILD-TYPE   2  93
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 30(20Q13.33) MUTATED      8  234
  AMP PEAK 30(20Q13.33) WILD-TYPE    2   93
                        clus
vv                       AMP PEAK 30(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           234
                        clus
vv                       AMP PEAK 30(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                              93
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(22Q12.2) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 31(22Q12.2) MUTATED    35  55
  AMP PEAK 31(22Q12.2) WILD-TYPE 193 276
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                            90                            469 
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                            55                            276 
$`AMP PEAK 31(22Q12.2) MUTATED`
TCGA-3P-A9WA TCGA-04-1341 TCGA-04-1348 TCGA-04-1356 TCGA-04-1364 TCGA-04-1517 
       13.81         1.08        48.76        49.28        33.67        19.99 
TCGA-04-1536 TCGA-04-1648 TCGA-04-1649 TCGA-04-1654 TCGA-09-1661 TCGA-09-1665 
       29.10        28.64        64.64        47.70        38.43        41.62 
TCGA-09-1667 TCGA-09-1675 TCGA-13-1403 TCGA-13-1405 TCGA-13-1482 TCGA-13-1488 
       61.87        97.55        77.10        28.54        61.71        70.82 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1504 TCGA-13-1511 TCGA-13-2061 TCGA-20-1685 
       90.38       127.27        34.82        54.25        76.90        16.70 
TCGA-20-1686 TCGA-23-1031 TCGA-23-1119 TCGA-23-1122 TCGA-23-2072 TCGA-23-2077 
        2.93        18.90       129.96        39.09        24.95       115.89 
TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 TCGA-24-1556 TCGA-24-1842 
       17.39        43.53        72.92         9.11        70.62         8.32 
TCGA-24-1845 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2026 
        3.81        30.21        16.44        11.05         4.87        34.82 
TCGA-24-2030 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 TCGA-25-1329 
       55.92        70.45        44.61        36.23        33.11        15.02 
TCGA-25-1627 TCGA-25-1878 TCGA-25-2398 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       12.95        85.05        45.01        36.36        16.93        23.93 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1777 TCGA-29-1778 TCGA-29-2425 
       62.93        31.30        24.36        12.30        14.93        65.00 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-A5NZ TCGA-30-1857 TCGA-30-1861 
       62.47        13.84        42.25        35.77         0.26        34.78 
TCGA-31-1950 TCGA-36-2534 TCGA-36-2547 TCGA-57-1583 TCGA-57-1585 TCGA-61-1727 
       18.77        29.82        20.52        11.38         1.74        18.54 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1904 TCGA-61-1911 TCGA-61-2000 
       35.80         2.43        43.69         9.07        42.51        14.50 
TCGA-61-2101 TCGA-61-2111 TCGA-61-2113 TCGA-10-0930 TCGA-10-0936 TCGA-13-0724 
       55.50       125.75        22.22        34.19        36.92         2.73 
TCGA-13-0762 TCGA-13-0794 TCGA-13-0795 TCGA-13-0883 TCGA-13-0888 TCGA-13-0901 
      111.78        63.09        20.35        68.94        92.42        19.36 

$`AMP PEAK 31(22Q12.2) WILD-TYPE`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       20.52        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        2.01        46.62        18.51        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 
       21.57        63.98        65.46         0.53        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 
       76.57       103.40        82.39        56.55        41.59         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
       36.23        31.86        45.37         9.99        89.33        74.93 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
        8.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       81.17        83.31        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       32.35        54.64        87.06        29.42       124.44        20.68 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 
       22.39        83.93        52.44       125.56        93.90         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       66.15       115.07        13.97        43.20        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       65.52        80.15        44.68        14.53        80.02        78.48 
TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       77.88        65.52        70.45         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 
       26.20        72.20        27.52        25.38        19.10         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        29.13         2.76        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        3.22        31.20        68.68        19.46        33.30        86.01 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2078 
        4.27         6.38        33.47        58.13         0.53        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        5.36         4.83        28.37        18.64        18.67         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14       105.99         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 
       51.91        41.39        58.09        88.50        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 
       90.15        88.37        48.33        38.24         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
       81.11       152.02        44.84        58.16       109.71        14.43 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 
        0.79         0.36        47.54        31.63         0.82        67.36 
TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        55.86        53.26         1.02        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       52.04        42.05         2.01        34.98        65.00        37.97 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       33.96         2.99        12.99        18.58        27.62        17.03 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       52.04        14.96        24.99        24.00        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04         3.02        12.00        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       68.32        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 
       17.36        86.60        66.81        39.42        22.98        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       17.33        12.36        11.84         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       36.30        86.17        45.11        21.47        11.47         9.76 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       38.07        51.91        36.26         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       44.91         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       30.05        48.79        45.57        30.18        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 
       24.23        24.69        35.05        33.01        29.49        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       14.17         6.05        16.18        11.47        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       28.93        42.02        10.42        40.77         1.48        24.03 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       21.14        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        11.11         8.09        20.94        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       33.67         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       34.13        31.30        37.05        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 
       43.43        15.75        38.17         2.01         5.52        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
        4.01        30.64        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       58.39        60.62        65.52         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       44.52         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
        0.79         9.99        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 
       35.57        54.31        25.91        81.86        18.51        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       14.66         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       38.01        61.84        56.71        58.65        40.24       118.42 
TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
      107.28        69.73        83.34        87.48        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        35.31        13.61       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        95.15       145.45       102.84        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       71.74        66.15       134.04       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      118.98        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       58.68        84.53        48.79        48.76        83.74        85.94 
TCGA-13-2071 
       25.41 

  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                          0.26                           0.30 
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                        129.96                         180.20 
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                         34.80                          31.86 
[1] "0.3 - 130.0 (34.8)" "0.3 - 180.2 (31.9)"
[1] "hr=" "1"  
D31V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 31(22Q12.2) MUTATED         2    89                0
  AMP PEAK 31(22Q12.2) WILD-TYPE       1   469                2
D31V3, multiclass
                  clus
vv                 AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                      89                            469
  PERITONEUM OVARY                            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"
D31V4, binary
                                cls
clus                               0   1
  AMP PEAK 31(22Q12.2) MUTATED    86   0
  AMP PEAK 31(22Q12.2) WILD-TYPE 455   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(22Q12.2) MUTATED     86    0
  AMP PEAK 31(22Q12.2) WILD-TYPE  455    5
     clus
vv    AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE
  NO                            86                            455
  YES                            0                              5
[1] 2 2
[1] FALSE
D31V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 31(22Q12.2) MUTATED    2  4  0  1
  AMP PEAK 31(22Q12.2) WILD-TYPE 13 22  5  2
D31V6, multiclass
    clus
vv   AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE
  R0                            2                             13
  R1                            4                             22
  R2                            0                              5
  RX                            1                              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"
D31V7, binary
                                cls
clus                               0   1
  AMP PEAK 31(22Q12.2) MUTATED     3  47
  AMP PEAK 31(22Q12.2) WILD-TYPE   7 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(22Q12.2) MUTATED      3   47
  AMP PEAK 31(22Q12.2) WILD-TYPE    7  280
                        clus
vv                       AMP PEAK 31(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       AMP PEAK 31(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            280
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(XP11.23) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 32(XP11.23) MUTATED    61  96
  AMP PEAK 32(XP11.23) WILD-TYPE 167 235
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                           157                            402 
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                            96                            235 
$`AMP PEAK 32(XP11.23) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       20.52        11.87        41.00         1.08        18.51        11.87 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.09        21.57        65.46        32.52        44.32        33.67 
TCGA-04-1530 TCGA-04-1652 TCGA-09-1661 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 
      119.08        31.86        38.43         8.55        35.15         4.54 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 TCGA-13-1485 TCGA-13-1488 TCGA-13-1496 
       28.54        55.23        81.01        20.68        70.82         4.24 
TCGA-13-1497 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 
      127.27        34.82        65.69        34.16        65.52        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FU TCGA-20-0991 TCGA-20-1686 TCGA-23-1022 
       78.48        77.88         8.42        26.20         2.93        49.68 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 
       18.90         2.76        54.51         3.22        68.68        33.30 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        4.27         6.38        33.47        58.13         0.53       115.89 
TCGA-23-2084 TCGA-24-0970 TCGA-24-1423 TCGA-24-1427 TCGA-24-1428 TCGA-24-1466 
       49.84        11.64         6.25         4.83        17.39        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1549 TCGA-24-1556 TCGA-24-1564 TCGA-24-1604 
        9.11         3.45        56.58        70.62        25.87        88.37 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       48.33         8.32         3.48         3.72         4.37        11.28 
TCGA-24-1850 TCGA-24-1924 TCGA-24-2023 TCGA-24-2030 TCGA-24-2038 TCGA-24-2260 
        5.52        30.21        44.84        55.92        44.52        36.16 
TCGA-24-2261 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-25-1315 
        0.79        70.45        44.61        67.36        36.23        52.04 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1633 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       65.00        37.97        62.17        14.96        24.99        24.00 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-29-1699 TCGA-29-1703 
        3.02        12.00        45.01        42.02        36.36        59.67 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1775 
       17.36        66.81        62.93        39.42        31.30        12.36 
TCGA-29-1776 TCGA-29-1781 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 
       11.84         8.38        11.47        35.77         2.47        15.68 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-31-1951 TCGA-31-1953 TCGA-36-1578 
       44.91         6.12         1.22        22.49         6.71        27.85 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2547 TCGA-36-2551 TCGA-42-2589 
       24.69        35.05         2.24        20.52        16.18        42.02 
TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2352 TCGA-59-2372 
        1.74        25.08        25.02       180.20         9.40        44.81 
TCGA-61-1722 TCGA-61-1911 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-2003 
        8.09        42.51        43.43        38.17         2.01         4.01 
TCGA-61-2098 TCGA-61-2109 TCGA-61-2113 TCGA-VG-A8LO TCGA-10-0928 TCGA-10-0933 
       65.52        20.68        22.22         0.79        18.51        14.66 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 TCGA-13-0723 TCGA-13-0726 
       35.44        36.92        19.99        24.59        39.58        31.20 
TCGA-13-0727 TCGA-13-0751 TCGA-13-0757 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 
       15.19        55.17        11.18        58.65        40.24       107.28 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0807 TCGA-13-0884 TCGA-13-0887 TCGA-13-0890 
       20.35        87.48        13.61       107.18        66.67       145.45 
TCGA-13-0897 TCGA-13-0901 TCGA-13-0904 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 
       71.74        19.36        50.37        58.68        48.79        83.74 
TCGA-13-2071 
       25.41 

$`AMP PEAK 32(XP11.23) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       13.81        43.92         1.81        49.15         2.01        46.62 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1365 
       65.52        48.76        63.98         0.53        49.28        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        82.39        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37        29.10        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       28.64        64.64        36.23        47.70        45.37         9.99 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       89.33        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       30.51        17.98         5.85         3.02        97.55         6.18 
TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        6.12       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 
       26.93        12.46        77.10        81.17        83.31        57.27 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
      124.44        22.39        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1509 
       90.38        66.15       115.07        13.97        43.20        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       44.68        54.25        14.53        76.90        65.52        70.45 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        72.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       16.70         2.66        47.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1113 
       32.09        49.41         8.81        29.13        51.35        31.20 
TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 
       19.46        86.01       129.96        39.09        24.95        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       91.66        77.00         2.76         4.70         4.50         7.63 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 
        0.76         6.02         5.95         5.36        28.37        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 
       18.67        43.53         8.55        72.92        12.46       105.99 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        1.18        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 
       41.06        51.91        41.39        58.09        88.50        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 
       19.53        44.09        45.50        47.70        10.26        17.23 
TCGA-24-1603 TCGA-24-1616 TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
       90.15        38.24         3.81         5.79         9.80        22.68 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 
       16.44        11.05        81.11         4.87       152.02        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       34.82       109.71        14.43        18.48        28.18        64.01 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2288 TCGA-24-2293 
       57.07         0.36        47.54        31.63         0.82        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       33.11        55.86        53.26         1.02        26.96        33.01 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       42.05         2.01        34.98        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       15.02        18.58        27.62        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 TCGA-25-1878 
       38.20         0.30        59.15        35.87        52.04        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2399 TCGA-25-2401 
       13.02        49.05         1.02        38.04        19.99         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       29.03        31.00        26.99        78.90        47.61        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        39.02        40.41        33.93        31.20        68.32 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       16.93        23.93        18.25        41.98        31.27        34.62 
TCGA-29-1762 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1777 
       86.60        22.98        24.36        22.55        17.33        12.30 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       14.93         7.23         5.36        36.30        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
       62.47        45.11        13.84        42.25        21.47         9.76 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       38.07        51.91        36.26         0.26        48.10        34.78 
TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       36.62        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       30.18        18.77        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       25.74        24.23        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 
       25.08        23.80        21.60        20.98        18.31        14.17 
TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
        6.05        11.47        47.57        23.74        28.93        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       40.77         1.48        24.03        11.38        21.14        22.32 
TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 
       29.00        80.12        22.32       116.12        34.39         2.14 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
        5.42        11.11        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1998 TCGA-61-2000 
       48.92        56.61        67.76        15.75         5.52        14.50 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98        30.64        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 
       58.39        60.62        55.50         6.48        76.87        44.52 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75         6.35        31.07         8.61        39.68        18.94 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        9.99        29.16         9.47        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
       54.31        25.91        81.86        34.19        32.88         6.71 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0730 
       20.91         6.21        44.55         2.73        12.39        17.82 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
        2.50        11.38        11.54        38.01       111.78        61.84 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       56.71       118.42        63.09        69.73        83.34        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0885 
       51.02        43.86        35.28        35.31        68.94       111.39 
TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
      153.37        92.42        95.15       102.84        43.36        66.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      134.04       127.79       123.16       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 
       44.55        37.64       109.32        84.53        48.76        85.94 

  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                          0.53                           0.26 
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                        180.20                         153.37 
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                         31.86                          33.01 
[1] "0.5 - 180.2 (31.9)" "0.3 - 153.4 (33.0)"
[1] "hr=" "1.2"
D32V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 32(XP11.23) MUTATED         2   154                2
  AMP PEAK 32(XP11.23) WILD-TYPE       1   404                0
D32V3, multiclass
                  clus
vv                 AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     154                            404
  PERITONEUM OVARY                            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"
D32V4, binary
                                cls
clus                               0   1
  AMP PEAK 32(XP11.23) MUTATED   153   1
  AMP PEAK 32(XP11.23) WILD-TYPE 388   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(XP11.23) MUTATED    153    1
  AMP PEAK 32(XP11.23) WILD-TYPE  388    4
     clus
vv    AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE
  NO                           153                            388
  YES                            1                              4
[1] 2 2
[1] FALSE
D32V5, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 32(XP11.23) MUTATED    6  4  2  0
  AMP PEAK 32(XP11.23) WILD-TYPE  9 22  3  3
D32V6, multiclass
    clus
vv   AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE
  R0                            6                              9
  R1                            4                             22
  R2                            2                              3
  RX                            0                              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"
D32V7, binary
                                cls
clus                               0   1
  AMP PEAK 32(XP11.23) MUTATED     3  94
  AMP PEAK 32(XP11.23) WILD-TYPE   7 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(XP11.23) MUTATED      3   94
  AMP PEAK 32(XP11.23) WILD-TYPE    7  233
                        clus
vv                       AMP PEAK 32(XP11.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK 32(XP11.23) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            233
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 33(XQ28) MUTATION ANALYSIS
D33V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 33(XQ28) MUTATED    89 125
  AMP PEAK 33(XQ28) WILD-TYPE 139 206
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                        214                         345 
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                        125                         206 
$`AMP PEAK 33(XQ28) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       20.52        11.87         1.81        18.51        11.87        65.52 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1367 TCGA-04-1519 
       65.46        49.28        32.52        33.67       103.40         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 
       38.37       119.08        29.10        31.86        45.37         9.99 
TCGA-09-1666 TCGA-09-1669 TCGA-09-2043 TCGA-09-2049 TCGA-09-2051 TCGA-09-2056 
       57.60        30.51         6.18       112.41        63.09        12.46 
TCGA-13-1404 TCGA-13-1409 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       81.17        57.27        32.35        87.06        61.71        29.42 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       20.68        22.39        70.82        93.90        90.38         4.24 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1511 TCGA-13-2057 TCGA-13-2065 TCGA-20-0987 
       34.82        65.69        54.25        80.02        65.52        23.05 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       26.20        27.52        25.38        16.70         2.93         2.66 
TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 
       49.68        32.09        49.41        18.90        51.35         3.22 
TCGA-23-1120 TCGA-23-1809 TCGA-23-2079 TCGA-23-2081 TCGA-24-0979 TCGA-24-0980 
        4.27         0.53        91.66        77.00        41.56         7.66 
TCGA-24-1104 TCGA-24-1417 TCGA-24-1419 TCGA-24-1435 TCGA-24-1474 TCGA-24-1546 
       63.55         7.82         7.86        43.53        22.22        64.27 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1563 
       41.39        58.09        88.50        70.62        39.88        47.70 
TCGA-24-1564 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       25.87        38.24         8.32         3.81         4.37        11.28 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 TCGA-24-2262 
       81.11       152.02        18.48        44.52         0.79         0.36 
TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2297 TCGA-25-1313 
       47.54        44.61         0.82        67.36        55.86        26.96 
TCGA-25-1314 TCGA-25-1329 TCGA-25-1625 TCGA-25-1632 TCGA-25-1870 TCGA-25-1871 
       33.01        15.02        27.62        59.15        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       24.00        85.05        13.02         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 
       12.00        45.01        42.02        33.93        16.93        23.93 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       59.67        41.98        31.27        86.60        66.81        62.93 
TCGA-29-1770 TCGA-29-1777 TCGA-29-1778 TCGA-29-1784 TCGA-29-2414 TCGA-29-2432 
       24.36        12.30        14.93         5.36        86.17        21.47 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1857 TCGA-30-1862 
       11.47        35.77        38.07        51.91         0.26         6.12 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       24.26        30.05        45.57        30.18        18.77        22.49 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1575 TCGA-36-1577 
       42.51        44.12        28.77        29.10         8.55        25.74 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2538 TCGA-36-2542 TCGA-36-2544 
       27.85        24.69        35.05        25.08        21.60        20.98 
TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-57-1584 
       18.31         6.05        47.57        23.74        28.93        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2354 
        1.74        22.32        25.02       180.20       116.12        34.39 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 TCGA-61-1738 TCGA-61-1740 
       44.81         8.09        31.43         4.34        35.80         2.43 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1911 TCGA-61-1915 
       43.69         1.45         8.42         5.79        42.51        67.76 
TCGA-61-1917 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 
       43.43        17.98        30.64        39.85        30.64        45.40 
TCGA-61-2088 TCGA-61-2101 TCGA-61-2104 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 
        4.77        55.50        76.87       125.75         6.35         8.61 
TCGA-09-0367 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0936 TCGA-13-0714 
       17.98        81.86        32.88        14.66        36.92         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0755 
       24.59        44.55        39.58        12.39        15.19         2.50 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 
       11.18        11.54        38.01       111.78        56.71       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0807 
       63.09        20.35        69.73        83.34        87.48        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0888 TCGA-13-0889 TCGA-13-0903 TCGA-13-0904 
       68.94       111.39        92.42        95.15       127.79        50.37 
TCGA-13-0908 TCGA-13-0912 TCGA-13-0921 TCGA-13-0924 
       60.59        37.64        48.76        85.94 

$`AMP PEAK 33(XQ28) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       13.81        43.92        41.00        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
        1.08        63.09        48.76        21.57        63.98         0.53 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       44.32        76.57        82.39        56.55        41.59        19.99 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       36.23        47.70        38.43        89.33        74.93        41.62 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       61.87        55.36        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2053 
       97.55         6.12        35.15         4.54        71.11        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       20.94        26.93        77.10        28.54        83.31        55.23 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1484 TCGA-13-1489 TCGA-13-1491 
       81.01        17.46        54.64       124.44        83.93        52.44 
TCGA-13-1492 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
      125.56       127.27        66.15       115.07        13.97        43.20 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 
       34.16        65.52        80.15        44.68        14.53        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 
       77.88        76.90        70.45         8.42        25.94        72.20 
TCGA-20-1684 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 
       19.10        47.54        40.54        15.39        26.83         8.81 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       29.13         2.76        54.51        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       33.30        86.01       129.96         6.38        39.09        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 
       58.13        24.95       115.89        87.48        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0982 
        4.70         4.50         7.63        11.64        21.80        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1422 
       54.12        47.41         6.31         6.38         7.99         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        18.64        18.67         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 
       45.14       105.99         9.11         3.45         1.18        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1558 
       57.40        16.21        56.58        41.06        51.91        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       44.09        45.50        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1843 TCGA-24-1844 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
       48.33         3.48         3.72         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2023 
       22.68        30.21        16.44        11.05         4.87        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 
       58.16        34.82       109.71        14.43        55.92        28.18 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 
       64.01        57.07        36.16        31.63        70.45        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 
       16.64        33.11        53.26         1.02        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       12.99        18.58        17.03        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2391 TCGA-25-2399 
        0.30        62.17        35.87        52.04        49.05        19.99 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       48.33       101.79        39.02        40.41        31.20        68.32 
TCGA-29-1699 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1768 
       36.36        18.25        34.62        17.36        39.42        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1781 
       22.98        22.55        17.33        12.36        11.84         8.38 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        7.23        36.30        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2436 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       42.25         9.76        36.26         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1892 
       44.91        34.78        36.62         1.22        57.57        48.79 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
        6.71         2.20        21.53        22.85        22.55        30.08 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 
       24.23        33.01        29.49        29.82        25.91        23.80 
TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 
        2.24        20.52        14.17        16.18        11.47        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1992 
       10.42        40.77         1.48        24.03        11.38        29.00 
TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
       25.08        80.12        22.32         9.40         2.14         5.42 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 
       11.11        20.94        18.54        27.88        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       48.79        44.84        33.67        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 
       34.13        31.30        37.05        48.92        56.61        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2016 
       38.17         2.01         5.52        14.50         4.01         1.18 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.96         4.80        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 
       60.62        65.52         6.48        20.68        44.52        22.22 
TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
       31.07        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
        9.47        57.76        35.57        54.31        25.91        18.51 
TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0724 
       34.19         6.71        35.44        19.99        20.91         2.73 
TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0758 TCGA-13-0764 TCGA-13-0768 
       31.20        17.82        55.17        11.38        61.84        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       40.24       118.42        45.99        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 
       35.31       107.18       153.37        66.67       145.45       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0905 
       43.36        71.74        66.15       134.04        19.36       123.16 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      118.98       116.65        44.55       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0923 TCGA-13-2071 
       48.79        83.74        25.41 

  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                       0.26                        0.30 
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                     180.20                      153.37 
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                     31.975                      33.470 
[1] "0.3 - 180.2 (32.0)" "0.3 - 153.4 (33.5)"
[1] "hr=" "1.1"
D33V2, continuous
                             vv
clus                          OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 33(XQ28) MUTATED         1   212                1
  AMP PEAK 33(XQ28) WILD-TYPE       2   346                1
D33V3, multiclass
                  clus
vv                 AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE
  OMENTUM                                  1                           2
  OVARY                                  212                         346
  PERITONEUM OVARY                         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"
D33V4, binary
                             cls
clus                            0   1
  AMP PEAK 33(XQ28) MUTATED   204   3
  AMP PEAK 33(XQ28) WILD-TYPE 337   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 33(XQ28) MUTATED    204    3
  AMP PEAK 33(XQ28) WILD-TYPE  337    2
     clus
vv    AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE
  NO                        204                         337
  YES                         3                           2
[1] 2 2
[1] FALSE
D33V5, continuous
                             vv
clus                          R0 R1 R2 RX
  AMP PEAK 33(XQ28) MUTATED    6 11  1  0
  AMP PEAK 33(XQ28) WILD-TYPE  9 15  4  3
D33V6, multiclass
    clus
vv   AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE
  R0                         6                           9
  R1                        11                          15
  R2                         1                           4
  RX                         0                           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"
D33V7, binary
                             cls
clus                            0   1
  AMP PEAK 33(XQ28) MUTATED     6 131
  AMP PEAK 33(XQ28) WILD-TYPE   4 196
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 33(XQ28) MUTATED      6  131
  AMP PEAK 33(XQ28) WILD-TYPE    4  196
                        clus
vv                       AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             6                           4
  NOT HISPANIC OR LATINO                       131                         196
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   117 145
  DEL PEAK  1(1P36.11) WILD-TYPE 111 186
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           262                            297 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           145                            186 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1346 
       43.92         1.81         2.01        46.62         1.08        65.52 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 
       63.98        65.46         0.53        49.28        32.52        33.67 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 
      103.40        56.55        19.99         0.79       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       84.20        55.43        48.89        64.64        36.23        47.70 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 
        9.99        89.33        74.93        41.62        57.60        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-2048 TCGA-09-2049 TCGA-09-2055 
       30.51        17.98         5.85         4.54       112.41        26.93 
TCGA-09-2056 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       12.46        55.23        57.27        81.01        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 
       87.06        61.71       124.44        20.68        22.39        52.44 
TCGA-13-1494 TCGA-13-1497 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
       93.90       127.27        65.69        34.16        80.15        44.68 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       78.48        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       26.20        27.52        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 TCGA-23-1029 TCGA-23-1031 TCGA-23-1110 
       49.68        40.54        32.09         8.81        18.90        54.51 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 
       86.01       129.96         4.27        87.48        49.84         2.76 
TCGA-23-2643 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 
        4.70        21.80         7.66        54.12        47.41         6.31 
TCGA-24-1417 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 
        7.82         0.76         6.25         6.02         5.95         4.83 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1545 TCGA-24-1546 
       43.53        72.92        12.46         9.11        57.40        64.27 
TCGA-24-1557 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 TCGA-24-1616 
       39.88        25.87        10.26        17.23        48.33        38.24 
TCGA-24-1842 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
        8.32         3.81         4.37        11.28         5.52         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 
       30.21        16.44        11.05        81.11       152.02        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2254 TCGA-24-2271 TCGA-24-2288 TCGA-24-2290 
      109.71        14.43        57.07        31.63         0.82        36.23 
TCGA-25-1313 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 TCGA-25-1627 
       26.96        42.05         2.01        37.97        12.99        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1871 
       38.20         0.30        59.15        62.17        35.87        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 
       24.00        85.05        49.05         3.02        45.01        42.02 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1696 TCGA-29-1705 
       31.00        78.90        47.61       101.79        33.93        18.25 
TCGA-29-1707 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 
       41.98        17.36        86.60        66.81        62.93        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
        5.36        36.30        86.17        65.00        62.47        13.84 
TCGA-29-2436 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 
        9.76        51.91        36.26         2.47        48.10        44.91 
TCGA-30-1861 TCGA-30-1891 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       34.78        30.05        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2534 
       29.10        30.08        25.74        24.23        33.01        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2588 TCGA-42-2589 
       18.31        20.52         6.05        11.47        28.93        42.02 
TCGA-42-2590 TCGA-57-1584 TCGA-57-1992 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       10.42        21.14        29.00        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 
       34.39         2.14         5.42        44.81         8.09        31.43 
TCGA-61-1727 TCGA-61-1734 TCGA-61-1737 TCGA-61-1740 TCGA-61-1901 TCGA-61-1903 
       18.54        28.47        44.84         2.43        11.41        13.02 
TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 
       48.92        67.76        43.43        15.75        38.17         5.52 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
        4.01        39.85        45.96        45.40         4.80        51.72 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2612 TCGA-61-2614 TCGA-09-0364 
       60.62        65.52        55.50         6.35         8.61        29.16 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0935 
       35.57        54.31        18.51        34.19        32.88        35.44 
TCGA-10-0937 TCGA-13-0724 TCGA-13-0725 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 
       19.99         2.73        12.39         2.50        11.38        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0794 TCGA-13-0801 
       38.01       111.78        61.84        56.71        63.09        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0890 
       51.02        43.86        68.94       153.37        66.67       145.45 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 
      134.04       127.79       123.16       118.98        60.59        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0924 
      109.32        58.68        84.53        85.94 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1336 TCGA-04-1342 
       13.81        20.52        11.87        41.00        49.15        18.51 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1362 TCGA-04-1365 
       11.87        63.09        48.76        21.57        44.32        76.57 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1646 TCGA-04-1648 TCGA-04-1652 
       82.39        41.59        38.37        27.88        28.64        31.86 
TCGA-04-1655 TCGA-09-1661 TCGA-09-1667 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       45.37        38.43        61.87         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.18         6.12        35.15        71.11        63.09        39.75 
TCGA-09-2054 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 
       20.94        77.10        81.17        28.54        83.31        17.46 
TCGA-13-1483 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
       29.42        70.82        83.93       125.56        90.38         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1507 
       66.15       115.07        13.97        43.20        34.82        65.52 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-20-0990 TCGA-20-0996 
       54.25        14.53        80.02        77.88        25.94        72.20 
TCGA-20-1683 TCGA-20-1684 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1030 
       25.38        19.10        15.39        26.83        49.41        29.13 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.76        51.35         3.22        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
       33.30         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2645 TCGA-24-0966 
       24.95       115.89        91.66        77.00         4.50         7.63 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1416 TCGA-24-1418 
       11.64        41.56        22.32        63.55         6.38         7.99 
TCGA-24-1419 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        7.86         5.36        17.39        28.37        18.64        18.67 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
        8.55        45.14       105.99         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       26.96        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       58.09        88.50        70.62        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 TCGA-24-1844 TCGA-24-1849 
       47.70        90.15        88.37         3.48         3.72         5.79 
TCGA-24-1923 TCGA-24-2019 TCGA-24-2023 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 
       22.68         4.87        44.84        34.82        55.92        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        64.01        44.52        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 
       47.54        70.45        44.61        67.36        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1318 
       55.86        53.26         1.02        33.01        52.04        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       65.00        33.96         2.99        15.02        18.58        27.62 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 TCGA-25-2392 
       17.03        20.61        52.04        14.96        13.02         1.02 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
       38.04        12.00        19.99         2.96        29.03        26.99 
TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       48.33        39.02        40.41        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1711 TCGA-29-1766 
       16.93        23.93        59.67        31.27        34.62        39.42 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-2428 TCGA-29-2431 
       12.30        14.93         8.38         7.23        45.11        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1856 TCGA-30-1857 
       21.47        11.47        35.77        38.07        15.68         0.26 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 
        6.12        36.62         1.22        57.57        24.26        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-36-1570 
       45.57        30.18        18.77        22.49         6.71        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
       22.85        22.55         8.55        27.85        24.69        35.05 
TCGA-36-2532 TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2591 
       29.49        14.17        16.18        47.57        23.74        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 
        1.48        24.03        11.38         1.74        22.32        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-61-1721 TCGA-61-1724 TCGA-61-1728 
       25.02       180.20        80.12        11.11        20.94        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 
        4.34        31.79        48.79        35.80        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        1.45         8.42         5.79         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 
       37.05        42.51        56.61         2.01        14.50        17.98 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 
       30.64        30.64         1.18         4.77        71.74        61.64 
TCGA-61-2096 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       58.39         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       22.22        31.07        39.68        18.94         0.79         9.99 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 
        9.47        57.76        17.98        25.91        81.86        14.66 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
        6.71        36.92        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       39.58        31.20        15.19        17.82        55.17        11.18 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       58.65        40.24       118.42       107.28        20.35        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 
       83.34        87.48        35.28        35.31        13.61       107.18 
TCGA-13-0885 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
      111.39        92.42        95.15       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 TCGA-13-0920 
       66.15        19.36        50.37       116.65        44.55        48.79 
TCGA-13-0921 TCGA-13-0923 TCGA-13-2071 
       48.76        83.74        25.41 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        153.37                         180.20 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        34.175                         31.200 
[1] "0.3 - 153.4 (34.2)" "0.3 - 180.2 (31.2)"
[1] "hr=" "1.3"
D34V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  1(1P36.11) MUTATED         1   264                0
  DEL PEAK  1(1P36.11) WILD-TYPE       2   294                2
D34V3, multiclass
                  clus
vv                 DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     264                            294
  PERITONEUM OVARY                            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"
D34V4, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   251   2
  DEL PEAK  1(1P36.11) WILD-TYPE 290   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    251    2
  DEL PEAK  1(1P36.11) WILD-TYPE  290    3
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                           251                            290
  YES                            2                              3
[1] 2 2
[1] FALSE
D34V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  1(1P36.11) MUTATED    8 16  2  1
  DEL PEAK  1(1P36.11) WILD-TYPE  7 10  3  2
D34V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                            8                              7
  R1                           16                             10
  R2                            2                              3
  RX                            1                              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"
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     6 152
  DEL PEAK  1(1P36.11) WILD-TYPE   4 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      6  152
  DEL PEAK  1(1P36.11) WILD-TYPE    4  175
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          152
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            175
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  2(1Q41) MUTATION ANALYSIS
D35V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1Q41) MUTATED    38  52
  DEL PEAK  2(1Q41) WILD-TYPE 190 279
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                         90                         469 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                         52                         279 
$`DEL PEAK  2(1Q41) MUTATED`
TCGA-59-A5PD TCGA-04-1338 TCGA-04-1349 TCGA-04-1353 TCGA-04-1362 TCGA-04-1517 
       20.52        46.62        21.57         0.53        44.32        19.99 
TCGA-04-1536 TCGA-04-1651 TCGA-04-1654 TCGA-09-1675 TCGA-09-2050 TCGA-09-2051 
       29.10        36.23        47.70        97.55        71.11        63.09 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1485 TCGA-13-1488 TCGA-13-1492 TCGA-13-1497 
       83.31        55.23        20.68        70.82       125.56       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-2059 TCGA-13-2065 TCGA-20-0987 TCGA-20-1687 
       66.15       115.07        78.48        65.52        23.05         2.66 
TCGA-23-1022 TCGA-23-1029 TCGA-23-1032 TCGA-23-1109 TCGA-23-1117 TCGA-23-1121 
       49.68         8.81         2.76        51.35        33.30         6.38 
TCGA-23-1124 TCGA-23-2641 TCGA-23-2645 TCGA-24-0979 TCGA-24-1103 TCGA-24-1418 
       58.13         2.76         4.50        41.56        54.12         7.99 
TCGA-24-1425 TCGA-24-1428 TCGA-24-1435 TCGA-24-1466 TCGA-24-1567 TCGA-24-1844 
        5.95        17.39        43.53        45.14        17.23         3.72 
TCGA-24-1920 TCGA-24-2020 TCGA-24-2026 TCGA-24-2280 TCGA-25-1314 TCGA-25-1315 
        9.80       152.02        34.82        70.45        33.01        52.04 
TCGA-25-1632 TCGA-25-2391 TCGA-25-2409 TCGA-29-1691 TCGA-29-1705 TCGA-29-1707 
       59.15        49.05        26.99        48.33        18.25        41.98 
TCGA-29-1763 TCGA-29-1768 TCGA-29-1776 TCGA-29-1781 TCGA-29-1783 TCGA-30-1718 
       66.81        31.30        11.84         8.38         7.23        51.91 
TCGA-30-1891 TCGA-36-2548 TCGA-42-2591 TCGA-57-1582 TCGA-57-1585 TCGA-59-2348 
       30.05        14.17        40.77        24.03         1.74       180.20 
TCGA-61-1724 TCGA-61-1737 TCGA-61-1895 TCGA-61-1901 TCGA-61-1907 TCGA-61-1914 
       20.94        44.84         1.45        11.41        31.30        56.61 
TCGA-61-2012 TCGA-61-2102 TCGA-61-2612 TCGA-WR-A838 TCGA-09-0367 TCGA-10-0928 
       30.64         6.48         6.35         9.99        17.98        18.51 
TCGA-10-0930 TCGA-13-0714 TCGA-13-0720 TCGA-13-0726 TCGA-13-0755 TCGA-13-0792 
       34.19         6.21        44.55        31.20         2.50       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0807 TCGA-13-0885 TCGA-13-0893 TCGA-13-0900 
      107.28        63.09        13.61       111.39        43.36       134.04 

$`DEL PEAK  2(1Q41) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        2.01         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 
       48.76        63.98        65.46        49.28        32.52        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 
       76.57       103.40        82.39        56.55        41.59         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       28.64        64.64        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       89.33        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 
       30.51        17.98         5.85         3.02         8.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 
        6.12        35.15         4.54       112.41        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 
       26.93        12.46        77.10        81.17        28.54        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       81.01        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
       29.42       124.44        22.39        83.93        52.44        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       90.38         4.24        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       34.16        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       80.02        77.88        76.90        70.45         8.42        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.93        47.54        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       49.41        29.13        18.90        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
       68.68        19.46        86.01       129.96         4.27        39.09 
TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47         0.53        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       77.00        49.84         4.70         7.63        11.64        21.80 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        22.32        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 
        7.82         7.86         0.76         6.25         6.02         5.36 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 
        4.83        28.37        18.64        18.67         8.55        72.92 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       90.15        88.37        48.33        38.24         8.32         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 
        3.81         4.37        11.28         5.79         5.52        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
       30.21        16.44        11.05        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       58.16       109.71        14.43        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       64.01        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       47.54        31.63        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       42.05         2.01        34.98        65.00        37.97        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.99        15.02        18.58        27.62        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       12.95        20.61        38.20         0.30        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       52.04        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       42.02         2.96        29.03        31.00        78.90        47.61 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        39.02        40.41        33.93        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1711 
       36.36        16.93        23.93        59.67        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 
       17.36        86.60        62.93        39.42        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1784 
       22.55        17.33        12.36        12.30        14.93         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       36.26         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       18.31        20.52         6.05        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 
       23.74        28.93        42.02        10.42         1.48        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 
       21.14        22.32        29.00        25.08        25.02        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       44.81        11.11         8.09        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        28.47        48.79        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 
       33.67        43.69         8.42         5.79        13.02         9.07 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 
       34.13        37.05        42.51        48.92        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        30.64        39.85         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        55.50        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 
        0.79        29.16         9.47        57.76        35.57        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       25.91        81.86        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 
       36.92        19.99        20.91        24.59        39.58         2.73 
TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
       12.39        15.19        17.82        55.17        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        38.01       111.78        61.84        56.71        58.65 
TCGA-13-0791 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       40.24        20.35        69.73        83.34        87.48        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 
       51.02        43.86        35.28        35.31        68.94       107.18 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      153.37        66.67        92.42        95.15       145.45       102.84 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       71.74        66.15        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      118.98        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       58.68        84.53        48.79        48.76        83.74        85.94 
TCGA-13-2071 
       25.41 

  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                       0.53                        0.26 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                     180.20                      153.37 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                     33.745                      32.350 
[1] "0.5 - 180.2 (33.7)" "0.3 - 153.4 (32.4)"
[1] "hr=" "1.2"
D35V2, continuous
                             vv
clus                          OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  2(1Q41) MUTATED         0    92                0
  DEL PEAK  2(1Q41) WILD-TYPE       3   466                2
D35V3, multiclass
                  clus
vv                 DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  OMENTUM                                  0                           3
  OVARY                                   92                         466
  PERITONEUM OVARY                         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"
D35V4, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q41) MUTATED    87   2
  DEL PEAK  2(1Q41) WILD-TYPE 454   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q41) MUTATED     87    2
  DEL PEAK  2(1Q41) WILD-TYPE  454    3
     clus
vv    DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  NO                         87                         454
  YES                         2                           3
[1] 2 2
[1] FALSE
D35V5, continuous
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  2(1Q41) MUTATED    0  3  0  0
  DEL PEAK  2(1Q41) WILD-TYPE 15 23  5  3
D35V6, multiclass
    clus
vv   DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  R0                         0                          15
  R1                         3                          23
  R2                         0                           5
  RX                         0                           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"
D35V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q41) MUTATED     0  55
  DEL PEAK  2(1Q41) WILD-TYPE  10 272
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q41) MUTATED      0   55
  DEL PEAK  2(1Q41) WILD-TYPE   10  272
                        clus
vv                       DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  HISPANIC OR LATINO                             0                          10
  NOT HISPANIC OR LATINO                        55                         272
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  3(2P25.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P25.3) MUTATED    42  75
  DEL PEAK  3(2P25.3) WILD-TYPE 186 256
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                          117                           442 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           75                           256 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-04-1331 TCGA-04-1343 TCGA-04-1348 TCGA-04-1356 TCGA-04-1362 TCGA-04-1514 
       43.92        11.87        48.76        49.28        44.32        56.55 
TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-09-1673 TCGA-09-2044 TCGA-09-2050 
       19.99       119.08        29.10         3.02         6.12        71.11 
TCGA-13-1408 TCGA-13-1411 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1498 
       55.23        17.46       124.44        70.82        83.93        66.15 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1509 TCGA-13-1510 TCGA-20-0990 TCGA-23-1022 
      115.07        43.20        80.15        44.68        25.94        49.68 
TCGA-23-1029 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 
        8.81       129.96         4.27         6.38        33.47        58.13 
TCGA-23-2077 TCGA-23-2078 TCGA-24-1103 TCGA-24-1413 TCGA-24-1430 TCGA-24-1436 
      115.89        87.48        54.12         6.31        28.37         8.55 
TCGA-24-1464 TCGA-24-1546 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 
       12.46        64.27        70.62        39.88        19.53        48.33 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-1930 
        8.32         3.72        11.28         5.79        22.68        81.11 
TCGA-24-2033 TCGA-24-2254 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 TCGA-24-2290 
       18.48        57.07        47.54        70.45         0.82        36.23 
TCGA-24-2298 TCGA-25-1321 TCGA-25-1329 TCGA-25-1630 TCGA-25-1878 TCGA-25-2392 
       53.26        33.96        15.02        38.20        85.05         1.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 
        3.02        12.00         2.96        26.99        78.90       101.79 
TCGA-29-1695 TCGA-29-1699 TCGA-29-1769 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       40.41        36.36        22.98        42.25        21.47        11.47 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1861 TCGA-36-1574 TCGA-36-1577 TCGA-36-1581 
       51.91         2.47        34.78        22.55        25.74        24.69 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2591 
       18.31        20.52         6.05        16.18        47.57        40.77 
TCGA-57-1582 TCGA-57-1993 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 
       24.03        25.08        20.94        18.54        27.88        28.47 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1917 TCGA-61-1918 TCGA-61-2002 
        2.43        33.67        43.69        43.43        15.75        17.98 
TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2096 TCGA-61-2109 TCGA-10-0928 
        1.18        45.40         4.80        58.39        20.68        18.51 
TCGA-10-0930 TCGA-10-0938 TCGA-13-0714 TCGA-13-0751 TCGA-13-0758 TCGA-13-0762 
       34.19        20.91         6.21        55.17        11.38       111.78 
TCGA-13-0794 TCGA-13-0803 TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 TCGA-13-0891 
       63.09        43.86        68.94       153.37        95.15       102.84 
TCGA-13-0904 TCGA-13-0916 TCGA-13-0923 
       50.37        58.68        83.74 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
        2.01        46.62         1.08        18.51        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1364 
       21.57        63.98        65.46         0.53        32.52        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 
       76.57       103.40        82.39        41.59         0.79        38.37 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       36.23        31.86        47.70        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       89.33        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       30.51        17.98         5.85         8.55        97.55         6.18 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
       35.15         4.54       112.41        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       26.93        12.46        77.10        81.17        28.54        83.31 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       57.27        81.01        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       29.42        20.68        22.39        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
       90.38         4.24       127.27        13.97        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       34.16        65.52        54.25        14.53        80.02        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       77.88        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.93         2.66        47.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       32.09        49.41        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68        19.46        33.30 
TCGA-23-1118 TCGA-23-1122 TCGA-23-1809 TCGA-23-2072 TCGA-23-2079 TCGA-23-2081 
       86.01        39.09         0.53        24.95        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56         7.66        22.32        63.55        47.41 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       18.67        43.53        72.92        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
        3.45         1.18        22.22        26.96        57.40        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       90.15        88.37        38.24         3.48         3.81         4.37 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        5.52         9.80        30.21        16.44        11.05         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
      152.02        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
       55.92        28.18        64.01        44.52        36.16         0.79 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 
        0.36        31.63        44.61        67.36        16.64        33.11 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86         1.02        26.96        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
        2.01        34.98        65.00        37.97         2.99        12.99 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       18.58        27.62        17.03        12.95        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2398 TCGA-25-2399 
       24.00        13.02        49.05        38.04        45.01        19.99 
TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 
       42.02        29.03        31.00        47.61        48.33        39.02 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.93        31.20        68.32        16.93        23.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 
       66.81        62.93        39.42        31.30        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        7.23         5.36        36.30        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 
       45.11        13.84         9.76        35.77        38.07        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
       15.68         0.26        48.10        44.91         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 
        2.20        28.77        29.10        21.53        22.85         8.55 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       30.08        27.85        24.23        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2548 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       20.98        14.17        11.47        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       10.42         1.48        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.02       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
        9.40        34.39         2.14         5.42        44.81        11.11 
TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 
        8.09        31.43         4.34        31.79        48.79        44.84 
TCGA-61-1738 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
        9.07        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        67.76        38.17         2.01         5.52        14.50 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2088 
        4.01        30.64        39.85        30.64        45.96         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       51.72        71.74        61.64        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
        6.48        76.87        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 
       29.16         9.47        57.76        17.98        35.57        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       25.91        81.86        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       36.92        19.99        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 
       12.39        31.20        15.19        17.82         2.50        11.18 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54        38.01        61.84        56.71        58.65        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
      118.42       107.28        20.35        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 
       45.99        51.02        35.28        35.31        13.61       107.18 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
      111.39        66.67        92.42       145.45        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       66.15       134.04        19.36       127.79       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 
       60.59       116.65        44.55        37.64       109.32        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 TCGA-13-2071 
       48.79        48.76        85.94        25.41 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         0.82                          0.26 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       153.37                        180.20 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       34.190                        31.975 
[1] "0.8 - 153.4 (34.2)" "0.3 - 180.2 (32.0)"
[1] "hr=" "1"  
D36V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  3(2P25.3) MUTATED         1   118                0
  DEL PEAK  3(2P25.3) WILD-TYPE       2   440                2
D36V3, multiclass
                  clus
vv                 DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  OMENTUM                                    1                             2
  OVARY                                    118                           440
  PERITONEUM OVARY                           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"
D36V4, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED   114   1
  DEL PEAK  3(2P25.3) WILD-TYPE 427   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED    114    1
  DEL PEAK  3(2P25.3) WILD-TYPE  427    4
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                          114                           427
  YES                           1                             4
[1] 2 2
[1] FALSE
D36V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  3(2P25.3) MUTATED    7  3  0  0
  DEL PEAK  3(2P25.3) WILD-TYPE  8 23  5  3
D36V6, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                           7                             8
  R1                           3                            23
  R2                           0                             5
  RX                           0                             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"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     3  69
  DEL PEAK  3(2P25.3) WILD-TYPE   7 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      3   69
  DEL PEAK  3(2P25.3) WILD-TYPE    7  258
                        clus
vv                       DEL PEAK  3(2P25.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK  3(2P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           258
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q22.1) MUTATED    53  77
  DEL PEAK  4(2Q22.1) WILD-TYPE 175 254
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          130                           429 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           77                           254 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-04-1336 TCGA-04-1338 TCGA-04-1346 TCGA-04-1349 TCGA-04-1356 TCGA-04-1362 
       49.15        46.62        65.52        21.57        49.28        44.32 
TCGA-04-1364 TCGA-04-1517 TCGA-04-1651 TCGA-04-1654 TCGA-09-1665 TCGA-09-1673 
       33.67        19.99        36.23        47.70        41.62         3.02 
TCGA-09-1674 TCGA-09-2048 TCGA-09-2054 TCGA-13-1404 TCGA-13-1411 TCGA-13-1484 
        8.55         4.54        20.94        81.17        17.46       124.44 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1506 TCGA-13-A5FU 
       52.44        93.90       127.27        66.15        34.16         8.42 
TCGA-20-0987 TCGA-20-0991 TCGA-20-1682 TCGA-20-1686 TCGA-23-1031 TCGA-23-1116 
       23.05        26.20        27.52         2.93        18.90        19.46 
TCGA-23-1117 TCGA-23-1121 TCGA-23-2641 TCGA-23-2645 TCGA-24-1104 TCGA-24-1413 
       33.30         6.38         2.76         4.50        63.55         6.31 
TCGA-24-1417 TCGA-24-1428 TCGA-24-1469 TCGA-24-1474 TCGA-24-1546 TCGA-24-1555 
        7.82        17.39         9.11        22.22        64.27        88.50 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1614 TCGA-24-1846 TCGA-24-1847 
       39.88        19.53        47.70        48.33         4.37        11.28 
TCGA-24-1920 TCGA-24-1923 TCGA-24-2029 TCGA-24-2260 TCGA-24-2288 TCGA-24-2289 
        9.80        22.68        14.43        36.16         0.82        67.36 
TCGA-25-1318 TCGA-25-1323 TCGA-25-1627 TCGA-25-1635 TCGA-25-2392 TCGA-25-2398 
       34.98        12.99        12.95        52.04         1.02        45.01 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1695 TCGA-29-1699 TCGA-29-1701 
       26.99        78.90       101.79        40.41        36.36        16.93 
TCGA-29-1702 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1770 TCGA-29-1774 
       23.93        31.27        17.36        66.81        24.36        17.33 
TCGA-29-2414 TCGA-29-2434 TCGA-30-1853 TCGA-30-1860 TCGA-30-1861 TCGA-30-1887 
       86.17        11.47        36.26        44.91        34.78        24.26 
TCGA-31-1951 TCGA-36-1575 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 
       22.49         8.55        24.69        35.05        29.49        29.82 
TCGA-36-2538 TCGA-36-2543 TCGA-36-2545 TCGA-36-2551 TCGA-42-2587 TCGA-57-1584 
       25.08         2.24        18.31        16.18        23.74        21.14 
TCGA-57-1585 TCGA-59-2350 TCGA-59-2352 TCGA-59-2363 TCGA-61-1725 TCGA-61-1736 
        1.74        22.32         9.40         5.42        31.43        48.79 
TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 TCGA-61-1919 TCGA-61-2009 TCGA-61-2016 
       31.30        42.51        48.92        38.17        39.85         1.18 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2102 TCGA-61-2109 TCGA-61-2614 TCGA-09-0367 
        4.80        51.72         6.48        20.68         8.61        17.98 
TCGA-10-0928 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0758 TCGA-13-0764 
       18.51         2.73        12.39        31.20        11.38        61.84 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0799 TCGA-13-0800 TCGA-13-0807 TCGA-13-0885 
       40.24       118.42        83.34        87.48        13.61       111.39 
TCGA-13-0886 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0911 
      153.37       145.45       102.84        43.36       134.04        44.55 
TCGA-13-0913 TCGA-13-0921 TCGA-13-0924 TCGA-13-2071 
      109.32        48.76        85.94        25.41 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 
        2.01         1.08        18.51        11.87        63.09        48.76 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 
       63.98        65.46         0.53        32.52        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        41.59         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       64.64        31.86        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       74.93        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        5.85        97.55         6.18         6.12        35.15       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       71.11        63.09        39.75        26.93        12.46        77.10 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
       28.54        83.31        55.23        57.27        81.01        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 
       54.64        87.06        61.71        29.42        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1499 
       70.82        83.93       125.56        90.38         4.24       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 
       13.97        43.20        34.82        65.69        65.52        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       44.68        54.25        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 
       76.90        65.52        70.45        25.94        72.20        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       19.10        16.70         2.66        47.54        49.68        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
        2.76        51.35        54.51         3.22        31.20        68.68 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       86.01       129.96         4.27        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       49.84         4.70         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1418 
        7.66        22.32        54.12        47.41         6.38         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        4.83        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14       105.99         3.45         1.18 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       26.96        57.40        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 
       41.39        58.09        70.62        44.09        45.50        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 
       10.26        17.23        90.15        88.37        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1849 TCGA-24-1850 TCGA-24-1924 
        3.48         3.72         3.81         5.79         5.52        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       16.44        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       58.16        34.82       109.71        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       64.01        44.52        57.07         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       31.63        70.45        44.61        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       42.05         2.01        65.00        37.97        33.96         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 
       15.02        18.58        27.62        17.03        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
        0.30        59.15        62.17        35.87        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       24.00        85.05        13.02        49.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       12.00        19.99        42.02         2.96        29.03        31.00 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       47.61        48.33        39.02        33.93        31.20        68.32 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 
       59.67        18.25        41.98        34.62        86.60        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       39.42        31.30        22.98        22.55        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       65.00        62.47        45.11        13.84        42.25        21.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
        9.76        35.77        38.07        51.91         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
        0.26        48.10         6.12        36.62         1.22        57.57 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 
       30.05        48.79        45.57        30.18        18.77         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55        30.08        25.74        27.85        24.23 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 
       33.01        25.91        23.80        21.60        20.98        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
       14.17         6.05        11.47        47.57        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 
       10.42        40.77         1.48        24.03        11.38        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 
       29.00        25.08        25.02       180.20        80.12       116.12 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       34.39         2.14        44.81        11.11         8.09        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 
       18.54        27.88         4.34        31.79        28.47        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 
        5.79        11.41        13.02         9.07        34.13        37.05 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       56.61        67.76        43.43        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 
       14.50        17.98         4.01        30.64        30.64        45.96 
TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
       45.40         4.77        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       65.52        55.50        76.87        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        6.35        31.07        39.68        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
       29.16         9.47        57.76        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.86        34.19        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       36.92        19.99        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       39.58        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0793 
       11.54        38.01       111.78        56.71        58.65       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       63.09        20.35        69.73        45.99        51.02        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 
       35.28        35.31        68.94       107.18        66.67        92.42 
TCGA-13-0889 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       95.15        71.74        66.15        19.36       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0916 
      123.16       118.98        60.59       116.65        37.64        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       84.53        48.79        83.74 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.82                          0.26 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       153.37                        180.20 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       28.505                        33.930 
[1] "0.8 - 153.4 (28.5)" "0.3 - 180.2 (33.9)"
[1] "hr=" "1.1"
D37V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  4(2Q22.1) MUTATED         0   130                1
  DEL PEAK  4(2Q22.1) WILD-TYPE       3   428                1
D37V3, multiclass
                  clus
vv                 DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  OMENTUM                                    0                             3
  OVARY                                    130                           428
  PERITONEUM OVARY                           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"
D37V4, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED   125   1
  DEL PEAK  4(2Q22.1) WILD-TYPE 416   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED    125    1
  DEL PEAK  4(2Q22.1) WILD-TYPE  416    4
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                          125                           416
  YES                           1                             4
[1] 2 2
[1] FALSE
D37V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  4(2Q22.1) MUTATED    4 10  1  0
  DEL PEAK  4(2Q22.1) WILD-TYPE 11 16  4  3
D37V6, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                           4                            11
  R1                          10                            16
  R2                           1                             4
  RX                           0                             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"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     5  75
  DEL PEAK  4(2Q22.1) WILD-TYPE   5 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      5   75
  DEL PEAK  4(2Q22.1) WILD-TYPE    5  252
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          75
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           252
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.3) MUTATED    79  88
  DEL PEAK  5(2Q37.3) WILD-TYPE 149 243
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          167                           392 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           88                           243 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1336 TCGA-04-1338 TCGA-04-1349 TCGA-04-1516 
       13.81        20.52        49.15        46.62        21.57        41.59 
TCGA-04-1536 TCGA-04-1646 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 
       29.10        27.88        55.36        30.51         3.02         8.55 
TCGA-09-2044 TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
        6.12        81.17        28.54        17.46        32.35        87.06 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1494 TCGA-13-1497 TCGA-13-1501 
      124.44        22.39        70.82        93.90       127.27        43.20 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-20-0991 
       65.69        34.16        14.53        77.88        76.90        26.20 
TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 
       27.52         2.93         2.66        49.41        18.90         2.76 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 
       54.51        68.68        19.46        33.30        86.01         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-2077 TCGA-23-2084 TCGA-23-2641 TCGA-24-0982 
       39.09        58.13       115.89        49.84         2.76        22.32 
TCGA-24-1103 TCGA-24-1413 TCGA-24-1417 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 
       54.12         6.31         7.82         5.95         4.83        17.39 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1470 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       18.67         8.55         3.45        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1563 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
       70.62        47.70         3.81        11.28         5.79         5.52 
TCGA-24-1923 TCGA-24-2019 TCGA-24-2020 TCGA-24-2260 TCGA-24-2280 TCGA-24-2290 
       22.68         4.87       152.02        36.16        70.45        36.23 
TCGA-25-1314 TCGA-25-1318 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1635 
       33.01        34.98        27.62        12.95        38.20        52.04 
TCGA-25-1877 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
       24.00         2.96        26.99        78.90        48.33       101.79 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       36.36        16.93        59.67        18.25        41.98        34.62 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1781 TCGA-29-1784 TCGA-30-1718 
       22.98        24.36        17.33         8.38         5.36        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1860 TCGA-30-1861 TCGA-30-1887 TCGA-30-1891 
       36.26         2.47        44.91        34.78        24.26        30.05 
TCGA-31-1951 TCGA-31-1953 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 
       22.49         6.71        22.55         8.55        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2537 TCGA-36-2543 TCGA-36-2545 
       24.23        24.69        35.05        25.91         2.24        18.31 
TCGA-36-2547 TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-57-1585 TCGA-57-1993 
       20.52        28.93        42.02        40.77         1.74        25.08 
TCGA-57-1994 TCGA-59-2351 TCGA-59-2363 TCGA-61-1724 TCGA-61-1728 TCGA-61-1738 
       25.02       116.12         5.42        20.94        27.88        35.80 
TCGA-61-1740 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 
        2.43         5.79        13.02        31.30        48.92        56.61 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2104 
       30.64         1.18         4.80        51.72        71.74        76.87 
TCGA-61-2109 TCGA-61-2612 TCGA-61-2614 TCGA-09-0369 TCGA-10-0928 TCGA-10-0930 
       20.68         6.35         8.61        35.57        18.51        34.19 
TCGA-10-0931 TCGA-10-0934 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       32.88         6.71        24.59        44.55        39.58        12.39 
TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0799 
       55.17        11.38        11.54        38.01       111.78        83.34 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0904 
       45.99        43.86       145.45       102.84        43.36        50.37 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 
      123.16        60.59        58.68        48.79        83.74 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1341 
       11.87        43.92        41.00         1.81         2.01         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
       18.51        11.87        65.52        63.09        48.76        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       65.46         0.53        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 
       76.57       103.40        82.39        56.55        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       38.37       119.08        84.20        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       64.64        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 
       17.98         5.85        97.55         6.18        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       12.46        77.10        83.31        55.23        57.27        81.01 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 
       54.64        61.71        29.42        20.68        83.93        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
      125.56        90.38         4.24        66.15       115.07        13.97 
TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 
       34.82        65.52        80.15        44.68        54.25        80.02 
TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       78.48        65.52        70.45         8.42        23.05        25.94 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 
       72.20        25.38        19.10        16.70        47.54        49.68 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        26.83        32.09         8.81        29.13 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 
       51.35         3.22        31.20       129.96         4.27        33.47 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2643 
        0.53        24.95        87.48        91.66        77.00         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       63.55        47.41         6.38         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        6.25         6.02         5.36        28.37        18.64        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 
       72.92        12.46        45.14       105.99         9.11         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       41.06        51.91        39.88        19.53        44.09        45.50 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1920 
       38.24         8.32         3.48         3.72         4.37         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
       30.21        16.44        11.05        81.11        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       64.01        44.52        57.07         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 
       31.63        44.61         0.82        67.36        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        26.96        52.04        42.05 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
        2.01        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       15.02        18.58        17.03        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 
       62.17        35.87        14.96        24.99        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       49.05         1.02        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1694 
       19.99        42.02        29.03        31.00        47.61        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1702 TCGA-29-1710 
       40.41        33.93        31.20        68.32        23.93        31.27 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       17.36        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 
       22.55        12.36        11.84        12.30        14.93         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68         0.26        48.10         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1955 
       57.57        48.79        45.57        30.18        18.77        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1576 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 
       30.08        33.01        29.49        29.82        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       21.60        20.98        14.17         6.05        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       47.57        23.74        10.42         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       21.14        22.32        29.00       180.20        80.12        22.32 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
        9.40        34.39         2.14        44.81        11.11         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       31.43        18.54         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 
       44.84        33.67        43.69         1.45         8.42        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 
        9.07        34.13        37.05        42.51        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 
        4.01        30.64        39.85        45.96        45.40         4.77 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
       44.52       125.75        22.22        31.07        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
        0.79         9.99        29.16         9.47        57.76        17.98 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 
       54.31        25.91        81.86        14.66        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 
       19.99        20.91         6.21         2.73        31.20        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       17.82         2.50        11.18        61.84        56.71        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       40.24       118.42       107.28        63.09        20.35        69.73 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       87.48        51.02        35.28        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18       111.39       153.37        66.67        92.42        95.15 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 
       71.74        66.15       134.04        19.36       127.79       118.98 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 
      116.65        44.55        37.64       109.32        84.53        48.76 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         1.18                          0.26 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       152.02                        180.20 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        30.05                         33.80 
[1] "1.2 - 152.0 (30.1)" "0.3 - 180.2 (33.8)"
[1] "hr=" "1.1"
D38V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  5(2Q37.3) MUTATED         1   168                1
  DEL PEAK  5(2Q37.3) WILD-TYPE       2   390                1
D38V3, multiclass
                  clus
vv                 DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  OMENTUM                                    1                             2
  OVARY                                    168                           390
  PERITONEUM OVARY                           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"
D38V4, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED   163   3
  DEL PEAK  5(2Q37.3) WILD-TYPE 378   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED    163    3
  DEL PEAK  5(2Q37.3) WILD-TYPE  378    2
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                          163                           378
  YES                           3                             2
[1] 2 2
[1] FALSE
D38V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  5(2Q37.3) MUTATED    6  5  1  1
  DEL PEAK  5(2Q37.3) WILD-TYPE  9 21  4  2
D38V6, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  R0                           6                             9
  R1                           5                            21
  R2                           1                             4
  RX                           1                             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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     4  96
  DEL PEAK  5(2Q37.3) WILD-TYPE   6 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      4   96
  DEL PEAK  5(2Q37.3) WILD-TYPE    6  231
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          96
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           231
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  6(3P26.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P26.2) MUTATED    83 118
  DEL PEAK  6(3P26.2) WILD-TYPE 145 213
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          201                           358 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          118                           213 
$`DEL PEAK  6(3P26.2) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1353 
       43.92        49.15        65.52        63.09        65.46         0.53 
TCGA-04-1356 TCGA-04-1365 TCGA-04-1371 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       49.28        76.57        82.39        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1644 TCGA-04-1652 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 
       84.20        48.89        31.86         9.99        38.43        61.87 
TCGA-09-1670 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-13-1407 
       17.98       112.41        71.11        39.75        20.94        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1481 TCGA-13-1487 TCGA-13-1489 
       55.23        57.27        17.46        87.06        22.39        83.93 
TCGA-13-1492 TCGA-13-1497 TCGA-13-1499 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
      125.56       127.27       115.07        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-20-0991 TCGA-20-1684 TCGA-20-1685 
       80.02        76.90        65.52        26.20        19.10        16.70 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 
        2.66        47.54        15.39        18.90         2.76        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1119 TCGA-23-1122 TCGA-23-1124 TCGA-23-2077 
        3.22        68.68       129.96        39.09        58.13       115.89 
TCGA-24-0970 TCGA-24-0975 TCGA-24-1103 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 
       11.64        21.80        54.12         7.82         7.99         0.76 
TCGA-24-1426 TCGA-24-1430 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
        5.36        28.37        18.67         8.55        72.92        12.46 
TCGA-24-1469 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1553 TCGA-24-1564 
        9.11        57.40        16.21        41.06        58.09        25.87 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       48.33         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2026 
        5.52         9.80        30.21        11.05        81.11        34.82 
TCGA-24-2027 TCGA-24-2035 TCGA-24-2261 TCGA-24-2262 TCGA-24-2280 TCGA-24-2288 
      109.71        28.18         0.79         0.36        70.45         0.82 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 
       36.23        16.64        55.86         1.02         2.01        37.97 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1627 TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 
       33.96        12.99        12.95        59.15        62.17        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
       24.99        24.00        38.04        78.90        48.33       101.79 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1710 
       40.41        31.20        68.32        36.36        16.93        31.27 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1769 TCGA-29-1777 TCGA-29-1783 
       17.36        86.60        62.93        22.98        12.30         7.23 
TCGA-29-1784 TCGA-29-2429 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
        5.36        13.84        38.07        51.91        36.26         2.47 
TCGA-30-1862 TCGA-30-1887 TCGA-31-1959 TCGA-36-1569 TCGA-36-1575 TCGA-36-1576 
        6.12        24.26         2.20        29.10         8.55        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2534 TCGA-36-2543 TCGA-36-2545 
       25.74        24.23        33.01        29.82         2.24        18.31 
TCGA-36-2547 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2593 
       20.52        11.47        47.57        23.74        42.02         1.48 
TCGA-57-1582 TCGA-57-1992 TCGA-59-2351 TCGA-59-2363 TCGA-61-1722 TCGA-61-1730 
       24.03        29.00       116.12         5.42         8.09         4.34 
TCGA-61-1733 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 
       31.79         2.43        33.67        43.69         1.45         5.79 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
        9.07        34.13        56.61        43.43        15.75        38.17 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2098 
        5.52        14.50        17.98        30.64         1.18        65.52 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2113 TCGA-09-0364 TCGA-09-0365 
        6.48        76.87        20.68        22.22        29.16         9.47 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0928 TCGA-10-0938 TCGA-13-0724 TCGA-13-0730 
       17.98        35.57        18.51        20.91         2.73        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0764 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 
       55.17        11.18        61.84       118.42        63.09        20.35 
TCGA-13-0802 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       51.02       111.39       153.37        66.67        92.42       145.45 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0916 TCGA-13-0920 
       50.37       123.16       118.98        60.59        58.68        48.79 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       48.76        83.74        85.94 

$`DEL PEAK  6(3P26.2) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 
       13.81        20.52        11.87        41.00         1.81         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 
       46.62         1.08        18.51        11.87        48.76        21.57 
TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1514 
       63.98        32.52        44.32        33.67       103.40        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 
       41.59        19.99         0.79        55.43        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1662 TCGA-09-1664 
       64.64        36.23        47.70        45.37        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        55.36        30.51         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       63.09        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       81.01        32.35        54.64        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       20.68        70.82        52.44        93.90        90.38         4.24 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15        13.97        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT TCGA-13-A5FU 
       65.52        80.15        78.48        77.88        70.45         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1686 
       23.05        25.94        72.20        27.52        25.38         2.93 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       49.68        40.54        26.83        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1109 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       29.13        51.35        31.20        19.46        33.30        86.01 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 
        4.27         6.38        33.47         0.53        24.95        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
        7.63        41.56         7.66        22.32        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        6.31         6.38         7.86         6.25         6.02         5.95 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1435 TCGA-24-1466 TCGA-24-1467 
        4.83        17.39        18.64        43.53        45.14       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 
        3.45         1.18        22.22        26.96        64.27        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       51.91        41.39        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       44.09        45.50        47.70        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 
       88.37        38.24        11.28         5.79        22.68        16.44 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2030 
        4.87       152.02        44.84        58.16        14.43        55.92 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2267 
       18.48        64.01        44.52        57.07        36.16        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2295 TCGA-24-2298 TCGA-25-1313 
       31.63        44.61        67.36        33.11        53.26        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 
       33.01        52.04        42.05        34.98        65.00         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 
       15.02        18.58        27.62        17.03        20.61        38.20 
TCGA-25-1631 TCGA-25-1634 TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
        0.30        35.87        52.04        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
        1.02         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 
        2.96        29.03        31.00        26.99        47.61        39.02 
TCGA-29-1696 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       33.93        23.93        59.67        18.25        41.98        34.62 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       66.81        39.42        31.30        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 
       12.36        11.84        14.93         8.38        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        62.47        45.11        42.25        21.47        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
        9.76        35.77        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       34.78        36.62         1.22        57.57        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1578 
       44.12        28.77        21.53        22.85        22.55        27.85 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       24.69        35.05        29.49        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2588 
       21.60        20.98        14.17         6.05        16.18        28.93 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       10.42        40.77        11.38        21.14         1.74        22.32 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 
       25.08        25.02       180.20        80.12        22.32         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
       34.39         2.14        44.81        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54        27.88        28.47        48.79        44.84        35.80 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
        8.42        11.41        13.02        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
       48.92        67.76         2.01         4.01        30.64        39.85 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2110 TCGA-61-2111 
       61.64        58.39        60.62        55.50        44.52       125.75 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 
        9.99        57.76        54.31        25.91        81.86        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       32.88        14.66         6.71        35.44        36.92        19.99 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55        39.58        12.39        31.20 
TCGA-13-0727 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       15.19         2.50        11.38        11.54        38.01       111.78 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 
       56.71        58.65        40.24       107.28        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       87.48        45.99        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       68.94       107.18        95.15       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0910 TCGA-13-0911 
       66.15       134.04        19.36       127.79       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-2071 
       37.64       109.32        84.53        25.41 

  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                         0.36                          0.26 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                       153.37                        180.20 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                       31.200                        33.385 
[1] "0.4 - 153.4 (31.2)" "0.3 - 180.2 (33.4)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  6(3P26.2) MUTATED         2   202                0
  DEL PEAK  6(3P26.2) WILD-TYPE       1   356                2
D39V3, multiclass
                  clus
vv                 DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    202                           356
  PERITONEUM OVARY                           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"
D39V4, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.2) MUTATED   196   2
  DEL PEAK  6(3P26.2) WILD-TYPE 345   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED    196    2
  DEL PEAK  6(3P26.2) WILD-TYPE  345    3
     clus
vv    DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  NO                          196                           345
  YES                           2                             3
[1] 2 2
[1] FALSE
D39V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  6(3P26.2) MUTATED    6  6  1  0
  DEL PEAK  6(3P26.2) WILD-TYPE  9 20  4  3
D39V6, multiclass
    clus
vv   DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  R0                           6                             9
  R1                           6                            20
  R2                           1                             4
  RX                           0                             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"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.2) MUTATED     3 112
  DEL PEAK  6(3P26.2) WILD-TYPE   7 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED      3  112
  DEL PEAK  6(3P26.2) WILD-TYPE    7  215
                        clus
vv                       DEL PEAK  6(3P26.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         112
                        clus
vv                       DEL PEAK  6(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           215
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  7(3Q13.31) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(3Q13.31) MUTATED    30  52
  DEL PEAK  7(3Q13.31) WILD-TYPE 198 279
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            82                            477 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            52                            279 
$`DEL PEAK  7(3Q13.31) MUTATED`
TCGA-04-1356 TCGA-04-1514 TCGA-04-1651 TCGA-04-1652 TCGA-09-2050 TCGA-13-1405 
       49.28        56.55        36.23        31.86        71.11        28.54 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1487 TCGA-13-1488 TCGA-13-1492 
       55.23        81.01        17.46        22.39        70.82       125.56 
TCGA-13-1507 TCGA-13-1512 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1024 
       65.52        14.53        19.10        16.70         2.66        15.39 
TCGA-23-1027 TCGA-23-1032 TCGA-23-1118 TCGA-23-1121 TCGA-24-0970 TCGA-24-1418 
       32.09         2.76        86.01         6.38        11.64         7.99 
TCGA-24-1422 TCGA-24-1426 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
        0.76         5.36         8.55        12.46        45.14         9.11 
TCGA-24-1471 TCGA-24-1545 TCGA-24-1927 TCGA-24-2020 TCGA-25-1317 TCGA-25-1318 
        1.18        57.40        16.44       152.02         2.01        34.98 
TCGA-25-1321 TCGA-25-1623 TCGA-25-1626 TCGA-25-2393 TCGA-29-1694 TCGA-29-1695 
       33.96        18.58        17.03        38.04        39.02        40.41 
TCGA-29-1697 TCGA-29-1710 TCGA-29-1777 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 
       31.20        31.27        12.30         7.23        65.00        45.11 
TCGA-36-1568 TCGA-36-1578 TCGA-36-2540 TCGA-42-2587 TCGA-42-2589 TCGA-59-2350 
       28.77        27.85        23.80        23.74        42.02        22.32 
TCGA-59-2354 TCGA-61-1724 TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-1904 
       34.39        20.94         4.34        33.67        43.69         9.07 
TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2018 TCGA-61-2096 TCGA-61-2101 
       38.17         4.01        30.64        45.40        58.39        55.50 
TCGA-61-2613 TCGA-09-0369 TCGA-10-0936 TCGA-10-0938 TCGA-13-0720 TCGA-13-0751 
       31.07        35.57        36.92        20.91        44.55        55.17 
TCGA-13-0762 TCGA-13-0791 TCGA-13-0794 TCGA-13-0803 TCGA-13-0807 TCGA-13-0887 
      111.78        40.24        63.09        43.86        13.61        66.67 
TCGA-13-0889 TCGA-13-0906 TCGA-13-0910 TCGA-13-0920 
       95.15       118.98       116.65        48.79 

$`DEL PEAK  7(3Q13.31) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       65.52        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
        0.53        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        41.59        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       64.64        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       74.93        41.62        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       17.98         5.85         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15         4.54       112.41        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 
       20.94        26.93        12.46        77.10        81.17        83.31 
TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       57.27        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 
      124.44        20.68        83.93        52.44        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24       127.27        66.15       115.07        13.97        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       34.82        65.69        34.16        80.15        44.68        54.25 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       80.02        78.48        77.88        76.90        65.52        70.45 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       25.38         2.93        47.54        49.68        40.54        26.83 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        29.13        18.90        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 
        3.22        31.20        68.68        19.46        33.30       129.96 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.70         4.50         7.63        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 
        7.82         7.86         6.25         6.02         5.95         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 
       17.39        28.37        18.64        18.67        43.53        72.92 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 
      105.99         3.45        22.22        26.96        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       11.05        81.11         4.87        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
      109.71        14.43        55.92        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       44.52        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       31.63        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 
       33.01        52.04        42.05        65.00        37.97         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       12.99        15.02        27.62        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        59.15        62.17        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        24.00        85.05        13.02        49.05         1.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        3.02        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       29.03        31.00        26.99        78.90        47.61        48.33 
TCGA-29-1693 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
      101.79        33.93        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       59.67        18.25        41.98        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 
       22.55        17.33        12.36        11.84        14.93         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        5.36        36.30        86.17        62.47        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       21.47        11.47         9.76        35.77        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       36.26         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51        44.12         2.20        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
       22.85        22.55         8.55        30.08        25.74        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.08        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 
       14.17         6.05        16.18        11.47        47.57        28.93 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       10.42        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       80.12       116.12         9.40         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
       11.11         8.09        31.43        18.54        27.88        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 
       28.47        48.79        44.84        35.80         2.43         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 
        8.42         5.79        11.41        13.02        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 
       15.75         2.01         5.52        14.50        17.98        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
       30.64         1.18        45.96         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 
       71.74        61.64        60.62        65.52         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 
       20.68        44.52       125.75        22.22         6.35         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       39.68        18.94         0.79         9.99        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       57.76        17.98        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       34.19        32.88        14.66         6.71        35.44        19.99 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        39.58         2.73        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       15.19        17.82         2.50        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 
       38.01        61.84        56.71        58.65       118.42       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       20.35        69.73        83.34        87.48        45.99        51.02 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        35.31        68.94       107.18       111.39       153.37 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       92.42       145.45       102.84        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 
      134.04        19.36       127.79        50.37       123.16        60.59 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       44.55        37.64       109.32        58.68        84.53        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                          0.76                           0.26 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                        152.02                         180.20 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                         32.88                          32.88 
[1] "0.8 - 152.0 (32.9)" "0.3 - 180.2 (32.9)"
[1] "hr=" "1.1"
D40V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  7(3Q13.31) MUTATED         0    82                0
  DEL PEAK  7(3Q13.31) WILD-TYPE       3   476                2
D40V3, multiclass
                  clus
vv                 DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  OMENTUM                                     0                              3
  OVARY                                      82                            476
  PERITONEUM OVARY                            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"
D40V4, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED    80   0
  DEL PEAK  7(3Q13.31) WILD-TYPE 461   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED     80    0
  DEL PEAK  7(3Q13.31) WILD-TYPE  461    5
     clus
vv    DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  NO                            80                            461
  YES                            0                              5
[1] 2 2
[1] FALSE
D40V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  7(3Q13.31) MUTATED    1  6  0  0
  DEL PEAK  7(3Q13.31) WILD-TYPE 14 20  5  3
D40V6, multiclass
    clus
vv   DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  R0                            1                             14
  R1                            6                             20
  R2                            0                              5
  RX                            0                              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"
D40V7, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED     1  54
  DEL PEAK  7(3Q13.31) WILD-TYPE   9 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      1   54
  DEL PEAK  7(3Q13.31) WILD-TYPE    9  273
                        clus
vv                       DEL PEAK  7(3Q13.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK  7(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            273
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  8(4Q22.1) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q22.1) MUTATED   160 216
  DEL PEAK  8(4Q22.1) WILD-TYPE  68 115
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                          376                           183 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                          216                           115 
$`DEL PEAK  8(4Q22.1) MUTATED`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1341 
       13.81        11.87        43.92        41.00        49.15         1.08 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 TCGA-04-1361 TCGA-04-1364 TCGA-04-1367 
       11.87        48.76        63.98        32.52        33.67       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 
       82.39        56.55        41.59        19.99       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       36.23        31.86        47.70        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        57.60        55.36        30.51        17.98 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        8.55        97.55         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 TCGA-13-1484 
       83.31        55.23        57.27        81.01        87.06       124.44 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       90.38       127.27       115.07        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       65.69        80.15        44.68        54.25        14.53        80.02 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1682 
       78.48        76.90        65.52        70.45        25.94        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       25.38        19.10         2.93         2.66        47.54        49.68 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 
       49.41         8.81        29.13         2.76        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       31.20        68.68        19.46        86.01       129.96        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 
       33.47        58.13         0.53        24.95        87.48        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-0982 
        2.76         4.70         4.50        11.64        21.80        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.99         7.86         0.76         6.02         5.95         5.36 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       72.92         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       16.21        51.91        41.39        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 
       19.53        44.09        45.50        47.70        17.23        90.15 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       48.33        38.24         8.32         3.72         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
      109.71        14.43        55.92        57.07        36.16         0.79 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 
       47.54        31.63        70.45        44.61         0.82        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 
       16.64        33.11        55.86        53.26         1.02        33.01 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       42.05         2.01        34.98        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       12.99        15.02        27.62        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       38.20         0.30        62.17        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2398 
       24.99        24.00        13.02        49.05         1.02        45.01 
TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 
       42.02        29.03        31.00        26.99        78.90        48.33 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1762 
       40.41        31.20        68.32        36.36        18.25        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 
       66.81        62.93        22.98        24.36        22.55        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 
       12.30        14.93         8.38         7.23         5.36        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 
       65.00        45.11        42.25        11.47        38.07        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1891 
        2.47        15.68        44.91        34.78        57.57        30.05 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1570 
       30.18        18.77         6.71        42.51         2.20        21.53 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       22.85         8.55        30.08        25.74        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 
       35.05        33.01        29.49        29.82        25.08        21.60 
TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
        2.24        20.52        14.17        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 
       24.03        21.14         1.74        29.00        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       22.32       116.12         9.40         2.14         5.42        44.81 
TCGA-61-1725 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       31.43         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80         2.43        33.67         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1917 
       11.41        13.02         9.07        34.13        31.30        43.43 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 TCGA-61-2097 
       39.85         1.18        45.40        51.72        71.74        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
      125.75        22.22         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       18.94         0.79        29.16        57.76        17.98        35.57 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0935 TCGA-10-0937 
       25.91        81.86        18.51        34.19        35.44        19.99 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       24.59        44.55         2.73        12.39        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0792 
       55.17        11.18        11.38        11.54       111.78       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 
      107.28        63.09        20.35        69.73        45.99        43.86 
TCGA-13-0804 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       35.28        68.94       107.18       111.39        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0899 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       95.15       145.45        66.15       127.79       123.16       118.98 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      116.65        44.55        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       48.79        48.76        83.74        85.94 

$`DEL PEAK  8(4Q22.1) WILD-TYPE`
TCGA-59-A5PD TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1346 
       20.52         1.81         2.01        46.62        18.51        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 
       63.09        21.57        65.46         0.53        49.28        44.32 
TCGA-04-1365 TCGA-04-1519 TCGA-04-1525 TCGA-09-1665 TCGA-09-1667 TCGA-09-1672 
       76.57         0.79        38.37        41.62        61.87         5.85 
TCGA-09-1673 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-13-1405 TCGA-13-1411 
        3.02         6.18        35.15         4.54        28.54        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1496 
       32.35        54.64        61.71        29.42        20.68         4.24 
TCGA-13-1498 TCGA-13-1506 TCGA-13-1507 TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 
       66.15        34.16        65.52        77.88         8.42        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1685 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       26.20        72.20        16.70        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1031 TCGA-23-1109 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 
       32.09        18.90        51.35        33.30         4.27         6.38 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0979 TCGA-24-0980 
      115.89        91.66        77.00         7.63        41.56         7.66 
TCGA-24-1423 TCGA-24-1427 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        6.25         4.83        12.46        45.14       105.99         9.11 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1553 TCGA-24-1564 TCGA-24-1565 
       64.27        56.58        41.06        58.09        25.87        10.26 
TCGA-24-1604 TCGA-24-1843 TCGA-24-1845 TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 
       88.37         3.48         3.81        34.82        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2289 TCGA-25-1313 TCGA-25-1315 
       64.01        44.52         0.36        67.36        26.96        52.04 
TCGA-25-1319 TCGA-25-1623 TCGA-25-1632 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 
       65.00        18.58        59.15        85.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 
       12.00        19.99         2.96        47.61       101.79        39.02 
TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 
       33.93        16.93        23.93        59.67        41.98        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1768 TCGA-29-1774 TCGA-29-1775 
       34.62        17.36        39.42        31.30        17.33        12.36 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ 
       36.30        62.47        13.84        21.47         9.76        35.77 
TCGA-30-1718 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       51.91         0.26        48.10         6.12        36.62         1.22 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 
       24.26        48.79        45.57        22.49        44.12        28.77 
TCGA-36-1569 TCGA-36-1574 TCGA-36-1578 TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 
       29.10        22.55        27.85        25.91        23.80        20.98 
TCGA-36-2545 TCGA-36-2549 TCGA-57-1583 TCGA-57-1586 TCGA-57-1994 TCGA-59-2349 
       18.31         6.05        11.38        22.32        25.02        80.12 
TCGA-59-2354 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 
       34.39        11.11         8.09        20.94        18.54        27.88 
TCGA-61-1743 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       43.69        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2012 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
       15.75        38.17        30.64        45.96         4.80         4.77 
TCGA-61-2095 TCGA-61-2096 TCGA-WR-A838 TCGA-09-0365 TCGA-10-0925 TCGA-10-0931 
       61.64        58.39         9.99         9.47        54.31        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0723 
       14.66         6.71        36.92        20.91         6.21        39.58 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       31.20         2.50        38.01        61.84        56.71        58.65 
TCGA-13-0791 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0805 TCGA-13-0807 
       40.24        83.34        87.48        51.02        35.31        13.61 
TCGA-13-0886 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
      153.37       102.84        43.36        71.74       134.04        19.36 
TCGA-13-0904 TCGA-13-0908 TCGA-13-2071 
       50.37        60.59        25.41 

  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                         0.30                          0.26 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                       180.20                        153.37 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                        33.06                         32.09 
[1] "0.3 - 180.2 (33.1)" "0.3 - 153.4 (32.1)"
[1] "hr=" "1.2"
D41V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  8(4Q22.1) MUTATED         2   377                1
  DEL PEAK  8(4Q22.1) WILD-TYPE       1   181                1
D41V3, multiclass
                  clus
vv                 DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    377                           181
  PERITONEUM OVARY                           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"
D41V4, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.1) MUTATED   367   3
  DEL PEAK  8(4Q22.1) WILD-TYPE 174   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED    367    3
  DEL PEAK  8(4Q22.1) WILD-TYPE  174    2
     clus
vv    DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  NO                          367                           174
  YES                           3                             2
[1] 2 2
[1] FALSE
D41V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  8(4Q22.1) MUTATED   12 18  4  3
  DEL PEAK  8(4Q22.1) WILD-TYPE  3  8  1  0
D41V6, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  R0                          12                             3
  R1                          18                             8
  R2                           4                             1
  RX                           3                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.1) MUTATED     9 213
  DEL PEAK  8(4Q22.1) WILD-TYPE   1 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED      9  213
  DEL PEAK  8(4Q22.1) WILD-TYPE    1  114
                        clus
vv                       DEL PEAK  8(4Q22.1) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         213
                        clus
vv                       DEL PEAK  8(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           114
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK  9(4Q34.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q34.3) MUTATED   170 235
  DEL PEAK  9(4Q34.3) WILD-TYPE  58  96
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          405                           154 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          235                            96 
$`DEL PEAK  9(4Q34.3) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       49.15        46.62         1.08        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       48.76        63.98        65.46        49.28        44.32        33.67 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 
      103.40        82.39        56.55        41.59        19.99        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 
       84.20        55.43        48.89        27.88        64.64        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 
       41.62        57.60        30.51        17.98         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 
       77.10        81.17        83.31        55.23        57.27        32.35 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       87.06        29.42       124.44        22.39        70.82        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
       52.44       125.56        90.38       127.27       115.07        13.97 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       34.82        65.69        80.15        14.53        80.02        78.48 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1683 TCGA-20-1685 
       76.90        65.52        70.45        25.94        25.38        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1026 TCGA-23-1027 
        2.93         2.66        47.54        49.68        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 
       86.01       129.96         4.27         6.38        39.09        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
        0.53        24.95       115.89        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        2.76         4.70        11.64        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 
       54.12        47.41         6.31         6.38         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        0.76         6.25         5.95         5.36        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 
       18.64        18.67         8.55        45.14         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        1.18        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       41.06        51.91        41.39        88.50        70.62        39.88 
TCGA-24-1560 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1842 
       44.09        47.70        17.23        90.15        88.37         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 
        3.48         3.72         3.81         4.37         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 
        9.80        22.68        30.21        11.05        81.11       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       57.07        36.16         0.79        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
       44.61        67.36        36.23        16.64        33.11        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       34.98        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-2042 
       59.15        62.17        35.87        52.04        24.99        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 
       49.05         1.02        12.00        45.01        42.02        29.03 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       31.00        78.90       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1707 
       31.20        68.32        36.36        16.93        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 
       31.27        34.62        17.36        86.60        62.93        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 
       22.98        22.55        11.84        12.30         8.38         7.23 
TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
        5.36        65.00        45.11        13.84        42.25        11.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91        36.26        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 
       44.91        34.78        36.62         1.22        57.57        30.05 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       45.57        30.18        18.77         6.71        42.51         2.20 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       21.53        22.85         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 
       24.23        24.69        35.05        33.01        29.49        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.08        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 
       14.17         6.05        16.18        11.47        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 
       42.02        10.42        40.77         1.48        24.03        21.14 
TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2351 
        1.74        29.00        25.08        25.02        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1727 
        9.40        34.39         2.14         5.42        44.81        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 
        2.43        33.67         8.42         5.79        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1917 
       34.13        31.30        37.05        42.51        56.61        43.43 
TCGA-61-1918 TCGA-61-1995 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       15.75         2.01         4.01        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 
        1.18        45.40        51.72        71.74        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 
       22.22         6.35         8.61        18.94         0.79        29.16 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       57.76        17.98        35.57        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 TCGA-10-0937 TCGA-13-0714 
       34.19        32.88        14.66        35.44        19.99         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       24.59        44.55         2.73        12.39        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       55.17        11.18        11.38        11.54        38.01       111.78 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       56.71       118.42       107.28        63.09        20.35        69.73 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       87.48        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0899 
       68.94       107.18       111.39        66.67       145.45        66.15 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      127.79        50.37       123.16       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0921 TCGA-13-0923 TCGA-13-2071 
       48.76        83.74        25.41 

$`DEL PEAK  9(4Q34.3) WILD-TYPE`
TCGA-04-1337 TCGA-04-1342 TCGA-04-1349 TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 
        2.01        18.51        21.57         0.53        32.52        76.57 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1648 TCGA-04-1651 TCGA-09-1667 
        0.79        38.37       119.08        28.64        36.23        61.87 
TCGA-09-1668 TCGA-09-1672 TCGA-13-1405 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 
       55.36         5.85        28.54        81.01        17.46        54.64 
TCGA-13-1482 TCGA-13-1485 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1501 
       61.71        20.68        93.90         4.24        66.15        43.20 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-2060 TCGA-13-A5FU 
       34.16        65.52        44.68        54.25        77.88         8.42 
TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-23-1023 
       23.05        26.20        72.20        27.52        19.10        40.54 
TCGA-23-1024 TCGA-23-1123 TCGA-23-2078 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 
       15.39        33.47        87.48         4.50         7.63        21.80 
TCGA-24-1104 TCGA-24-1417 TCGA-24-1424 TCGA-24-1427 TCGA-24-1435 TCGA-24-1463 
       63.55         7.82         6.02         4.83        43.53        72.92 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1549 TCGA-24-1553 TCGA-24-1558 TCGA-24-1562 
       12.46       105.99        56.58        58.09        19.53        45.50 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1614 TCGA-24-1616 TCGA-24-1847 TCGA-24-1927 
       25.87        10.26        48.33        38.24        11.28        16.44 
TCGA-24-2019 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 
        4.87        18.48        28.18        64.01        44.52         0.36 
TCGA-24-2288 TCGA-24-2297 TCGA-25-1319 TCGA-25-1320 TCGA-25-1870 TCGA-25-1877 
        0.82        55.86        65.00        37.97        14.96        24.00 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 
       85.05        38.04         3.02        19.99         2.96        26.99 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1702 TCGA-29-1703 TCGA-29-1763 TCGA-29-1766 
       47.61        48.33        23.93        59.67        66.81        39.42 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1785 TCGA-29-2414 
       24.36        17.33        12.36        14.93        36.30        86.17 
TCGA-29-2427 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1862 
       62.47        21.47         9.76        35.77         2.47         6.12 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       24.26        48.79        22.49        44.12        28.77        29.10 
TCGA-36-1574 TCGA-36-2534 TCGA-36-2540 TCGA-42-2582 TCGA-57-1583 TCGA-57-1586 
       22.55        29.82        23.80        47.57        11.38        22.32 
TCGA-59-2348 TCGA-59-2349 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
      180.20        80.12        11.11         8.09        20.94        31.43 
TCGA-61-1738 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1913 TCGA-61-1915 
       35.80        43.69         1.45        11.41        48.92        67.76 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2017 TCGA-61-2087 
       38.17         5.52        14.50        17.98        45.96         4.80 
TCGA-61-2088 TCGA-61-2095 TCGA-61-2096 TCGA-61-2613 TCGA-OY-A56P TCGA-WR-A838 
        4.77        61.64        58.39        31.07        39.68         9.99 
TCGA-09-0365 TCGA-10-0925 TCGA-10-0934 TCGA-10-0936 TCGA-10-0938 TCGA-13-0723 
        9.47        54.31         6.71        36.92        20.91        39.58 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0799 
       31.20         2.50        61.84        58.65        40.24        83.34 
TCGA-13-0807 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
       13.61       153.37        92.42        95.15       102.84        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0924 
       71.74       134.04        19.36        85.94 

  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                         0.26                          0.36 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                       152.02                        180.20 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                       33.010                        31.315 
[1] "0.3 - 152.0 (33.0)" "0.4 - 180.2 (31.3)"
[1] "hr=" "1.1"
D42V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  9(4Q34.3) MUTATED         2   405                1
  DEL PEAK  9(4Q34.3) WILD-TYPE       1   153                1
D42V3, multiclass
                  clus
vv                 DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    405                           153
  PERITONEUM OVARY                           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"
D42V4, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED   390   5
  DEL PEAK  9(4Q34.3) WILD-TYPE 151   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED    390    5
  DEL PEAK  9(4Q34.3) WILD-TYPE  151    0
     clus
vv    DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  NO                          390                           151
  YES                           5                             0
[1] 2 2
[1] FALSE
D42V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  9(4Q34.3) MUTATED   13 18  3  3
  DEL PEAK  9(4Q34.3) WILD-TYPE  2  8  2  0
D42V6, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  R0                          13                             2
  R1                          18                             8
  R2                           3                             2
  RX                           3                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    10 234
  DEL PEAK  9(4Q34.3) WILD-TYPE   0  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     10  234
  DEL PEAK  9(4Q34.3) WILD-TYPE    0   93
                        clus
vv                       DEL PEAK  9(4Q34.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         234
                        clus
vv                       DEL PEAK  9(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            93
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 10(5Q12.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q12.1) MUTATED   137 205
  DEL PEAK 10(5Q12.1) WILD-TYPE  91 126
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          342                           217 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          205                           126 
$`DEL PEAK 10(5Q12.1) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 
        1.08        18.51        63.09        21.57        65.46         0.53 
TCGA-04-1362 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 
       44.32        19.99         0.79        38.37        29.10        84.20 
TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       55.43        27.88        28.64        64.64        36.23        47.70 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       38.43        89.33        41.62        61.87        55.36        30.51 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55         6.18         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2054 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       63.09        20.94        77.10        81.17        28.54        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1482 TCGA-13-1484 
       55.23        57.27        17.46        32.35        61.71       124.44 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 
       70.82        83.93        52.44       125.56         4.24       127.27 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       43.20        34.82        65.69        80.15        44.68        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-20-0990 TCGA-20-0991 
       80.02        78.48        77.88        65.52        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 
       47.54        40.54        15.39        26.83        49.41         8.81 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       18.90         2.76        54.51        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
       33.30       129.96        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 
      115.89        77.00        49.84         4.70         4.50        11.64 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 
       41.56         7.66        22.32        63.55        47.41         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        7.99         7.86         5.95         4.83        17.39        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
        9.11         3.45        64.27        16.21        56.58        41.06 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 
       41.39        58.09        19.53        25.87        17.23        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
       48.33        38.24         8.32        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87       152.02        44.84        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       55.92        18.48        28.18        57.07        36.16         0.79 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 
       47.54        31.63        70.45        44.61         0.82        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1317 
       16.64        55.86        53.26         1.02        33.01         2.01 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       34.98        37.97        33.96         2.99        12.99        15.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       17.03        12.95        62.17        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 
       24.99        24.00        49.05         1.02        38.04        45.01 
TCGA-25-2400 TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 
       42.02        29.03        78.90        48.33        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 
       33.93        31.20        68.32        16.93        23.93        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       41.98        31.27        17.36        86.60        62.93        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 
       31.30        22.98        12.36        12.30        14.93         7.23 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 
       86.17        65.00        62.47        45.11        42.25        21.47 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 
       11.47        35.77        51.91         2.47         0.26        48.10 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1946 
       34.78        36.62         1.22        24.26        30.05        30.18 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 
        6.71        42.51         2.20         8.55        30.08        27.85 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       24.69        33.01        29.82        25.08        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       20.98        18.31        20.52         6.05        16.18        11.47 
TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 
       23.74        42.02        10.42        40.77        11.38        21.14 
TCGA-57-1585 TCGA-57-1992 TCGA-59-2348 TCGA-59-2351 TCGA-61-1722 TCGA-61-1724 
        1.74        29.00       180.20       116.12         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1737 TCGA-61-1740 
       31.43        18.54        27.88        31.79        44.84         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 
       33.67        43.69         1.45         8.42        11.41        13.02 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 
       34.13        31.30        48.92        56.61        43.43        15.75 
TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 
       38.17         4.01        30.64        45.40         4.77        71.74 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2111 TCGA-61-2113 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
      125.75        22.22        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0927 TCGA-10-0931 
        9.47        57.76        35.57        54.31        81.86        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 
       14.66         6.71        35.44        19.99        20.91        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       39.58         2.73        12.39        17.82        55.17        11.18 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 
       11.54        38.01       111.78        61.84        56.71       118.42 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
      107.28        20.35        69.73        83.34        87.48        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 
       51.02        43.86        35.28        35.31       107.18       111.39 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        92.42        95.15       145.45       102.84        43.36 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
      134.04        19.36       127.79        50.37       123.16       118.98 
TCGA-13-0911 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       44.55        58.68        48.79        48.76        83.74        85.94 

$`DEL PEAK 10(5Q12.1) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 
       11.87         2.01        46.62        11.87        65.52        48.76 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       63.98        49.28        32.52        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 TCGA-04-1644 TCGA-04-1652 
       82.39        56.55        41.59       119.08        48.89        31.86 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 TCGA-09-1670 TCGA-09-1672 
       45.37         9.99        74.93        57.60        17.98         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2048 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 
        3.02        97.55         4.54        39.75        26.93        12.46 
TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 
       81.01        54.64        87.06        29.42        20.68        22.39 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1506 
       93.90        90.38        66.15       115.07        13.97        34.16 
TCGA-13-1507 TCGA-13-1511 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       65.52        54.25        76.90        70.45         8.42        23.05 
TCGA-20-0996 TCGA-23-1022 TCGA-23-1027 TCGA-23-1030 TCGA-23-1109 TCGA-23-1111 
       72.20        49.68        32.09        29.13        51.35         3.22 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 
       86.01         4.27         6.38         0.53        87.48        91.66 
TCGA-23-2641 TCGA-24-0966 TCGA-24-0975 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 
        2.76         7.63        21.80        54.12         6.31         6.38 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 TCGA-24-1467 
        0.76         6.25         6.02         5.36        28.37       105.99 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1551 TCGA-24-1555 
        1.18        22.22        26.96        57.40        51.91        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 
       70.62        39.88        44.09        45.50        47.70        10.26 
TCGA-24-1603 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-2024 
       90.15         3.48         3.72         3.81         4.37        58.16 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2289 TCGA-24-2295 TCGA-25-1313 
       64.01        44.52         0.36        67.36        33.11        26.96 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 
       52.04        42.05        65.00        18.58        27.62        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1878 TCGA-25-2042 TCGA-25-2396 
       38.20         0.30        59.15        85.05        13.02         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 
       12.00        19.99         2.96        31.00        26.99        47.61 
TCGA-29-1693 TCGA-29-1699 TCGA-29-1703 TCGA-29-1711 TCGA-29-1763 TCGA-29-1770 
      101.79        36.36        59.67        34.62        66.81        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 
       22.55        17.33        11.84         8.38         5.36        36.30 
TCGA-29-2429 TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1860 
       13.84         9.76        38.07        36.26        15.68        44.91 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 
        6.12        57.57        48.79        45.57        18.77        22.49 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1577 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 TCGA-36-2540 
       25.74        24.23        35.05        29.49        25.91        23.80 
TCGA-36-2548 TCGA-42-2582 TCGA-42-2588 TCGA-42-2593 TCGA-57-1582 TCGA-57-1586 
       14.17        47.57        28.93         1.48        24.03        22.32 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 
       25.08        25.02        80.12        22.32         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1730 TCGA-61-1734 
        2.14         5.42        44.81        11.11         4.34        28.47 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1900 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 
       48.79        35.80         5.79         9.07        37.05        42.51 
TCGA-61-1915 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 
       67.76         2.01         5.52        14.50        17.98        30.64 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 
       39.85         1.18        45.96         4.80        51.72        61.64 
TCGA-61-2096 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       58.39        44.52         6.35        31.07         8.61        39.68 
TCGA-09-0367 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0936 TCGA-13-0714 
       17.98        25.91        18.51        34.19        36.92         6.21 
TCGA-13-0720 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0758 TCGA-13-0768 
       44.55        31.20        15.19         2.50        11.38        58.65 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0897 
       40.24        63.09        13.61        68.94       153.37        71.74 
TCGA-13-0899 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 
       66.15        60.59       116.65        37.64       109.32        84.53 
TCGA-13-2071 
       25.41 

  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                         0.26                          0.30 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                       180.20                        153.37 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                        33.57                         31.07 
[1] "0.3 - 180.2 (33.6)" "0.3 - 153.4 (31.1)"
[1] "hr=" "1"  
D43V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 10(5Q12.1) MUTATED         3   340                1
  DEL PEAK 10(5Q12.1) WILD-TYPE       0   218                1
D43V3, multiclass
                  clus
vv                 DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  OMENTUM                                    3                             0
  OVARY                                    340                           218
  PERITONEUM OVARY                           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"
D43V4, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED   332   3
  DEL PEAK 10(5Q12.1) WILD-TYPE 209   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED    332    3
  DEL PEAK 10(5Q12.1) WILD-TYPE  209    2
     clus
vv    DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  NO                          332                           209
  YES                           3                             2
[1] 2 2
[1] FALSE
D43V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 10(5Q12.1) MUTATED    7 16  1  2
  DEL PEAK 10(5Q12.1) WILD-TYPE  8 10  4  1
D43V6, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  R0                           7                             8
  R1                          16                            10
  R2                           1                             4
  RX                           2                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED     6 199
  DEL PEAK 10(5Q12.1) WILD-TYPE   4 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED      6  199
  DEL PEAK 10(5Q12.1) WILD-TYPE    4  128
                        clus
vv                       DEL PEAK 10(5Q12.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         199
                        clus
vv                       DEL PEAK 10(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           128
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 11(5Q13.2) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(5Q13.2) MUTATED   170 234
  DEL PEAK 11(5Q13.2) WILD-TYPE  58  97
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                          404                           155 
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                          234                            97 
$`DEL PEAK 11(5Q13.2) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
       46.62         1.08        18.51        63.09        21.57        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 
       65.46         0.53        49.28        32.52        76.57       103.40 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 
       41.59        19.99         0.79        29.10        84.20        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-1661 
       27.88        28.64        64.64        36.23        47.70        38.43 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       89.33        41.62        61.87        55.36        30.51        17.98 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        8.55        97.55         6.18         6.12        35.15       112.41 
TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       71.11        20.94        26.93        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       83.31        55.23        57.27        81.01        17.46        32.35 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 
       87.06        61.71        29.42       124.44        70.82        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 
       52.44       125.56         4.24       127.27       115.07        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
       34.82        65.69        80.15        44.68        14.53        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 
       78.48        77.88        76.90        65.52        70.45        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       26.20        27.52        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        18.90         2.76        51.35        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68        19.46        33.30        86.01       129.96 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 
       77.00        49.84         2.76         4.70         4.50        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.95         4.83        17.39        28.37        18.64        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 
       43.53         8.55        72.92        12.46        45.14         3.45 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 
       64.27        16.21        56.58        41.06        41.39        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 
       70.62        39.88        19.53        25.87        17.23        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       48.33        38.24         8.32         3.48         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       16.44        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       58.16        34.82       109.71        14.43        55.92        18.48 
TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 
       28.18        57.07        36.16         0.79        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       33.11        55.86        53.26         1.02        26.96        33.01 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
        2.01        34.98        37.97        33.96         2.99        12.99 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 
       27.62        17.03        12.95        38.20         0.30        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.87        52.04        14.96        24.99        24.00        85.05 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 
       49.05         1.02         3.02        12.00        45.01        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1694 
        2.96        29.03        26.99        78.90        48.33        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 
       40.41        33.93        31.20        16.93        23.93        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 
       62.93        39.42        31.30        22.98        24.36        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       11.84        12.30        14.93         8.38         7.23         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 
       86.17        65.00        62.47        45.11        42.25        21.47 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 
       11.47        35.77        51.91         2.47         0.26        48.10 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1946 
       34.78        36.62         1.22        24.26        30.05        30.18 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1575 
        6.71        42.51        44.12         2.20        29.10         8.55 
TCGA-36-1576 TCGA-36-1581 TCGA-36-2530 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 
       30.08        24.69        33.01        29.82        25.08        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 
       20.98        18.31        20.52         6.05        11.47        23.74 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 
       42.02        10.42        40.77        24.03        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 
       22.32        29.00        25.02       180.20       116.12         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        2.14         5.42         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 
       27.88        31.79        28.47        44.84         2.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       43.69         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 
       34.13        31.30        48.92        56.61        43.43        15.75 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
       38.17         5.52        17.98         4.01        30.64        30.64 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2101 
       45.40         4.80         4.77        71.74        60.62        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-OY-A56Q 
        6.48        76.87        20.68       125.75        22.22        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
        0.79         9.99        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 
       35.57        54.31        81.86        18.51        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 
        6.71        35.44        19.99        20.91        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       39.58         2.73        12.39        17.82        55.17        11.18 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 
       11.54        38.01       111.78        61.84        56.71       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
      107.28        63.09        20.35        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 
       45.99        51.02        43.86        35.28        35.31       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      111.39       153.37        66.67        92.42        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
      102.84        43.36        71.74        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0911 
      127.79        50.37       123.16       118.98        60.59        44.55 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
      109.32        58.68        84.53        48.79        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

$`DEL PEAK 11(5Q13.2) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1337 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1362 
       11.87         2.01        11.87        65.52        48.76        44.32 
TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 
       33.67        82.39        56.55        38.37       119.08        55.43 
TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 TCGA-09-1672 
       31.86        45.37         9.99        74.93        57.60         5.85 
TCGA-09-1673 TCGA-09-2048 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1477 
        3.02         4.54        63.09        39.75        12.46        54.64 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1500 
       20.68        22.39        93.90        90.38        66.15        13.97 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 
       34.16        65.52        54.25         8.42        23.05        72.20 
TCGA-20-1683 TCGA-23-1030 TCGA-23-1111 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 
       25.38        29.13         3.22         4.27         6.38         0.53 
TCGA-23-2079 TCGA-24-0966 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1426 
       91.66         7.63        47.41         6.31         6.38         5.36 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
      105.99         9.11         1.18        22.22        26.96        57.40 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 
       51.91        88.50        44.09        45.50        47.70        10.26 
TCGA-24-1603 TCGA-24-1844 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-25-1315 
       90.15         3.72        64.01        44.52         0.36        52.04 
TCGA-25-1316 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 TCGA-25-1632 
       42.05        65.00        15.02        18.58        20.61        59.15 
TCGA-25-2042 TCGA-25-2393 TCGA-25-2399 TCGA-25-2408 TCGA-29-1690 TCGA-29-1693 
       13.02        38.04        19.99        31.00        47.61       101.79 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1771 TCGA-29-1774 TCGA-29-1785 
       68.32        36.36        59.67        22.55        17.33        36.30 
TCGA-29-2429 TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1860 
       13.84         9.76        38.07        36.26        15.68        44.91 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 
        6.12        57.57        48.79        45.57        18.77        22.49 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 
       28.77        21.53        22.85        22.55        25.74        27.85 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 TCGA-36-2540 TCGA-36-2543 
       24.23        35.05        29.49        25.91        23.80         2.24 
TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2593 TCGA-57-1583 
       14.17        16.18        47.57        28.93         1.48        11.38 
TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 
       25.08        80.12        22.32        34.39        44.81        11.11 
TCGA-61-1730 TCGA-61-1736 TCGA-61-1738 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 
        4.34        48.79        35.80         9.07        37.05        42.51 
TCGA-61-1915 TCGA-61-1995 TCGA-61-2000 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 
       67.76         2.01        14.50        39.85         1.18        45.96 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2110 TCGA-61-2612 
       51.72        61.64        58.39        65.52        44.52         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-10-0926 TCGA-10-0930 TCGA-10-0936 
       31.07         8.61        39.68        25.91        34.19        36.92 
TCGA-13-0714 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0758 TCGA-13-0768 
        6.21        31.20        15.19         2.50        11.38        58.65 
TCGA-13-0791 TCGA-13-0807 TCGA-13-0883 TCGA-13-0910 TCGA-13-0912 
       40.24        13.61        68.94       116.65        37.64 

  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                         0.26                          0.36 
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                       180.20                        119.08 
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                        33.01                         31.20 
[1] "0.3 - 180.2 (33.0)" "0.4 - 119.1 (31.2)"
[1] "hr=" "1.2"
D44V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 11(5Q13.2) MUTATED         3   402                1
  DEL PEAK 11(5Q13.2) WILD-TYPE       0   156                1
D44V3, multiclass
                  clus
vv                 DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE
  OMENTUM                                    3                             0
  OVARY                                    402                           156
  PERITONEUM OVARY                           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"
D44V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q13.2) MUTATED   392   3
  DEL PEAK 11(5Q13.2) WILD-TYPE 149   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q13.2) MUTATED    392    3
  DEL PEAK 11(5Q13.2) WILD-TYPE  149    2
     clus
vv    DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE
  NO                          392                           149
  YES                           3                             2
[1] 2 2
[1] FALSE
D44V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 11(5Q13.2) MUTATED    9 15  1  3
  DEL PEAK 11(5Q13.2) WILD-TYPE  6 11  4  0
D44V6, multiclass
    clus
vv   DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE
  R0                           9                             6
  R1                          15                            11
  R2                           1                             4
  RX                           3                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q13.2) MUTATED     7 239
  DEL PEAK 11(5Q13.2) WILD-TYPE   3  88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q13.2) MUTATED      7  239
  DEL PEAK 11(5Q13.2) WILD-TYPE    3   88
                        clus
vv                       DEL PEAK 11(5Q13.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         239
                        clus
vv                       DEL PEAK 11(5Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            88
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 12(6Q27) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q27) MUTATED   150 213
  DEL PEAK 12(6Q27) WILD-TYPE  78 118
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        363                         196 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        213                         118 
$`DEL PEAK 12(6Q27) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 
       20.52        11.87        43.92        41.00         1.81         2.01 
TCGA-04-1338 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       46.62        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
        0.53        32.52        44.32        76.57       103.40        56.55 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       19.99         0.79       119.08        29.10        84.20        55.43 
TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       27.88        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1670 
       38.43        89.33        41.62        57.60        55.36        17.98 
TCGA-09-1672 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 
        5.85        97.55         6.12        35.15       112.41        63.09 
TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       39.75        26.93        12.46        81.17        28.54        83.31 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
       57.27        81.01        17.46        32.35        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
       29.42       124.44        70.82        83.93        52.44        93.90 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
       90.38       127.27       115.07        13.97        43.20        65.69 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 
       34.16        80.15        44.68        54.25        14.53        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       65.52        70.45        23.05        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 
       47.54        49.68        15.39        26.83        32.09         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       29.13        18.90         2.76        51.35        54.51        31.20 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       33.30        86.01       129.96         4.27        39.09        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13         0.53        24.95        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 
       21.80         7.66        22.32        54.12        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        6.38         7.82         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        28.37        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 TCGA-24-1545 
        8.55        72.92        45.14       105.99         1.18        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 
       64.27        41.06        51.91        41.39        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 
       19.53        44.09        45.50        47.70        25.87        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       90.15        88.37        38.24         8.32         3.72         3.81 
TCGA-24-1846 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 
        4.37         5.79        22.68        16.44         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2036 TCGA-24-2261 TCGA-24-2267 
       44.84        58.16        14.43        64.01         0.79        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       31.63        70.45        67.36        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        52.04        42.05         2.01        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1628 
       37.97        33.96         2.99        12.99        15.02        20.61 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       38.20        59.15        85.05        13.02        49.05         1.02 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
        3.02        45.01        19.99         2.96        29.03        26.99 
TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1705 
       78.90       101.79        39.02        33.93        31.20        18.25 
TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       41.98        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       22.98        24.36        22.55        12.36        11.84        12.30 
TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        8.38         5.36        36.30        65.00        62.47        45.11 
TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       21.47        11.47        38.07        51.91        36.26         2.47 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 
        0.26        48.10        44.91        34.78        36.62        57.57 
TCGA-30-1892 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       48.79        30.18        22.49         6.71        42.51        44.12 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
       28.77        29.10        21.53        22.85        22.55        30.08 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 
       24.23        33.01        29.49        25.91        25.08        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2552 TCGA-42-2582 
       20.98        18.31        20.52        14.17        11.47        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       28.93        42.02        10.42        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2355 
       21.14         1.74       180.20        22.32       116.12         2.14 
TCGA-59-2372 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1895 
       31.79        28.47        48.79        44.84         2.43         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       37.05        48.92        56.61        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2087 
        5.52        17.98         4.01        30.64        30.64         4.80 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       58.39        60.62        55.50        76.87        20.68        44.52 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-09-0364 TCGA-09-0365 
        6.35        31.07         8.61        39.68        29.16         9.47 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       17.98        54.31        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       32.88        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 
       24.59        44.55        12.39        31.20        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        38.01       111.78        61.84 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       56.71       118.42       107.28        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       45.99        51.02        43.86        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      153.37        66.67        92.42        95.15       145.45       102.84 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       71.74        66.15       134.04       123.16       118.98        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
      116.65        44.55       109.32        58.68        84.53        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

$`DEL PEAK 12(6Q27) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1336 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       13.81        49.15         1.08        18.51        11.87        65.52 
TCGA-04-1356 TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1644 
       49.28        33.67        82.39        41.59        38.37        48.89 
TCGA-04-1648 TCGA-04-1649 TCGA-09-1664 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 
       28.64        64.64        74.93        61.87        30.51         3.02 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-13-1403 
        8.55         6.18         4.54        71.11        20.94        77.10 
TCGA-13-1408 TCGA-13-1477 TCGA-13-1485 TCGA-13-1487 TCGA-13-1492 TCGA-13-1496 
       55.23        54.64        20.68        22.39       125.56         4.24 
TCGA-13-1498 TCGA-13-1504 TCGA-13-1507 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       66.15        34.82        65.52        80.02        78.48        77.88 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
        8.42        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-23-1023 TCGA-23-1028 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
       19.10        40.54        49.41         3.22        68.68        19.46 
TCGA-23-1121 TCGA-23-2077 TCGA-24-0979 TCGA-24-1104 TCGA-24-1418 TCGA-24-1419 
        6.38       115.89        41.56        63.55         7.99         7.86 
TCGA-24-1431 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       18.64        12.46         9.11         3.45        22.22        26.96 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1553 TCGA-24-1555 TCGA-24-1565 TCGA-24-1614 
       16.21        56.58        58.09        88.50        10.26        48.33 
TCGA-24-1843 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 
        3.48        11.28         5.52         9.80        30.21        11.05 
TCGA-24-1930 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       81.11        34.82       109.71        55.92        18.48        28.18 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2281 TCGA-24-2288 
       44.52        57.07        36.16         0.36        44.61         0.82 
TCGA-24-2290 TCGA-25-1312 TCGA-25-1314 TCGA-25-1319 TCGA-25-1623 TCGA-25-1625 
       36.23         1.02        33.01        65.00        18.58        27.62 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       17.03        12.95         0.30        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 TCGA-25-2397 TCGA-25-2400 
       14.96        24.99        24.00        38.04        12.00        42.02 
TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 
       31.00        47.61        48.33        40.41        68.32        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       16.93        23.93        59.67        31.27        34.62        17.36 
TCGA-29-1774 TCGA-29-1778 TCGA-29-1783 TCGA-29-2414 TCGA-29-2429 TCGA-29-2431 
       17.33        14.93         7.23        86.17        13.84        42.25 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 
        9.76        35.77        15.68         6.12         1.22        24.26 
TCGA-30-1891 TCGA-31-1944 TCGA-31-1950 TCGA-31-1959 TCGA-36-1575 TCGA-36-1577 
       30.05        45.57        18.77         2.20         8.55        25.74 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 TCGA-36-2540 TCGA-36-2543 
       27.85        24.69        35.05        29.82        23.80         2.24 
TCGA-36-2549 TCGA-36-2551 TCGA-42-2587 TCGA-42-2593 TCGA-57-1586 TCGA-57-1992 
        6.05        16.18        23.74         1.48        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
       25.08        25.02        80.12         9.40        34.39         5.42 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1907 
       11.11         8.09        35.80        33.67        43.69        31.30 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-2000 TCGA-61-2009 TCGA-61-2016 
       42.51        67.76        43.43        14.50        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.77        51.72        71.74        61.64 
TCGA-61-2098 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 TCGA-OY-A56Q TCGA-VG-A8LO 
       65.52         6.48       125.75        22.22        18.94         0.79 
TCGA-WR-A838 TCGA-09-0366 TCGA-09-0369 TCGA-10-0933 TCGA-10-0934 TCGA-13-0723 
        9.99        57.76        35.57        14.66         6.71        39.58 
TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0768 TCGA-13-0791 TCGA-13-0794 
        2.73        15.19        17.82        58.65        40.24        63.09 
TCGA-13-0795 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0893 TCGA-13-0901 
       20.35        35.28        35.31        13.61        43.36        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0912 TCGA-13-0920 
      127.79        50.37        37.64        48.79 

  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                       0.26                        0.30 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                     180.20                      127.79 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                      34.16                       28.82 
[1] "0.3 - 180.2 (34.2)" "0.3 - 127.8 (28.8)"
[1] "hr=" "1.3"
D45V2, continuous
                             vv
clus                          OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 12(6Q27) MUTATED         1   364                1
  DEL PEAK 12(6Q27) WILD-TYPE       2   194                1
D45V3, multiclass
                  clus
vv                 DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  OMENTUM                                  1                           2
  OVARY                                  364                         194
  PERITONEUM OVARY                         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"
D45V4, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED   351   4
  DEL PEAK 12(6Q27) WILD-TYPE 190   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED    351    4
  DEL PEAK 12(6Q27) WILD-TYPE  190    1
     clus
vv    DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  NO                        351                         190
  YES                         4                           1
[1] 2 2
[1] FALSE
D45V5, continuous
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK 12(6Q27) MUTATED    9 15  2  1
  DEL PEAK 12(6Q27) WILD-TYPE  6 11  3  2
D45V6, multiclass
    clus
vv   DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  R0                         9                           6
  R1                        15                          11
  R2                         2                           3
  RX                         1                           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"
D45V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED     7 215
  DEL PEAK 12(6Q27) WILD-TYPE   3 112
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED      7  215
  DEL PEAK 12(6Q27) WILD-TYPE    3  112
                        clus
vv                       DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             7                           3
  NOT HISPANIC OR LATINO                       215                         112
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 13(7P22.2) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7P22.2) MUTATED   108 137
  DEL PEAK 13(7P22.2) WILD-TYPE 120 194
  DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE 
                          245                           314 
  DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE 
                          137                           194 
$`DEL PEAK 13(7P22.2) MUTATED`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1347 
       20.52        43.92        49.15        46.62         1.08        63.09 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1371 TCGA-04-1514 
       21.57        65.46        49.28        32.52        82.39        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1651 TCGA-09-1659 
       19.99        38.37       119.08        29.10        36.23         9.99 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1673 TCGA-09-2044 TCGA-09-2045 
       41.62        57.60        55.36         3.02         6.12        35.15 
TCGA-09-2050 TCGA-09-2053 TCGA-09-2055 TCGA-13-1409 TCGA-13-1412 TCGA-13-1481 
       71.11        39.75        26.93        57.27        32.35        87.06 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1488 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
       29.42        22.39        70.82       127.27       115.07        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1509 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT 
       43.20        65.69        80.15        77.88        76.90        70.45 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       19.10        16.70        47.54        49.68        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       32.09        49.41         8.81        18.90        51.35        54.51 
TCGA-23-1114 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       68.68        33.30       129.96         4.27         6.38        39.09 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0979 
       87.48        91.66        49.84         2.76         4.50        41.56 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1425 TCGA-24-1427 
       22.32        54.12        63.55        47.41         5.95         4.83 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1545 
       18.67        43.53         8.55        72.92        12.46        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 
       64.27        16.21        41.06        41.39        70.62        39.88 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       45.50        47.70        17.23         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
        4.37        11.28         5.79         5.52         9.80        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2027 TCGA-24-2030 TCGA-24-2254 
       16.44        81.11         4.87       109.71        55.92        57.07 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 TCGA-24-2298 TCGA-25-1315 
        0.36        47.54        70.45         0.82        53.26        52.04 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1630 TCGA-25-1632 
        2.01        34.98        33.96         2.99        38.20        59.15 
TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
       62.17        52.04        13.02        49.05         1.02         3.02 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 
       19.99        42.02         2.96        29.03        78.90        48.33 
TCGA-29-1693 TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
      101.79        31.20        16.93        23.93        59.67        18.25 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 
       34.62        17.36        86.60        62.93        39.42        22.98 
TCGA-29-1770 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 
       24.36        11.84        12.30         8.38         5.36        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       65.00        45.11        42.25        38.07        51.91        36.26 
TCGA-30-1860 TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       44.91        36.62        24.26        30.05        48.79        45.57 
TCGA-31-1955 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       42.51        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1578 TCGA-36-2530 TCGA-36-2534 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       27.85        33.01        29.82        20.98        18.31        20.52 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2591 TCGA-57-1582 
       11.47        47.57        23.74        42.02        40.77        24.03 
TCGA-57-1583 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 
       11.38         1.74        29.00        25.08        25.02       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        9.40        34.39         5.42         8.09        20.94        31.43 
TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 
       27.88        48.79        44.84        35.80         2.43         1.45 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       34.13        37.05        48.92        56.61        67.76        43.43 
TCGA-61-1919 TCGA-61-1995 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       38.17         2.01        17.98        30.64        39.85        30.64 
TCGA-61-2087 TCGA-61-2094 TCGA-61-2096 TCGA-61-2102 TCGA-61-2109 TCGA-61-2111 
        4.80        71.74        58.39         6.48        20.68       125.75 
TCGA-61-2612 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 TCGA-10-0928 TCGA-10-0931 
        6.35        39.68         0.79         9.99        18.51        32.88 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0724 TCGA-13-0751 TCGA-13-0755 
       35.44        19.99        20.91         2.73        55.17         2.50 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 
       11.38        11.54        61.84        69.73        87.48        45.99 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 
       68.94       107.18       111.39        66.67       145.45       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       43.36        71.74       134.04       127.79        50.37       118.98 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
       37.64       109.32        48.79        85.94        25.41 

$`DEL PEAK 13(7P22.2) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 
       13.81        11.87        41.00         1.81         2.01        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1353 TCGA-04-1362 
       11.87        65.52        48.76        63.98         0.53        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 TCGA-04-1519 TCGA-04-1542 
       33.67        76.57       103.40        41.59         0.79        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 
       55.43        48.89        27.88        28.64        64.64        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1667 
       47.70        45.37        38.43        89.33        74.93        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       30.51        17.98         5.85         8.55        97.55         6.18 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 TCGA-09-2056 TCGA-13-1403 
        4.54       112.41        63.09        20.94        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
       81.17        28.54        83.31        55.23        81.01        17.46 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 
       54.64        61.71       124.44        20.68        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1504 
      125.56        93.90        90.38         4.24        66.15        34.82 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       34.16        65.52        44.68        54.25        14.53        80.02 
TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       78.48        65.52         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1024 
       72.20        27.52        25.38         2.93         2.66        15.39 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 
       29.13         2.76         3.22        31.20        19.46        86.01 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 
       33.47        58.13         0.53        24.95       115.89        77.00 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1413 
        4.70         7.63        11.64        21.80         7.66         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1466 
        6.02         5.36        17.39        28.37        18.64        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 
       56.58        51.91        58.09        88.50        19.53        44.09 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       25.87        10.26        90.15        88.37        48.33        38.24 
TCGA-24-1845 TCGA-24-1923 TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
        3.81        22.68        11.05       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       34.82        14.43        18.48        28.18        64.01        44.52 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 
       36.16         0.79        31.63        44.61        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        55.86         1.02        26.96        33.01 
TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       42.05        65.00        37.97        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 
       27.62        17.03        12.95        20.61         0.30        35.87 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2397 
       14.96        24.99        24.00        85.05        38.04        12.00 
TCGA-25-2398 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 
       45.01        31.00        26.99        47.61        39.02        40.41 
TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1707 TCGA-29-1710 TCGA-29-1763 
       33.93        68.32        36.36        41.98        31.27        66.81 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 
       31.30        22.55        17.33        12.36        14.93         7.23 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       36.30        62.47        13.84        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       35.77         2.47        15.68         0.26        48.10        34.78 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
        6.12         1.22        57.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
        6.71        44.12         2.20         8.55        30.08        25.74 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
       24.23        24.69        35.05        29.49        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       23.80        21.60         2.24        14.17         6.05        16.18 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2593 TCGA-57-1584 TCGA-57-1586 TCGA-59-2348 
       28.93        10.42         1.48        21.14        22.32       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1727 
       80.12        22.32         2.14        44.81        11.11        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
        4.34        31.79        28.47        33.67        43.69         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1911 
        5.79        11.41        13.02         9.07        31.30        42.51 
TCGA-61-1918 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2016 TCGA-61-2017 
       15.75         5.52        14.50         4.01         1.18        45.96 
TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 
       45.40         4.77        51.72        61.64        60.62        65.52 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 
       55.50        76.87        44.52        22.22        31.07         8.61 
TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       18.94        29.16         9.47        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 
       54.31        25.91        81.86        34.19        14.66         6.71 
TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       36.92         6.21        24.59        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0761 TCGA-13-0762 
       31.20        15.19        17.82        11.18        38.01       111.78 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       56.71        58.65        40.24       118.42       107.28        63.09 
TCGA-13-0795 TCGA-13-0799 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       20.35        83.34        51.02        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0899 TCGA-13-0901 
       13.61       153.37        92.42        95.15        66.15        19.36 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 
      123.16        60.59       116.65        44.55        58.68        84.53 
TCGA-13-0921 TCGA-13-0923 
       48.76        83.74 

  DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE 
                         0.36                          0.26 
  DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE 
                       145.45                        180.20 
  DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE 
                        36.26                         30.13 
[1] "0.4 - 145.4 (36.3)" "0.3 - 180.2 (30.1)"
[1] "hr=" "1.2"
D46V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 13(7P22.2) MUTATED         0   246                1
  DEL PEAK 13(7P22.2) WILD-TYPE       3   312                1
D46V3, multiclass
                  clus
vv                 DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE
  OMENTUM                                    0                             3
  OVARY                                    246                           312
  PERITONEUM OVARY                           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"
D46V4, binary
                               cls
clus                              0   1
  DEL PEAK 13(7P22.2) MUTATED   239   3
  DEL PEAK 13(7P22.2) WILD-TYPE 302   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7P22.2) MUTATED    239    3
  DEL PEAK 13(7P22.2) WILD-TYPE  302    2
     clus
vv    DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE
  NO                          239                           302
  YES                           3                             2
[1] 2 2
[1] FALSE
D46V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 13(7P22.2) MUTATED    8  8  2  1
  DEL PEAK 13(7P22.2) WILD-TYPE  7 18  3  2
D46V6, multiclass
    clus
vv   DEL PEAK 13(7P22.2) MUTATED DEL PEAK 13(7P22.2) WILD-TYPE
  R0                           8                             7
  R1                           8                            18
  R2                           2                             3
  RX                           1                             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"
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(7P22.2) MUTATED     5 143
  DEL PEAK 13(7P22.2) WILD-TYPE   5 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7P22.2) MUTATED      5  143
  DEL PEAK 13(7P22.2) WILD-TYPE    5  184
                        clus
vv                       DEL PEAK 13(7P22.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         143
                        clus
vv                       DEL PEAK 13(7P22.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           184
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.3) MUTATED   160 214
  DEL PEAK 14(8P23.3) WILD-TYPE  68 117
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          374                           185 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          214                           117 
$`DEL PEAK 14(8P23.3) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 
       13.81        20.52        11.87        43.92        41.00        46.62 
TCGA-04-1341 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 
        1.08        65.52        48.76        21.57        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       32.52        44.32        33.67        76.57       103.40        82.39 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1646 TCGA-04-1652 
       41.59        19.99        38.37       119.08        27.88        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       47.70        45.37        38.43        89.33        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1675 
       61.87        55.36        30.51        17.98         3.02        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2056 
        6.18         6.12        71.11        63.09        20.94        12.46 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
       81.17        83.31        55.23        81.01        17.46        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1494 
       61.71        29.42       124.44        22.39        83.93        93.90 
TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       90.38        66.15       115.07        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 
       65.69        65.52        80.15        44.68        14.53        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       77.88        76.90        65.52        70.45         8.42        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        27.52        25.38        19.10        16.70         2.93 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        49.68        15.39        26.83        32.09        49.41 
TCGA-23-1031 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       18.90        68.68        19.46        86.01       129.96         4.27 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       33.47        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 
       47.41         6.31         6.38         7.82         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        6.25         6.02         4.83        17.39        18.64        18.67 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
        8.55        12.46        45.14         3.45        22.22        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 
       64.27        16.21        56.58        41.06        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 TCGA-24-1567 TCGA-24-1604 
       88.50        70.62        19.53        47.70        17.23        88.37 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       48.33         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        5.52         9.80        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 
        4.87       152.02        44.84        58.16       109.71        55.92 
TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2280 TCGA-24-2288 
       28.18        57.07        36.16         0.79        70.45         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 
       67.36        36.23        16.64        55.86         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       33.01        52.04        34.98        65.00        37.97        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
        2.99        12.99        18.58        27.62        17.03        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 
       38.20         0.30        62.17        52.04        24.00        85.05 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 
       13.02         1.02        38.04         3.02        12.00        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 
       42.02         2.96        29.03        26.99        48.33       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       39.02        40.41        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 
       23.93        59.67        41.98        31.27        17.36        86.60 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       62.93        39.42        24.36        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 
       12.30         8.38         7.23         5.36        86.17        65.00 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-30-1718 TCGA-30-1855 
       45.11        13.84        21.47        11.47        51.91         2.47 
TCGA-30-1856 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       24.26        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       42.51        44.12        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 
       35.05        33.01        29.82        25.91        25.08        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 
        2.24        20.98        18.31        20.52         6.05        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 
       47.57        23.74        42.02        10.42         1.48        24.03 
TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       11.38         1.74        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
      180.20        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        5.42         8.09        18.54        27.88         4.34        31.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 
       44.84         2.43        33.67         1.45         5.79        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 TCGA-61-1915 
        9.07        34.13        31.30        37.05        56.61        67.76 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2012 
       15.75        38.17         5.52        14.50        17.98        30.64 
TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 
        1.18        45.40         4.80         4.77        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2613 TCGA-61-2614 TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 
       31.07         8.61         9.99        57.76        17.98        54.31 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0936 TCGA-13-0723 TCGA-13-0724 
       81.86        18.51        34.19        36.92        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       12.39        31.20        17.82         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54        38.01        61.84        56.71        58.65        40.24 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
      118.42        63.09        20.35        69.73        83.34        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       51.02        43.86        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
      111.39        66.67       145.45        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
      134.04        19.36       127.79       123.16       118.98        60.59 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 
        1.81        49.15         2.01        18.51        11.87        63.09 
TCGA-04-1350 TCGA-04-1353 TCGA-04-1514 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 
       63.98         0.53        56.55         0.79        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-09-1659 
       55.43        48.89        28.64        64.64        36.23         9.99 
TCGA-09-1664 TCGA-09-1672 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       74.93         5.85         8.55        35.15         4.54       112.41 
TCGA-09-2053 TCGA-09-2055 TCGA-13-1403 TCGA-13-1405 TCGA-13-1409 TCGA-13-1412 
       39.75        26.93        77.10        28.54        57.27        32.35 
TCGA-13-1477 TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 
       54.64        20.68        70.82        52.44       125.56         4.24 
TCGA-13-1497 TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-20-0987 TCGA-20-0996 
      127.27        34.16        54.25        80.02        23.05        72.20 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 
        2.66        40.54         8.81        29.13         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1121 TCGA-23-1122 
       54.51         3.22        31.20        33.30         6.38        39.09 
TCGA-24-0966 TCGA-24-0970 TCGA-24-1418 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 
        7.63        11.64         7.99         5.95         5.36        28.37 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 
       43.53        72.92       105.99         9.11         1.18        57.40 
TCGA-24-1551 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       51.91        39.88        44.09        45.50        25.87        10.26 
TCGA-24-1603 TCGA-24-1616 TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-2026 
       90.15        38.24        11.28         5.79        22.68        34.82 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2267 
       14.43        18.48        64.01        44.52         0.36        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2295 TCGA-24-2298 TCGA-25-1316 TCGA-25-1317 
       31.63        44.61        33.11        53.26        42.05         2.01 
TCGA-25-1329 TCGA-25-1628 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       15.02        20.61        59.15        35.87        14.96        24.99 
TCGA-25-2391 TCGA-25-2398 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1696 
       49.05        45.01        31.00        78.90        47.61        33.93 
TCGA-29-1705 TCGA-29-1711 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       18.25        34.62        66.81        31.30        22.98        22.55 
TCGA-29-1778 TCGA-29-1785 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ 
       14.93        36.30        62.47        42.25         9.76        35.77 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1880 TCGA-30-1891 
       38.07        36.26         0.26        48.10        57.57        30.05 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-2532 TCGA-36-2540 TCGA-36-2548 
        6.71         2.20        28.77        29.49        23.80        14.17 
TCGA-36-2551 TCGA-42-2588 TCGA-42-2591 TCGA-57-1584 TCGA-59-2349 TCGA-59-2372 
       16.18        28.93        40.77        21.14        80.12        44.81 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 
       11.11        20.94        31.43        28.47        48.79        35.80 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1901 TCGA-61-1911 TCGA-61-1913 TCGA-61-1917 
       43.69         8.42        11.41        42.51        48.92        43.43 
TCGA-61-1995 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 
        2.01         4.01        30.64        39.85        45.96        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 TCGA-61-2612 TCGA-OY-A56P 
       71.74        61.64        58.39        20.68         6.35        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-10-0926 
       18.94         0.79        29.16         9.47        35.57        25.91 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0727 TCGA-13-0751 TCGA-13-0762 
        6.21        24.59        44.55        15.19        55.17       111.78 
TCGA-13-0793 TCGA-13-0800 TCGA-13-0804 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 
      107.28        87.48        35.28       153.37        92.42        95.15 
TCGA-13-0891 TCGA-13-0904 TCGA-13-0910 TCGA-13-0921 TCGA-13-0923 
      102.84        50.37       116.65        48.76        83.74 

  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                         0.30                          0.26 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       180.20                        153.37 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       31.545                        34.160 
[1] "0.3 - 180.2 (31.5)" "0.3 - 153.4 (34.2)"
[1] "hr=" "1.2"
D47V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 14(8P23.3) MUTATED         2   374                2
  DEL PEAK 14(8P23.3) WILD-TYPE       1   184                0
D47V3, multiclass
                  clus
vv                 DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    374                           184
  PERITONEUM OVARY                           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"
D47V4, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED   362   3
  DEL PEAK 14(8P23.3) WILD-TYPE 179   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED    362    3
  DEL PEAK 14(8P23.3) WILD-TYPE  179    2
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  NO                          362                           179
  YES                           3                             2
[1] 2 2
[1] FALSE
D47V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 14(8P23.3) MUTATED   11 19  2  2
  DEL PEAK 14(8P23.3) WILD-TYPE  4  7  3  1
D47V6, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  R0                          11                             4
  R1                          19                             7
  R2                           2                             3
  RX                           2                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     9 217
  DEL PEAK 14(8P23.3) WILD-TYPE   1 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      9  217
  DEL PEAK 14(8P23.3) WILD-TYPE    1  110
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         217
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           110
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 15(8P21.2) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P21.2) MUTATED   164 228
  DEL PEAK 15(8P21.2) WILD-TYPE  64 103
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                          392                           167 
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                          228                           103 
$`DEL PEAK 15(8P21.2) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1332 TCGA-04-1338 TCGA-04-1341 TCGA-04-1346 
       13.81        20.52        41.00        46.62         1.08        65.52 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       48.76        21.57        65.46         0.53        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       44.32        33.67        76.57       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1646 
       41.59        19.99       119.08        29.10        55.43        27.88 
TCGA-04-1652 TCGA-04-1655 TCGA-09-1661 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       31.86        45.37        38.43        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 
       61.87        55.36        30.51        17.98         3.02         8.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2056 
        6.18         6.12        71.11        63.09        20.94        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
       77.10        81.17        83.31        55.23        81.01        17.46 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
       87.06        61.71        29.42       124.44        22.39        83.93 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
       52.44        93.90        90.38         4.24        66.15       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 
       13.97        43.20        34.82        65.69        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       44.68        14.53        78.48        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       70.45         8.42        23.05        25.94        26.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 
       25.38        19.10        16.70         2.93        47.54        49.68 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       15.39        26.83        32.09        49.41         8.81        18.90 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       68.68        19.46        86.01       129.96         4.27         6.38 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       33.47        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 
       91.66        49.84         2.76         4.70         4.50        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.82         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        6.02         4.83        17.39        18.64        18.67        43.53 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
        8.55        12.46       105.99         3.45        22.22        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 
       64.27        16.21        56.58        41.06        41.39        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 
       70.62        39.88        19.53        47.70        25.87        17.23 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       88.37        48.33         8.32         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 
        4.37        11.28         5.52         9.80        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 
      109.71        14.43        55.92        18.48        28.18        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       36.16         0.79        47.54        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
       67.36        36.23        16.64        33.11        55.86         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       26.96        33.01        52.04        34.98        65.00        37.97 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       33.96         2.99        12.99        18.58        27.62        17.03 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
       12.95        38.20         0.30        59.15        62.17        52.04 
TCGA-25-1871 TCGA-25-1878 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       24.99        85.05         1.02        38.04         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 
       19.99        42.02         2.96        29.03        26.99        48.33 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       39.02        40.41        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       23.93        18.25        41.98        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 
       86.60        62.93        39.42        31.30        24.36        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        12.30        14.93         7.23         5.36 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-30-1718 
       65.00        45.11        13.84        21.47        11.47        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
        2.47        15.68         0.26        44.91        34.78         6.12 
TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       36.62        24.26        30.05        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       22.49        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        24.69        35.05        29.82        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.08        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       11.47        23.74        28.93        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        24.03        11.38         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02       180.20        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       34.39         2.14         5.42         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 TCGA-61-1740 
       18.54        27.88         4.34        31.79        44.84         2.43 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1904 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 
       33.67         1.45         9.07        31.30        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       67.76        15.75        38.17         5.52        14.50         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2096 
       30.64        30.64         1.18        45.40         4.80        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0927 
        0.79         9.99        57.76        17.98        54.31        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 TCGA-13-0714 TCGA-13-0723 
       18.51        34.19        32.88        36.92         6.21        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 
        2.73        12.39        31.20        17.82         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        38.01       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       58.65        40.24       118.42       107.28        63.09        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       69.73        83.34        45.99        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 
       35.31        13.61        68.94       111.39       153.37        92.42 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0908 
      145.45        43.36        71.74        66.15        19.36        60.59 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

$`DEL PEAK 15(8P21.2) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       11.87        43.92         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1350 TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 
       11.87        63.09        63.98         0.79        38.37        84.20 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-1659 
       48.89        28.64        64.64        36.23        47.70         9.99 
TCGA-09-1662 TCGA-09-1672 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       89.33         5.85        97.55        35.15         4.54       112.41 
TCGA-09-2053 TCGA-09-2055 TCGA-13-1405 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 
       39.75        26.93        28.54        57.27        32.35        54.64 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1492 TCGA-13-1497 TCGA-13-1506 TCGA-13-1511 
       20.68        70.82       125.56       127.27        34.16        54.25 
TCGA-13-2057 TCGA-20-0996 TCGA-20-1687 TCGA-23-1023 TCGA-23-1030 TCGA-23-1032 
       80.02        72.20         2.66        40.54        29.13         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1122 
       51.35        54.51         3.22        31.20        33.30        39.09 
TCGA-23-2081 TCGA-24-0966 TCGA-24-0970 TCGA-24-1418 TCGA-24-1425 TCGA-24-1426 
       77.00         7.63        11.64         7.99         5.95         5.36 
TCGA-24-1430 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 
       28.37        72.92        45.14         9.11         1.18        57.40 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1603 
       51.91        88.50        44.09        45.50        10.26        90.15 
TCGA-24-1616 TCGA-24-1849 TCGA-24-1923 TCGA-24-2026 TCGA-24-2036 TCGA-24-2038 
       38.24         5.79        22.68        34.82        64.01        44.52 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2298 TCGA-25-1316 TCGA-25-1317 TCGA-25-1329 
        0.36        31.63        53.26        42.05         2.01        15.02 
TCGA-25-1628 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       20.61        35.87        14.96        24.00        13.02        49.05 
TCGA-25-2398 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1696 
       45.01        31.00        78.90        47.61       101.79        33.93 
TCGA-29-1703 TCGA-29-1763 TCGA-29-1769 TCGA-29-1771 TCGA-29-1781 TCGA-29-1785 
       59.67        66.81        22.98        22.55         8.38        36.30 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       86.17        62.47        42.25         9.76        35.77        38.07 
TCGA-30-1853 TCGA-30-1859 TCGA-30-1867 TCGA-30-1880 TCGA-30-1892 TCGA-31-1953 
       36.26        48.10         1.22        57.57        48.79         6.71 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2540 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       33.01        29.49        23.80        14.17         6.05        16.18 
TCGA-42-2582 TCGA-57-1584 TCGA-59-2349 TCGA-59-2372 TCGA-61-1721 TCGA-61-1734 
       47.57        21.14        80.12        44.81        11.11        28.47 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       48.79        35.80        43.69         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 TCGA-61-1995 
       13.02        34.13        37.05        42.51        43.43         2.01 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2017 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       17.98        39.85        45.96         4.77        51.72        71.74 
TCGA-61-2095 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 
       61.64        39.68        18.94        29.16         9.47        35.57 
TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       25.91        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0727 TCGA-13-0751 TCGA-13-0800 TCGA-13-0884 
       24.59        44.55        15.19        55.17        87.48       107.18 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
       66.67        95.15       102.84       134.04       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0921 TCGA-13-0923 
      123.16       118.98       116.65        48.76        83.74 

  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                         0.26                          0.36 
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                       180.20                        134.04 
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                       30.575                        36.260 
[1] "0.3 - 180.2 (30.6)" "0.4 - 134.0 (36.3)"
[1] "hr=" "1.1"
D48V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 15(8P21.2) MUTATED         2   391                2
  DEL PEAK 15(8P21.2) WILD-TYPE       1   167                0
D48V3, multiclass
                  clus
vv                 DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    391                           167
  PERITONEUM OVARY                           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"
D48V4, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.2) MUTATED   378   3
  DEL PEAK 15(8P21.2) WILD-TYPE 163   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.2) MUTATED    378    3
  DEL PEAK 15(8P21.2) WILD-TYPE  163    2
     clus
vv    DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE
  NO                          378                           163
  YES                           3                             2
[1] 2 2
[1] FALSE
D48V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 15(8P21.2) MUTATED    8 19  4  2
  DEL PEAK 15(8P21.2) WILD-TYPE  7  7  1  1
D48V6, multiclass
    clus
vv   DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE
  R0                           8                             7
  R1                          19                             7
  R2                           4                             1
  RX                           2                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.2) MUTATED     9 226
  DEL PEAK 15(8P21.2) WILD-TYPE   1 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.2) MUTATED      9  226
  DEL PEAK 15(8P21.2) WILD-TYPE    1  101
                        clus
vv                       DEL PEAK 15(8P21.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         226
                        clus
vv                       DEL PEAK 15(8P21.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           101
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 16(9P24.3) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(9P24.3) MUTATED    98 151
  DEL PEAK 16(9P24.3) WILD-TYPE 130 180
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                          249                           310 
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                          151                           180 
$`DEL PEAK 16(9P24.3) MUTATED`
TCGA-59-A5PD TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       20.52         2.01        46.62        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       21.57        63.98        65.46        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1371 TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 
       76.57        82.39         0.79        38.37        29.10        84.20 
TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       55.43        27.88        31.86         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       41.62        61.87        17.98         3.02        97.55         6.12 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 
        4.54       112.41        63.09        39.75        20.94        12.46 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 
       57.27        81.01        17.46        32.35        87.06        29.42 
TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1500 
       20.68        83.93        52.44        93.90        90.38        13.97 
TCGA-13-1509 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       80.15        44.68        80.02        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0991 TCGA-20-1682 TCGA-23-1021 TCGA-23-1022 
       70.45         8.42        26.20        27.52        47.54        49.68 
TCGA-23-1027 TCGA-23-1030 TCGA-23-1031 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 
       32.09        29.13        18.90        68.68        86.01       129.96 
TCGA-23-1121 TCGA-23-1123 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2643 
        6.38        33.47       115.89        87.48        77.00         4.70 
TCGA-23-2645 TCGA-24-0970 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1418 
        4.50        11.64        22.32        47.41         6.31         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 
        7.86         0.76         5.36         4.83        28.37        18.64 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1545 TCGA-24-1550 TCGA-24-1552 TCGA-24-1560 
       72.92        12.46        57.40        41.06        41.39        44.09 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 TCGA-24-2023 
       25.87        17.23        90.15        88.37         3.48        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       58.16       109.71        14.43        55.92        28.18        64.01 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
       36.16         0.79        67.36        16.64        33.11        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
        1.02        26.96        33.01        42.05         2.01        34.98 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1632 
       33.96        12.99        27.62        17.03        12.95        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 
       62.17        35.87        14.96        24.99        24.00         1.02 
TCGA-25-2393 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-29-1691 TCGA-29-1693 
       38.04        19.99        42.02         2.96        48.33       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       18.25        31.27        39.42        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1783 TCGA-29-2425 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       12.36         7.23        65.00        13.84        42.25        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
        9.76        38.07        51.91        36.26        15.68         0.26 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1891 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 
       34.78        36.62        30.05        42.51         2.20        29.10 
TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2534 TCGA-36-2537 
       22.85        30.08        24.23        35.05        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 
       25.08        23.80        21.60        14.17         6.05        11.47 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1992 
       42.02        10.42         1.48        24.03        11.38        29.00 
TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1728 
       25.02       116.12         9.40         5.42        44.81        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 
        4.34        31.79        35.80         5.79        13.02        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 
       37.05        42.51        56.61        67.76        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 
       39.85        30.64         1.18        61.64        60.62        65.52 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2113 TCGA-61-2612 TCGA-VG-A8LO 
       55.50        76.87        20.68        22.22         6.35         0.79 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0927 TCGA-10-0928 
       29.16         9.47        17.98        35.57        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       34.19        32.88        19.99        20.91         6.21        24.59 
TCGA-13-0724 TCGA-13-0730 TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 TCGA-13-0800 
        2.73        17.82        11.54       111.78        20.35        87.48 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 
       35.28        35.31        68.94       111.39       153.37        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0906 
       95.15       145.45        66.15       134.04        19.36       118.98 
TCGA-13-0908 TCGA-13-0921 TCGA-13-0924 
       60.59        48.76        85.94 

$`DEL PEAK 16(9P24.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1348 TCGA-04-1353 TCGA-04-1356 TCGA-04-1367 
        1.08        18.51        48.76         0.53        49.28       103.40 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1644 TCGA-04-1648 
       56.55        41.59        19.99       119.08        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1664 TCGA-09-1666 
       64.64        36.23        47.70        45.37        74.93        57.60 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 
       55.36        30.51         5.85         8.55         6.18        35.15 
TCGA-09-2050 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       71.11        26.93        77.10        81.17        28.54        83.31 
TCGA-13-1408 TCGA-13-1477 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       55.23        54.64        61.71       124.44        22.39        70.82 
TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
      125.56         4.24       127.27        66.15       115.07        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 
       34.82        65.69        34.16        65.52        54.25        14.53 
TCGA-13-2059 TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
       78.48        23.05        25.94        72.20        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       16.70         2.93         2.66        40.54        15.39        26.83 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       49.41         8.81         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1122 TCGA-23-1124 
       31.20        19.46        33.30         4.27        39.09        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 
        0.53        24.95        91.66        49.84         2.76         7.63 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 
       21.80        41.56         7.66        54.12        63.55         6.38 
TCGA-24-1417 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1428 TCGA-24-1434 
        7.82         6.25         6.02         5.95        17.39        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       43.53         8.55        45.14       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        64.27        16.21        56.58 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       51.91        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       45.50        47.70        10.26        48.33        38.24         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.72         3.81         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2033 TCGA-24-2038 TCGA-24-2254 
        4.87       152.02        34.82        18.48        44.52        57.07 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2290 TCGA-24-2297 TCGA-25-1315 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 
       36.23        55.86        52.04        65.00        37.97         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1635 
       15.02        18.58        20.61        38.20         0.30        52.04 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       85.05        13.02        49.05         3.02        12.00        45.01 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1701 
       29.03        31.00        26.99        78.90        47.61        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       23.93        59.67        41.98        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1777 
       66.81        62.93        31.30        22.98        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       14.93         8.38         5.36        36.30        86.17        62.47 
TCGA-29-2428 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 
       45.11        21.47        35.77         2.47        48.10        44.91 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
        6.12         1.22        57.57        24.26        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 
       30.18        18.77        22.49         6.71        44.12        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 
       21.53        22.55         8.55        25.74        27.85        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       33.01        29.49         2.24        20.98        18.31        20.52 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1584 
       16.18        47.57        23.74        28.93        40.77        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
        1.74        22.32        25.08       180.20        80.12        22.32 
TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       34.39         2.14        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 
       18.54        28.47        48.79        44.84         2.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 
       43.69         1.45         8.42        11.41         9.07        34.13 
TCGA-61-1913 TCGA-61-1917 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       48.92        43.43        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2096 TCGA-61-2102 TCGA-61-2110 TCGA-61-2111 
       51.72        71.74        58.39         6.48        44.52       125.75 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0366 
       31.07         8.61        39.68        18.94         9.99        57.76 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       54.31        25.91        14.66         6.71        35.44        36.92 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 
       44.55        39.58        12.39        31.20        15.19        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.38        38.01        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
       58.65        40.24       118.42       107.28        63.09        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0884 
       83.34        45.99        51.02        43.86        13.61       107.18 
TCGA-13-0887 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0903 TCGA-13-0904 
       66.67       102.84        43.36        71.74       127.79        50.37 
TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      123.16       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-2071 
       84.53        48.79        83.74        25.41 

  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                         0.26                          0.30 
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                       153.37                        180.20 
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                       31.860                        34.145 
[1] "0.3 - 153.4 (31.9)" "0.3 - 180.2 (34.1)"
[1] "hr=" "1"  
D49V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 16(9P24.3) MUTATED         1   248                2
  DEL PEAK 16(9P24.3) WILD-TYPE       2   310                0
D49V3, multiclass
                  clus
vv                 DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE
  OMENTUM                                    1                             2
  OVARY                                    248                           310
  PERITONEUM OVARY                           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"
D49V4, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P24.3) MUTATED   241   2
  DEL PEAK 16(9P24.3) WILD-TYPE 300   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P24.3) MUTATED    241    2
  DEL PEAK 16(9P24.3) WILD-TYPE  300    3
     clus
vv    DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE
  NO                          241                           300
  YES                           2                             3
[1] 2 2
[1] FALSE
D49V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 16(9P24.3) MUTATED    8 11  3  1
  DEL PEAK 16(9P24.3) WILD-TYPE  7 15  2  2
D49V6, multiclass
    clus
vv   DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE
  R0                           8                             7
  R1                          11                            15
  R2                           3                             2
  RX                           1                             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"
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P24.3) MUTATED     4 147
  DEL PEAK 16(9P24.3) WILD-TYPE   6 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P24.3) MUTATED      4  147
  DEL PEAK 16(9P24.3) WILD-TYPE    6  180
                        clus
vv                       DEL PEAK 16(9P24.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         147
                        clus
vv                       DEL PEAK 16(9P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           180
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 17(9Q34.13) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(9Q34.13) MUTATED   139 191
  DEL PEAK 17(9Q34.13) WILD-TYPE  89 140
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                           330                            229 
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                           191                            140 
$`DEL PEAK 17(9Q34.13) MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 
       11.87        41.00        49.15        46.62         1.08        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1364 
       65.52        63.09        48.76        21.57        63.98        33.67 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 
       82.39        41.59        19.99         0.79        38.37        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       84.20        55.43        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1667 
       31.86        45.37         9.99        38.43        89.33        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       30.51        17.98         3.02         8.55        97.55         6.12 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       26.93        77.10        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
       17.46        87.06        29.42       124.44        22.39        83.93 
TCGA-13-1491 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 
       52.44        90.38       127.27        66.15        13.97        34.82 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 
       34.16        65.52        80.15        54.25        80.02        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-20-0990 TCGA-20-1682 TCGA-20-1683 
       77.88        76.90        65.52        25.94        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1028 
       19.10        16.70         2.93         2.66        47.54        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
        8.81        29.13        18.90        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1124 TCGA-23-2072 
       19.46        86.01       129.96         4.27        58.13        24.95 
TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
      115.89        77.00        49.84         4.70         4.50         7.63 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 
       21.80        41.56        22.32        47.41         6.31         7.82 
TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        0.76         6.02         5.36        17.39        28.37        18.64 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
       72.92        12.46         9.11         1.18        26.96        57.40 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1558 TCGA-24-1560 
       16.21        56.58        41.06        51.91        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       45.50        47.70        25.87        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
       38.24         8.32         3.48         3.81        11.28         5.79 
TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
       30.21        11.05        81.11         4.87        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       34.82        14.43        18.48        36.16         0.79        47.54 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 
       70.45         0.82        16.64        33.11        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        33.01        52.04        42.05         2.01        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1627 TCGA-25-1630 
       37.97        33.96         2.99        12.99        12.95        38.20 
TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
        0.30        62.17        35.87        14.96        24.99        24.00 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       49.05         1.02        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
       19.99        42.02         2.96        78.90        48.33       101.79 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 TCGA-29-1711 
       40.41        68.32        36.36        23.93        31.27        34.62 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       86.60        66.81        39.42        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 
       12.36        12.30         8.38         7.23         5.36        86.17 
TCGA-29-2425 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       65.00        11.47        38.07        51.91        36.26         2.47 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-31-1944 TCGA-31-1946 TCGA-31-1953 
       36.62         1.22        57.57        45.57        30.18         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1576 TCGA-36-1577 
       42.51         2.20        29.10        22.85        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2544 
       27.85        24.23        24.69        35.05         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2588 
       18.31        20.52        14.17         6.05        11.47        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 
       42.02        10.42        40.77         1.48        24.03        21.14 
TCGA-57-1585 TCGA-57-1992 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
        1.74        29.00       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
        5.42        44.81        20.94        31.43        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
       31.79        28.47        48.79        33.67        43.69         8.42 
TCGA-61-1904 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
        9.07        31.30        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 
       15.75        38.17         2.01        17.98         4.01        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 
       30.64         1.18        45.40        71.74        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       65.52        55.50         6.48        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
        6.35        31.07         8.61        39.68        18.94         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0927 
       29.16         9.47        17.98        35.57        54.31        81.86 
TCGA-10-0930 TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 
       34.19        35.44        20.91        24.59        44.55         2.73 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 
       17.82        55.17         2.50        11.18        11.54       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 
       61.84        56.71        58.65        40.24       118.42        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
       69.73        83.34        87.48        45.99        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.31        13.61       107.18       111.39       153.37        66.67 
TCGA-13-0899 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       66.15       127.79       123.16       118.98       116.65        44.55 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
      109.32        84.53        48.79        48.76        83.74        85.94 

$`DEL PEAK 17(9Q34.13) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 
       13.81        20.52        43.92         1.81         2.01        18.51 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       65.46         0.53        49.28        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1530 TCGA-04-1644 TCGA-04-1654 TCGA-09-1664 
      103.40        56.55       119.08        48.89        47.70        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 TCGA-09-2043 TCGA-09-2045 
       41.62        57.60        55.36         5.85         6.18        35.15 
TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
       12.46        81.17        28.54        32.35        54.64        61.71 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1499 
       20.68        70.82       125.56        93.90         4.24       115.07 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1510 TCGA-13-1512 TCGA-13-A5FT TCGA-13-A5FU 
       43.20        65.69        44.68        14.53        70.45         8.42 
TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       23.05        26.20        72.20        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1032 TCGA-23-1109 TCGA-23-1113 TCGA-23-1117 
       26.83        32.09         2.76        51.35        31.20        33.30 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 
        6.38        39.09        33.47         0.53        87.48        91.66 
TCGA-23-2641 TCGA-24-0970 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 
        2.76        11.64         7.66        54.12        63.55         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 
        7.99         7.86         6.25         5.95         4.83        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 
       43.53         8.55        45.14       105.99         3.45        22.22 
TCGA-24-1546 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       64.27        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1844 TCGA-24-1846 TCGA-24-1850 TCGA-24-1920 
       10.26        17.23         3.72         4.37         5.52         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-2020 TCGA-24-2027 TCGA-24-2030 TCGA-24-2035 
       22.68        16.44       152.02       109.71        55.92        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 
       64.01        44.52        57.07         0.36        31.63        44.61 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 
       67.36        36.23        55.86        65.00        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1632 TCGA-25-1635 TCGA-25-1878 
       27.62        17.03        20.61        59.15        52.04        85.05 
TCGA-25-2042 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 
       13.02        29.03        31.00        26.99        47.61        39.02 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       33.93        31.20        16.93        59.67        18.25        41.98 
TCGA-29-1761 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1778 
       17.36        62.93        31.30        22.98        11.84        14.93 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       36.30        62.47        45.11        13.84        42.25        21.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
        9.76        35.77        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1950 
       34.78         6.12        24.26        30.05        48.79        18.77 
TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 
       22.49        44.12        28.77        21.53        22.55         8.55 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-57-1583 TCGA-57-1586 
       21.60        16.18        47.57        23.74        11.38        22.32 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-61-1721 
       25.08        25.02       180.20        80.12        22.32        11.11 
TCGA-61-1722 TCGA-61-1727 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 
        8.09        18.54        44.84        35.80         2.43         1.45 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 
        5.79        11.41        13.02        34.13        37.05        42.51 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2008 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
        5.52        14.50        30.64        45.96         4.80         4.77 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2104 TCGA-61-2109 TCGA-VG-A8LO TCGA-09-0366 
       51.72        61.64        76.87        20.68         0.79        57.76 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 
       25.91        18.51        32.88        14.66         6.71        36.92 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       19.99         6.21        39.58        12.39        31.20        15.19 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0793 TCGA-13-0794 TCGA-13-0802 TCGA-13-0883 
       11.38        38.01       107.28        63.09        51.02        68.94 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       92.42        95.15       145.45       102.84        43.36        71.74 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0908 TCGA-13-0912 TCGA-13-0916 
      134.04        19.36        50.37        60.59        37.64        58.68 
TCGA-13-2071 
       25.41 

  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                        153.37                         180.20 
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                        34.175                         31.200 
[1] "0.3 - 153.4 (34.2)" "0.3 - 180.2 (31.2)"
[1] "hr=" "1.1"
D50V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 17(9Q34.13) MUTATED         1   331                2
  DEL PEAK 17(9Q34.13) WILD-TYPE       2   227                0
D50V3, multiclass
                  clus
vv                 DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     331                            227
  PERITONEUM OVARY                            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"
D50V4, binary
                                cls
clus                               0   1
  DEL PEAK 17(9Q34.13) MUTATED   322   3
  DEL PEAK 17(9Q34.13) WILD-TYPE 219   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(9Q34.13) MUTATED    322    3
  DEL PEAK 17(9Q34.13) WILD-TYPE  219    2
     clus
vv    DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE
  NO                           322                            219
  YES                            3                              2
[1] 2 2
[1] FALSE
D50V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 17(9Q34.13) MUTATED   10 13  3  1
  DEL PEAK 17(9Q34.13) WILD-TYPE  5 13  2  2
D50V6, multiclass
    clus
vv   DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE
  R0                           10                              5
  R1                           13                             13
  R2                            3                              2
  RX                            1                              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"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(9Q34.13) MUTATED     6 198
  DEL PEAK 17(9Q34.13) WILD-TYPE   4 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(9Q34.13) MUTATED      6  198
  DEL PEAK 17(9Q34.13) WILD-TYPE    4  129
                        clus
vv                       DEL PEAK 17(9Q34.13) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          198
                        clus
vv                       DEL PEAK 17(9Q34.13) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            129
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 18(10P15.3) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(10P15.3) MUTATED    47  65
  DEL PEAK 18(10P15.3) WILD-TYPE 181 266
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           112                            447 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            65                            266 
$`DEL PEAK 18(10P15.3) MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1351 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       43.92         1.81        65.46        44.32        33.67        76.57 
TCGA-04-1371 TCGA-04-1646 TCGA-04-1648 TCGA-09-2043 TCGA-09-2051 TCGA-09-2053 
       82.39        27.88        28.64         6.18        63.09        39.75 
TCGA-09-2055 TCGA-13-1404 TCGA-13-1408 TCGA-13-1412 TCGA-13-1482 TCGA-13-1492 
       26.93        81.17        55.23        32.35        61.71       125.56 
TCGA-13-1494 TCGA-13-1500 TCGA-13-1510 TCGA-13-2057 TCGA-13-2065 TCGA-20-0996 
       93.90        13.97        44.68        80.02        65.52        72.20 
TCGA-20-1684 TCGA-20-1687 TCGA-23-1109 TCGA-23-1114 TCGA-23-1119 TCGA-23-1809 
       19.10         2.66        51.35        68.68       129.96         0.53 
TCGA-23-2078 TCGA-23-2641 TCGA-23-2643 TCGA-24-0975 TCGA-24-0979 TCGA-24-1416 
       87.48         2.76         4.70        21.80        41.56         6.38 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1435 TCGA-24-1467 TCGA-24-1471 
        6.25         5.95         5.36        43.53       105.99         1.18 
TCGA-24-1474 TCGA-24-1546 TCGA-24-1558 TCGA-24-1567 TCGA-24-1842 TCGA-24-1844 
       22.22        64.27        19.53        17.23         8.32         3.72 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 
        5.79         5.52         9.80        22.68        16.44         4.87 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2036 TCGA-24-2254 TCGA-24-2293 TCGA-25-1313 
       58.16       109.71        64.01        57.07        16.64        26.96 
TCGA-25-1323 TCGA-25-1625 TCGA-25-1630 TCGA-25-1632 TCGA-25-2042 TCGA-25-2393 
       12.99        27.62        38.20        59.15        13.02        38.04 
TCGA-25-2399 TCGA-25-2400 TCGA-29-1688 TCGA-29-1694 TCGA-29-1697 TCGA-29-1698 
       19.99        42.02        78.90        39.02        31.20        68.32 
TCGA-29-1699 TCGA-29-1761 TCGA-29-1764 TCGA-30-1714 TCGA-30-1855 TCGA-30-1891 
       36.36        17.36        62.93        38.07         2.47        30.05 
TCGA-31-1946 TCGA-31-1959 TCGA-36-1570 TCGA-36-2534 TCGA-36-2538 TCGA-36-2544 
       30.18         2.20        21.53        29.82        25.08        20.98 
TCGA-36-2545 TCGA-42-2582 TCGA-57-1992 TCGA-61-1736 TCGA-61-1743 TCGA-61-1895 
       18.31        47.57        29.00        48.79        43.69         1.45 
TCGA-61-1899 TCGA-61-1907 TCGA-61-2016 TCGA-61-2096 TCGA-61-2097 TCGA-61-2614 
        8.42        31.30         1.18        58.39        60.62         8.61 
TCGA-09-0364 TCGA-09-0367 TCGA-10-0927 TCGA-10-0928 TCGA-10-0938 TCGA-13-0714 
       29.16        17.98        81.86        18.51        20.91         6.21 
TCGA-13-0761 TCGA-13-0766 TCGA-13-0799 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 
       38.01        56.71        83.34        95.15       145.45        71.74 
TCGA-13-0899 TCGA-13-0905 TCGA-13-0908 TCGA-13-0921 
       66.15       123.16        60.59        48.76 

$`DEL PEAK 18(10P15.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        11.87        41.00        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       46.62         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       48.76        21.57        63.98         0.53        49.28        32.52 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
      103.40        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 
      119.08        29.10        84.20        55.43        48.89        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       36.23        31.86        47.70        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       89.33        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 
        6.12        35.15         4.54       112.41        71.11        20.94 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
       12.46        77.10        28.54        83.31        57.27        81.01 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       17.46        54.64        87.06        29.42       124.44        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1495 TCGA-13-1496 
       22.39        70.82        83.93        52.44        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
      127.27        66.15       115.07        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
       34.16        65.52        80.15        54.25        14.53        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       77.88        76.90        70.45         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       26.20        27.52        25.38        16.70         2.93        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       49.68        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 
        8.81        29.13        18.90         2.76        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 
       31.20        19.46        33.30        86.01         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 
       39.09        33.47        58.13        24.95       115.89        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 
       77.00        49.84         4.50         7.63        11.64         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 
       22.32        54.12        63.55        47.41         6.31         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 
        7.99         7.86         0.76         6.02         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        18.64        18.67         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
       45.14         9.11         3.45        26.96        57.40        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       70.62        39.88        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       10.26        90.15        88.37        48.33        38.24         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 
        3.81         4.37        11.28        30.21        11.05        81.11 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
      152.02        44.84        34.82        14.43        55.92        18.48 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       28.18        44.52        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       31.63        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86        53.26         1.02        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       42.05         2.01        34.98        65.00        37.97        33.96 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.99        15.02        18.58        17.03        12.95        20.61 
TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
        0.30        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
       24.00        85.05        49.05         1.02         3.02        12.00 
TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 
       45.01         2.96        29.03        31.00        26.99        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 
       48.33       101.79        40.41        33.93        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 
       59.67        18.25        41.98        31.27        34.62        86.60 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       66.81        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        7.23         5.36        36.30        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       45.11        13.84        42.25        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       35.77        51.91        36.26        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       24.26        48.79        45.57        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 
       42.51        44.12        28.77        29.10        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 
       35.05        33.01        29.49        25.91        23.80        21.60 
TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
        2.24        20.52        14.17         6.05        16.18        11.47 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 
       24.03        11.38        21.14         1.74        22.32        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
       34.39         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.94        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1900 
       28.47        44.84        35.80         2.43        33.67         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02         9.07        34.13        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       48.92        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       39.85        30.64        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       51.72        71.74        61.64        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       76.87        20.68        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0365 
       31.07        39.68        18.94         0.79         9.99         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0930 TCGA-10-0931 
       57.76        35.57        54.31        25.91        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 
       14.66         6.71        35.44        36.92        19.99        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       44.55        39.58         2.73        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
      111.78        61.84        58.65        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       63.09        20.35        69.73        87.48        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0893 
      111.39       153.37        66.67        92.42       102.84        43.36 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0910 
      134.04        19.36       127.79        50.37       118.98       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                          0.53                           0.26 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        145.45                         180.20 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        31.825                         33.010 
[1] "0.5 - 145.4 (31.8)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 18(10P15.3) MUTATED         1   113                0
  DEL PEAK 18(10P15.3) WILD-TYPE       2   445                2
D51V3, multiclass
                  clus
vv                 DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     113                            445
  PERITONEUM OVARY                            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"
D51V4, binary
                                cls
clus                               0   1
  DEL PEAK 18(10P15.3) MUTATED   110   0
  DEL PEAK 18(10P15.3) WILD-TYPE 431   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED    110    0
  DEL PEAK 18(10P15.3) WILD-TYPE  431    5
     clus
vv    DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  NO                           110                            431
  YES                            0                              5
[1] 2 2
[1] FALSE
D51V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 18(10P15.3) MUTATED    2  4  0  0
  DEL PEAK 18(10P15.3) WILD-TYPE 13 22  5  3
D51V6, multiclass
    clus
vv   DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  R0                            2                             13
  R1                            4                             22
  R2                            0                              5
  RX                            0                              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"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(10P15.3) MUTATED     1  60
  DEL PEAK 18(10P15.3) WILD-TYPE   9 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      1   60
  DEL PEAK 18(10P15.3) WILD-TYPE    9  267
                        clus
vv                       DEL PEAK 18(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 18(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            267
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 19(10Q23.31) MUTATION ANALYSIS
D52V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 19(10Q23.31) MUTATED    92 123
  DEL PEAK 19(10Q23.31) WILD-TYPE 136 208
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            215                             344 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            123                             208 
$`DEL PEAK 19(10Q23.31) MUTATED`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1342 TCGA-04-1343 
       13.81        43.92        41.00         1.81        18.51        11.87 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1525 
       48.76        21.57        33.67        76.57       103.40        38.37 
TCGA-04-1536 TCGA-04-1648 TCGA-04-1649 TCGA-04-1654 TCGA-09-1667 TCGA-09-1668 
       29.10        28.64        64.64        47.70        61.87        55.36 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2051 TCGA-09-2053 TCGA-13-1405 
        3.02        97.55         6.18        63.09        39.75        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1496 
       83.31        55.23        70.82        83.93       125.56         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 
      127.27        66.15       115.07        43.20        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
       44.68        14.53        80.02        78.48        76.90        65.52 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       27.52        19.10         2.93         2.66        47.54        49.68 
TCGA-23-1023 TCGA-23-1032 TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 TCGA-23-1119 
       40.54         2.76         3.22        68.68        33.30       129.96 
TCGA-23-1122 TCGA-23-1123 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       39.09        33.47       115.89        77.00        49.84         2.76 
TCGA-23-2645 TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 
        4.50        41.56        54.12        63.55         6.38         7.82 
TCGA-24-1418 TCGA-24-1423 TCGA-24-1424 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        7.99         6.25         6.02        28.37        18.64        18.67 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
        8.55        45.14       105.99         1.18        22.22        26.96 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 TCGA-24-1563 TCGA-24-1567 
       41.06        41.39        70.62        39.88        47.70        17.23 
TCGA-24-1614 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1928 
       48.33         3.72         3.81        11.28         5.52        11.05 
TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 TCGA-24-2254 
      152.02        58.16        34.82        55.92        64.01        57.07 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 
       47.54        70.45         0.82        67.36        36.23        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1320 TCGA-25-1329 TCGA-25-1631 TCGA-25-1632 
       53.26         1.02        37.97        15.02         0.30        59.15 
TCGA-25-1635 TCGA-25-2391 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-29-1691 
       52.04        49.05        45.01        19.99        42.02        48.33 
TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.93        68.32        36.36        16.93        23.93        59.67 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       41.98        34.62        17.36        66.81        62.93        39.42 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 
       22.98        24.36        12.36        14.93         8.38         5.36 
TCGA-29-1785 TCGA-29-2429 TCGA-29-2434 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       36.30        13.84        11.47        51.91         2.47        15.68 
TCGA-30-1859 TCGA-30-1860 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       48.10        44.91        45.57        30.18        22.49         6.71 
TCGA-31-1959 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1581 TCGA-36-2532 
        2.20        21.53        22.55        25.74        24.69        29.49 
TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-36-2551 TCGA-42-2587 TCGA-42-2589 
       21.60        18.31        20.52        16.18        23.74        42.02 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1994 TCGA-61-1727 TCGA-61-1728 TCGA-61-1737 
       40.77        24.03        25.02        18.54        27.88        44.84 
TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 
       35.80        33.67        43.69         1.45         5.79        11.41 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-2012 TCGA-61-2088 
       48.92        56.61        43.43        15.75        30.64         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2113 TCGA-OY-A56P TCGA-09-0366 TCGA-09-0367 
       51.72        71.74        22.22        39.68        57.76        17.98 
TCGA-09-0369 TCGA-10-0930 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0720 
       35.57        34.19        35.44        36.92        20.91        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 
       39.58         2.73        55.17        11.38        11.54        61.84 
TCGA-13-0768 TCGA-13-0794 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0807 
       58.65        63.09        87.48        45.99        43.86        13.61 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
      111.39        66.67        95.15       102.84        43.36        66.15 
TCGA-13-0900 TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 
      134.04        50.37       123.16       116.65        44.55       109.32 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       58.68        48.79        48.76        83.74        85.94 

$`DEL PEAK 19(10Q23.31) WILD-TYPE`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       20.52        11.87        49.15         2.01        46.62         1.08 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       65.52        63.09        63.98        65.46         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       32.52        44.32        82.39        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
        0.79       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       36.23        31.86        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       74.93        41.62        57.60        30.51        17.98         5.85 
TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        8.55         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 
       20.94        26.93        12.46        77.10        81.17        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       81.01        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 TCGA-13-1494 
       29.42       124.44        20.68        22.39        52.44        93.90 
TCGA-13-1495 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 
       90.38        13.97        34.82        65.69        34.16        54.25 
TCGA-13-2060 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       77.88        70.45         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       72.20        25.38        16.70        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        29.13        18.90        51.35        54.51 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 
       31.20        19.46        86.01         4.27         6.38        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2643 TCGA-24-0966 
        0.53        24.95        87.48        91.66         4.70         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 
       11.64        21.80         7.66        22.32        47.41         6.31 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        7.86         0.76         5.95         5.36         4.83        17.39 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 TCGA-24-1545 
       43.53        72.92        12.46         9.11         3.45        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 
       64.27        16.21        56.58        51.91        58.09        88.50 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 
       19.53        44.09        45.50        25.87        10.26        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 
       88.37        38.24         8.32         3.48         4.37         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        9.80        22.68        30.21        16.44        81.11         4.87 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 
       44.84       109.71        14.43        18.48        28.18        44.52 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2293 
       36.16         0.79         0.36        31.63        44.61        16.64 
TCGA-24-2295 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       33.11        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
       34.98        65.00        33.96         2.99        12.99        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 
       27.62        17.03        12.95        20.61        38.20        62.17 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       35.87        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2401 TCGA-25-2404 
        1.02        38.04         3.02        12.00         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 
       31.00        26.99        78.90        47.61       101.79        39.02 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1705 TCGA-29-1710 TCGA-29-1762 TCGA-29-1768 
       40.41        31.20        18.25        31.27        86.60        31.30 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1783 TCGA-29-2414 
       22.55        17.33        11.84        12.30         7.23        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
       65.00        62.47        45.11        42.25        21.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 
       35.77        38.07        36.26         0.26        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       36.62         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1950 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 
       18.77        42.51        44.12        28.77        29.10        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
        8.55        30.08        27.85        24.23        35.05        33.01 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 
       29.82        25.91        25.08        23.80         2.24        20.98 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 
       14.17         6.05        11.47        47.57        28.93        10.42 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        11.38        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
       34.39         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       20.94        31.43         4.34        31.79        28.47        48.79 
TCGA-61-1740 TCGA-61-1899 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        2.43         8.42        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       37.05        42.51        67.76        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 
       14.50        17.98         4.01        30.64        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
       45.96        45.40         4.80        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO 
      125.75         6.35        31.07         8.61        18.94         0.79 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        9.99        29.16         9.47        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0937 TCGA-13-0714 
       18.51        32.88        14.66         6.71        19.99         6.21 
TCGA-13-0717 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 
       24.59        12.39        31.20        15.19        17.82         2.50 
TCGA-13-0757 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.18        38.01       111.78        56.71        40.24       118.42 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0802 TCGA-13-0804 
      107.28        20.35        69.73        83.34        51.02        35.28 
TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 
       35.31        68.94       107.18       153.37        92.42       145.45 
TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 
       71.74        19.36       127.79       118.98        60.59        37.64 
TCGA-13-0919 TCGA-13-2071 
       84.53        25.41 

  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                           0.30                            0.26 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         152.02                          180.20 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         39.680                          29.935 
[1] "0.3 - 152.0 (39.7)" "0.3 - 180.2 (29.9)"
[1] "hr=" "1.2"
D52V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 19(10Q23.31) MUTATED         1   215                1
  DEL PEAK 19(10Q23.31) WILD-TYPE       2   343                1
D52V3, multiclass
                  clus
vv                 DEL PEAK 19(10Q23.31) MUTATED
  OMENTUM                                      1
  OVARY                                      215
  PERITONEUM OVARY                             1
                  clus
vv                 DEL PEAK 19(10Q23.31) WILD-TYPE
  OMENTUM                                        2
  OVARY                                        343
  PERITONEUM OVARY                               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"
D52V4, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED   210   3
  DEL PEAK 19(10Q23.31) WILD-TYPE 331   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED    210    3
  DEL PEAK 19(10Q23.31) WILD-TYPE  331    2
     clus
vv    DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  NO                            210                             331
  YES                             3                               2
[1] 2 2
[1] FALSE
D52V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 19(10Q23.31) MUTATED    5  6  1  1
  DEL PEAK 19(10Q23.31) WILD-TYPE 10 20  4  2
D52V6, multiclass
    clus
vv   DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  R0                             5                              10
  R1                             6                              20
  R2                             1                               4
  RX                             1                               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"
D52V7, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     4 122
  DEL PEAK 19(10Q23.31) WILD-TYPE   6 205
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      4  122
  DEL PEAK 19(10Q23.31) WILD-TYPE    6  205
                        clus
vv                       DEL PEAK 19(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           122
                        clus
vv                       DEL PEAK 19(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             205
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 20(10Q25.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(10Q25.1) MUTATED   100 132
  DEL PEAK 20(10Q25.1) WILD-TYPE 128 199
  DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE 
                           232                            327 
  DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE 
                           132                            199 
$`DEL PEAK 20(10Q25.1) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1341 TCGA-04-1342 
       13.81        20.52        43.92        41.00         1.08        18.51 
TCGA-04-1343 TCGA-04-1356 TCGA-04-1364 TCGA-04-1525 TCGA-04-1530 TCGA-04-1644 
       11.87        49.28        33.67        38.37       119.08        48.89 
TCGA-04-1648 TCGA-04-1649 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       28.64        64.64        41.62        57.60        61.87        55.36 
TCGA-09-1673 TCGA-09-2045 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-13-1404 
        3.02        35.15        71.11        63.09        39.75        81.17 
TCGA-13-1405 TCGA-13-1410 TCGA-13-1483 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 
       28.54        81.01        29.42        70.82        83.93       125.56 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1507 TCGA-13-1509 
       90.38         4.24       127.27        66.15        65.52        80.15 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 
       14.53        80.02        78.48        76.90        65.52        23.05 
TCGA-20-1684 TCGA-20-1686 TCGA-23-1021 TCGA-23-1027 TCGA-23-1032 TCGA-23-1110 
       19.10         2.93        47.54        32.09         2.76        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 
        3.22        68.68        33.30       129.96         6.38        33.47 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 TCGA-23-2641 TCGA-24-0979 
        0.53        24.95       115.89        77.00         2.76        41.56 
TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 TCGA-24-1425 
       63.55         6.38         7.82         7.99         6.25         5.95 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 
       28.37        18.64        18.67        43.53         8.55        45.14 
TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1549 TCGA-24-1551 
      105.99         1.18        22.22        26.96        56.58        51.91 
TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 TCGA-24-1563 TCGA-24-1604 TCGA-24-1614 
       41.39        70.62        39.88        47.70        88.37        48.33 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1849 TCGA-24-1850 TCGA-24-1928 
        8.32         3.72         3.81         5.79         5.52        11.05 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 
       58.16        34.82        55.92        64.01        57.07        47.54 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       70.45         0.82        36.23        55.86        53.26         1.02 
TCGA-25-1320 TCGA-25-1329 TCGA-25-1625 TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 
       37.97        15.02        27.62         0.30        59.15        52.04 
TCGA-25-2042 TCGA-25-2399 TCGA-25-2400 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 
       13.02        19.99        42.02        26.99        78.90        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
      101.79        39.02        33.93        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 
       16.93        23.93        59.67        41.98        34.62        17.36 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 
       66.81        62.93        39.42        22.98        24.36        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1784 TCGA-29-2427 TCGA-30-1853 
       12.36        11.84        14.93         5.36        62.47        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-31-1953 TCGA-31-1959 
        2.47        15.68        48.10        44.91         6.71         2.20 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2532 
       22.55         8.55        25.74        27.85        24.69        29.49 
TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 TCGA-36-2545 TCGA-36-2551 TCGA-42-2582 
       29.82        25.08        21.60        18.31        16.18        47.57 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1994 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
       40.77        24.03        25.02         8.09        20.94        18.54 
TCGA-61-1728 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       27.88        28.47        44.84        35.80         2.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 TCGA-61-1910 TCGA-61-1913 
       43.69         1.45         5.79        13.02        37.05        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-61-2008 
       56.61        67.76        43.43        15.75        14.50        30.64 
TCGA-61-2012 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2096 
       30.64         4.80         4.77        51.72        71.74        58.39 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 TCGA-OY-A56P TCGA-09-0366 TCGA-09-0367 
        6.48        76.87        22.22        39.68        57.76        17.98 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0931 TCGA-10-0935 TCGA-10-0938 TCGA-13-0714 
       35.57        54.31        32.88        35.44        20.91         6.21 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 
       39.58         2.73        12.39        55.17        11.38        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 
       38.01        61.84        56.71        58.65       118.42        63.09 
TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0807 
       20.35        83.34        87.48        45.99        43.86        13.61 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
      111.39        66.67        95.15       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 
       66.15        19.36        50.37       116.65        44.55       109.32 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       58.68        48.79        48.76        83.74 

$`DEL PEAK 20(10Q25.1) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 
       11.87         1.81        49.15         2.01        46.62        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       63.09        48.76        21.57        63.98        65.46         0.53 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        76.57       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       41.59        19.99         0.79        29.10        84.20        55.43 
TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       27.88        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       38.43        89.33        74.93        30.51        17.98         5.85 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 
        8.55        97.55         6.18         6.12         4.54       112.41 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 
       20.94        26.93        12.46        77.10        83.31        55.23 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       57.27        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 TCGA-13-1494 TCGA-13-1499 
      124.44        20.68        22.39        52.44        93.90       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 
       13.97        43.20        34.82        65.69        34.16        44.68 
TCGA-13-1511 TCGA-13-2060 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       54.25        77.88        70.45         8.42        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1687 TCGA-23-1022 
       72.20        27.52        25.38        16.70         2.66        49.68 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        26.83        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-1120 
       18.90        51.35        31.20        19.46        86.01         4.27 
TCGA-23-1122 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 
       39.09        58.13        87.48        91.66        49.84         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
        4.50         7.63        11.64        21.80         7.66        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 
       54.12        47.41         6.31         7.86         0.76         6.02 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 
        5.36         4.83        17.39        72.92        12.46         9.11 
TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1553 
        3.45        57.40        64.27        16.21        41.06        58.09 
TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       88.50        19.53        44.09        45.50        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 
       17.23        90.15        38.24         3.48         4.37        11.28 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        9.80        22.68        30.21        16.44        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 
      152.02        44.84       109.71        14.43        18.48        28.18 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 
       44.52        36.16         0.79         0.36        31.63        44.61 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       67.36        16.64        33.11        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 
       42.05         2.01        34.98        65.00        33.96         2.99 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       12.99        18.58        17.03        12.95        20.61        38.20 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       62.17        35.87        14.96        24.99        24.00        85.05 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       49.05         1.02        38.04         3.02        12.00        45.01 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1695 TCGA-29-1705 
        2.96        29.03        31.00        47.61        40.41        18.25 
TCGA-29-1710 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 TCGA-29-1777 TCGA-29-1781 
       31.27        86.60        31.30        22.55        12.30         8.38 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
        7.23        36.30        86.17        65.00        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       51.91         0.26        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       18.77        22.49        42.51        44.12        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
       21.53        22.85        30.08        24.23        35.05        33.01 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 
       25.91        23.80         2.24        20.98        20.52        14.17 
TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
        6.05        11.47        23.74        28.93        42.02        10.42 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        11.38        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1725 
       34.39         2.14         5.42        44.81        11.11        31.43 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1899 TCGA-61-1901 TCGA-61-1904 
        4.34        31.79        48.79         8.42        11.41         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       34.13        31.30        42.51        38.17         2.01         5.52 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98         4.01        39.85         1.18        45.96        45.40 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2109 TCGA-61-2110 
       61.64        60.62        65.52        55.50        20.68        44.52 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO 
      125.75         6.35        31.07         8.61        18.94         0.79 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
        9.99        29.16         9.47        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 
       34.19        14.66         6.71        36.92        19.99        24.59 
TCGA-13-0720 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 
       44.55        31.20        15.19        17.82         2.50        11.18 
TCGA-13-0762 TCGA-13-0791 TCGA-13-0793 TCGA-13-0797 TCGA-13-0802 TCGA-13-0804 
      111.78        40.24       107.28        69.73        51.02        35.28 
TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 
       35.31        68.94       107.18       153.37        92.42       145.45 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 
      134.04       127.79       123.16       118.98        60.59        37.64 
TCGA-13-0919 TCGA-13-0924 TCGA-13-2071 
       84.53        85.94        25.41 

  DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE 
                        129.96                         180.20 
  DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE 
                         36.31                          30.51 
[1] "0.3 - 130.0 (36.3)" "0.3 - 180.2 (30.5)"
[1] "hr=" "1.2"
D53V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 20(10Q25.1) MUTATED         1   231                1
  DEL PEAK 20(10Q25.1) WILD-TYPE       2   327                1
D53V3, multiclass
                  clus
vv                 DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     231                            327
  PERITONEUM OVARY                            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"
D53V4, binary
                                cls
clus                               0   1
  DEL PEAK 20(10Q25.1) MUTATED   227   3
  DEL PEAK 20(10Q25.1) WILD-TYPE 314   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q25.1) MUTATED    227    3
  DEL PEAK 20(10Q25.1) WILD-TYPE  314    2
     clus
vv    DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE
  NO                           227                            314
  YES                            3                              2
[1] 2 2
[1] FALSE
D53V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 20(10Q25.1) MUTATED    3  8  1  1
  DEL PEAK 20(10Q25.1) WILD-TYPE 12 18  4  2
D53V6, multiclass
    clus
vv   DEL PEAK 20(10Q25.1) MUTATED DEL PEAK 20(10Q25.1) WILD-TYPE
  R0                            3                             12
  R1                            8                             18
  R2                            1                              4
  RX                            1                              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"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(10Q25.1) MUTATED     5 131
  DEL PEAK 20(10Q25.1) WILD-TYPE   5 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q25.1) MUTATED      5  131
  DEL PEAK 20(10Q25.1) WILD-TYPE    5  196
                        clus
vv                       DEL PEAK 20(10Q25.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          131
                        clus
vv                       DEL PEAK 20(10Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            196
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 21(11P15.5) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(11P15.5) MUTATED   149 184
  DEL PEAK 21(11P15.5) WILD-TYPE  79 147
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           333                            226 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           184                            147 
$`DEL PEAK 21(11P15.5) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1338 TCGA-04-1341 TCGA-04-1346 
       13.81        20.52        43.92        46.62         1.08        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       63.09        21.57        65.46        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
      103.40        82.39        56.55        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       29.10        84.20        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1661 TCGA-09-1665 TCGA-09-1666 
       36.23        47.70        45.37        38.43        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 
       61.87        55.36        30.51        17.98         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2053 TCGA-09-2055 
        6.18         6.12        35.15       112.41        39.75        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 
       12.46        77.10        81.17        28.54        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
       81.01        17.46        32.35        54.64        61.71        29.42 
TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 
      124.44        70.82        83.93        93.90        90.38       127.27 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 
       13.97        43.20        65.69        34.16        65.52        80.02 
TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-1682 
       78.48        65.52        70.45         8.42        25.94        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       25.38        16.70         2.93         2.66        47.54        49.68 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       40.54        26.83        32.09        49.41         8.81        18.90 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       54.51        31.20        68.68        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1124 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
        4.27        39.09        58.13       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 
       77.00         2.76         4.70         4.50        11.64        21.80 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1424 
       54.12        63.55        47.41         6.31         7.82         6.02 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
        5.95         4.83        17.39        43.53         8.55        72.92 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       45.14         9.11         3.45        22.22        26.96        57.40 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1556 TCGA-24-1558 TCGA-24-1562 TCGA-24-1563 
       56.58        51.91        70.62        19.53        45.50        47.70 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       25.87        17.23        88.37        48.33        38.24         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.81         4.37        11.28         5.79         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2026 TCGA-24-2029 
       30.21        16.44        81.11         4.87        34.82        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       55.92        18.48        57.07        36.16         0.79         0.36 
TCGA-24-2280 TCGA-24-2295 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1318 
       70.45        33.11        26.96        33.01        52.04        34.98 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       12.99        15.02        27.62        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
        0.30        35.87        14.96        24.00        85.05        13.02 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2400 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 
        1.02        38.04        42.02         2.96        26.99        78.90 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1697 TCGA-29-1702 TCGA-29-1703 
       48.33       101.79        39.02        31.20        23.93        59.67 
TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 
       18.25        34.62        86.60        66.81        62.93        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       22.98        24.36        12.36        11.84        12.30         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2431 TCGA-29-2432 
        7.23         5.36        86.17        65.00        42.25        21.47 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 
       51.91        36.26        15.68         0.26        44.91        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1953 
        6.12        36.62        24.26        30.05        45.57         6.71 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 TCGA-36-1577 
       44.12         2.20        28.77        29.10        22.55        25.74 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       27.85        24.69        33.01        29.82        25.91        25.08 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 
       21.60         2.24        18.31        20.52         6.05        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-59-2350 
       24.03        21.14         1.74        29.00        25.08        22.32 
TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        9.40         5.42        44.81         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 
       18.54        27.88         4.34        28.47        44.84        35.80 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       43.69         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 
        9.07        34.13        37.05        48.92        56.61        38.17 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       17.98        39.85        30.64        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2102 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 
       51.72        71.74         6.48        20.68       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0926 TCGA-10-0928 
        9.99        57.76        17.98        35.57        25.91        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 TCGA-13-0714 TCGA-13-0723 TCGA-13-0724 
       34.19        32.88        19.99         6.21        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 
       12.39        31.20        55.17         2.50        11.38        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 
      111.78        61.84        56.71        58.65       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       63.09        20.35        69.73        45.99        51.02        43.86 
TCGA-13-0804 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0890 TCGA-13-0893 
       35.28        68.94       111.39       153.37       145.45        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 
      118.98        60.59       109.32        58.68        48.79        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

$`DEL PEAK 21(11P15.5) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       11.87        41.00         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1364 
       11.87        48.76        63.98         0.53        49.28        33.67 
TCGA-04-1516 TCGA-04-1519 TCGA-04-1638 TCGA-04-1652 TCGA-09-1659 TCGA-09-1662 
       41.59         0.79        55.43        31.86         9.99        89.33 
TCGA-09-1664 TCGA-09-1672 TCGA-09-1673 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 
       74.93         5.85         3.02         4.54        71.11        63.09 
TCGA-09-2054 TCGA-13-1407 TCGA-13-1481 TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 
       20.94        83.31        87.06        20.68        22.39        52.44 
TCGA-13-1492 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1504 TCGA-13-1509 
      125.56         4.24        66.15       115.07        34.82        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-20-0987 
       44.68        54.25        14.53        77.88        76.90        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1684 TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 
       26.20        72.20        19.10        15.39        29.13         2.76 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1116 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 
       51.35         3.22        19.46         6.38        33.47         0.53 
TCGA-23-2072 TCGA-23-2084 TCGA-24-0966 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       24.95        49.84         7.63        41.56         7.66        22.32 
TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1426 
        6.38         7.99         7.86         0.76         6.25         5.36 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1464 TCGA-24-1467 TCGA-24-1471 
       28.37        18.64        18.67        12.46       105.99         1.18 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       64.27        16.21        41.06        41.39        58.09        88.50 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1565 TCGA-24-1603 TCGA-24-1842 TCGA-24-1844 
       39.88        44.09        10.26        90.15         8.32         3.72 
TCGA-24-1850 TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
        5.52        11.05       152.02        44.84        58.16       109.71 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 
       28.18        64.01        44.52        47.54        31.63        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 
        0.82        67.36        36.23        16.64        55.86        53.26 
TCGA-25-1312 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
        1.02        42.05         2.01        65.00        37.97        33.96 
TCGA-25-1322 TCGA-25-1623 TCGA-25-1626 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
        2.99        18.58        17.03        59.15        62.17        52.04 
TCGA-25-1871 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       24.99        49.05         3.02        12.00        45.01        19.99 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 
       29.03        31.00        47.61        40.41        33.93        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1766 
       36.36        16.93        41.98        31.27        17.36        39.42 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1778 TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 
       22.55        17.33        14.93        36.30        62.47        45.11 
TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 
       13.84        11.47         9.76        35.77        38.07         2.47 
TCGA-30-1859 TCGA-30-1867 TCGA-30-1880 TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 
       48.10         1.22        57.57        48.79        30.18        18.77 
TCGA-31-1951 TCGA-31-1955 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
       22.49        42.51        21.53        22.85         8.55        30.08 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 
       24.23        35.05        29.49        23.80        20.98        14.17 
TCGA-36-2551 TCGA-42-2593 TCGA-57-1583 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 
       16.18         1.48        11.38        22.32        25.02       180.20 
TCGA-59-2349 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 TCGA-61-1733 
       80.12       116.12        34.39         2.14        11.11        31.79 
TCGA-61-1736 TCGA-61-1740 TCGA-61-1741 TCGA-61-1907 TCGA-61-1911 TCGA-61-1915 
       48.79         2.43        33.67        31.30        42.51        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       43.43        15.75         2.01         5.52        14.50         4.01 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
       30.64         1.18        45.96        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-09-0364 TCGA-09-0365 
       65.52        55.50        76.87        44.52        29.16         9.47 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       54.31        81.86        14.66         6.71        35.44        36.92 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 
       20.91        24.59        44.55        15.19        17.82        11.18 
TCGA-13-0761 TCGA-13-0791 TCGA-13-0799 TCGA-13-0800 TCGA-13-0805 TCGA-13-0807 
       38.01        40.24        83.34        87.48        35.31        13.61 
TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0897 
      107.18        66.67        92.42        95.15       102.84        71.74 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0919 
      116.65        44.55        37.64        84.53 

  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                        153.37                         180.20 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                        32.880                         32.665 
[1] "0.3 - 153.4 (32.9)" "0.5 - 180.2 (32.7)"
[1] "hr=" "1.2"
D54V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 21(11P15.5) MUTATED         0   336                0
  DEL PEAK 21(11P15.5) WILD-TYPE       3   222                2
D54V3, multiclass
                  clus
vv                 DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  OMENTUM                                     0                              3
  OVARY                                     336                            222
  PERITONEUM OVARY                            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"
D54V4, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED   326   4
  DEL PEAK 21(11P15.5) WILD-TYPE 215   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED    326    4
  DEL PEAK 21(11P15.5) WILD-TYPE  215    1
     clus
vv    DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  NO                           326                            215
  YES                            4                              1
[1] 2 2
[1] FALSE
D54V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 21(11P15.5) MUTATED   10 16  4  3
  DEL PEAK 21(11P15.5) WILD-TYPE  5 10  1  0
D54V6, multiclass
    clus
vv   DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  R0                           10                              5
  R1                           16                             10
  R2                            4                              1
  RX                            3                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED     6 200
  DEL PEAK 21(11P15.5) WILD-TYPE   4 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      6  200
  DEL PEAK 21(11P15.5) WILD-TYPE    4  127
                        clus
vv                       DEL PEAK 21(11P15.5) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          200
                        clus
vv                       DEL PEAK 21(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            127
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 22(11Q25) MUTATION ANALYSIS
D55V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 22(11Q25) MUTATED    76 120
  DEL PEAK 22(11Q25) WILD-TYPE 152 211
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                         196                          363 
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                         120                          211 
$`DEL PEAK 22(11Q25) MUTATED`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 
       20.52        43.92         1.81        46.62         1.08        18.51 
TCGA-04-1348 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1514 TCGA-04-1516 
       48.76        65.46        49.28        32.52        56.55        41.59 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1648 TCGA-04-1655 TCGA-09-1666 TCGA-09-1667 
      119.08        29.10        28.64        45.37        57.60        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-2044 TCGA-09-2050 TCGA-09-2053 
       30.51        17.98         3.02         6.12        71.11        39.75 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1409 TCGA-13-1411 TCGA-13-1482 TCGA-13-1483 
       26.93        12.46        57.27        17.46        61.71        29.42 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1501 
       22.39        83.93        93.90        90.38       127.27        43.20 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU 
       44.68        14.53        77.88        76.90        65.52         8.42 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-23-1022 TCGA-23-1028 
       26.20        27.52        25.38        19.10        49.68        49.41 
TCGA-23-1113 TCGA-23-1118 TCGA-23-1122 TCGA-23-2072 TCGA-23-2084 TCGA-23-2643 
       31.20        86.01        39.09        24.95        49.84         4.70 
TCGA-23-2645 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1418 TCGA-24-1427 
        4.50        11.64        41.56        22.32         7.99         4.83 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1544 TCGA-24-1546 
       72.92        12.46        45.14         9.11        26.96        64.27 
TCGA-24-1557 TCGA-24-1562 TCGA-24-1567 TCGA-24-1842 TCGA-24-1844 TCGA-24-1850 
       39.88        45.50        17.23         8.32         3.72         5.52 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2030 
       22.68        30.21        11.05         4.87       152.02        55.92 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2293 
       57.07        36.16         0.79        47.54        70.45        16.64 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1320 
       55.86        53.26        26.96        52.04        34.98        37.97 
TCGA-25-1321 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1635 TCGA-25-1870 
       33.96        15.02        12.95        20.61        52.04        14.96 
TCGA-25-1871 TCGA-25-2392 TCGA-25-2393 TCGA-29-1688 TCGA-29-1703 TCGA-29-1705 
       24.99         1.02        38.04        78.90        59.67        18.25 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 
       31.27        34.62        17.36        39.42        31.30        24.36 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-2414 TCGA-29-2428 TCGA-29-2434 
       12.36        12.30        14.93        86.17        45.11        11.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1861 TCGA-30-1866 TCGA-31-1946 
       38.07        51.91         2.47        34.78        36.62        30.18 
TCGA-31-1953 TCGA-31-1956 TCGA-36-1571 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
        6.71        44.12        22.85        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2543 TCGA-36-2545 TCGA-42-2582 TCGA-42-2589 TCGA-42-2593 
       33.01         2.24        18.31        47.57        42.02         1.48 
TCGA-57-1585 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 
        1.74        25.02       180.20       116.12        34.39         2.14 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.94        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1903 TCGA-61-1904 
       28.47        33.67        43.69         1.45        13.02         9.07 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1918 TCGA-61-1919 TCGA-61-2012 TCGA-61-2016 
       37.05        42.51        15.75        38.17        30.64         1.18 
TCGA-61-2018 TCGA-61-2092 TCGA-61-2096 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 
       45.40        51.72        58.39         6.48       125.75        22.22 
TCGA-61-2612 TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 
        6.35        18.94         9.99        29.16        57.76        35.57 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 TCGA-10-0938 
       25.91        81.86        34.19        32.88        19.99        20.91 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 TCGA-13-0757 TCGA-13-0758 
       44.55        39.58         2.73        17.82        11.18        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0801 TCGA-13-0885 
       11.54       111.78        58.65        20.35        45.99       111.39 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 TCGA-13-0906 
       92.42        95.15       102.84        66.15       134.04       118.98 
TCGA-13-0910 TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
      116.65        48.79        85.94        25.41 

$`DEL PEAK 22(11Q25) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1343 
       13.81        11.87        41.00        49.15         2.01        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1362 
       65.52        63.09        21.57        63.98         0.53        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 
       33.67        76.57       103.40        82.39        19.99         0.79 
TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 
       38.37        84.20        55.43        48.89        27.88        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       36.23        31.86        47.70         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1668 TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 
       74.93        41.62        55.36         5.85         8.55        97.55 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 
        6.18        35.15         4.54       112.41        63.09        20.94 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 
       77.10        81.17        28.54        83.31        55.23        81.01 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 
       32.35        54.64        87.06       124.44        20.68        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       52.44       125.56         4.24        66.15       115.07        13.97 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 
       34.82        65.69        34.16        65.52        80.15        54.25 
TCGA-13-2057 TCGA-13-2059 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 
       80.02        78.48        70.45        23.05        25.94        72.20 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 
       16.70         2.93         2.66        47.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       26.83        32.09         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       51.35        54.51         3.22        68.68        19.46        33.30 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
      129.96         4.27         6.38        33.47        58.13         0.53 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 
      115.89        87.48        91.66        77.00         2.76         7.63 
TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       21.80         7.66        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.38         7.82         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.95         5.36        17.39        28.37        18.64        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       43.53         8.55       105.99         3.45         1.18        22.22 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 
       58.09        88.50        70.62        19.53        44.09        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       25.87        10.26        90.15        88.37        48.33        38.24 
TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 
        3.48         3.81         4.37        11.28         5.79         9.80 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       16.44        81.11        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 
       14.43        18.48        28.18        64.01        44.52         0.36 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 
       31.63        44.61         0.82        67.36        36.23        33.11 
TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1322 
        1.02        33.01        42.05         2.01        65.00         2.99 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 
       12.99        18.58        27.62        17.03        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       59.15        62.17        35.87        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       49.05         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 
        2.96        29.03        31.00        26.99        47.61        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        39.02        40.41        33.93        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 
       36.36        16.93        23.93        41.98        86.60        66.81 
TCGA-29-1764 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1781 
       62.93        22.98        22.55        17.33        11.84         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
        7.23         5.36        36.30        65.00        62.47        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1856 
       42.25        21.47         9.76        35.77        36.26        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 
        0.26        48.10        44.91         6.12         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 
       24.26        30.05        48.79        45.57        18.77        22.49 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 
       42.51         2.20        28.77        29.10        21.53        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-2532 TCGA-36-2534 
        8.55        30.08        25.74        27.85        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 
       25.91        25.08        23.80        21.60        20.98        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 
       14.17         6.05        16.18        11.47        23.74        28.93 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       10.42        40.77        24.03        11.38        21.14        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2363 
       29.00        25.08        80.12        22.32         9.40         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       44.81        11.11         8.09        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 TCGA-61-1907 
        2.43         8.42         5.79        11.41        34.13        31.30 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        67.76        43.43         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 
       14.50        17.98         4.01        30.64        39.85        45.96 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 
        4.80         4.77        71.74        61.64        60.62        65.52 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 TCGA-61-2614 
       55.50        76.87        20.68        44.52        31.07         8.61 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0365 TCGA-09-0367 TCGA-10-0925 TCGA-10-0928 
       39.68         0.79         9.47        17.98        54.31        18.51 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 
       14.66         6.71        35.44        36.92         6.21        24.59 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0761 
       12.39        31.20        15.19        55.17         2.50        38.01 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       61.84        56.71        40.24       118.42       107.28        63.09 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       69.73        83.34        87.48        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 
       35.31        13.61        68.94       107.18       153.37        66.67 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
      145.45        43.36        71.74        19.36       127.79        50.37 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      123.16        60.59        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       84.53        48.76        83.74 

  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                        0.79                         0.26 
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                      180.20                       153.37 
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                       31.61                        33.30 
[1] "0.8 - 180.2 (31.6)" "0.3 - 153.4 (33.3)"
[1] "hr=" "1.1"
D55V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 22(11Q25) MUTATED         1   195                2
  DEL PEAK 22(11Q25) WILD-TYPE       2   363                0
D55V3, multiclass
                  clus
vv                 DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE
  OMENTUM                                   1                            2
  OVARY                                   195                          363
  PERITONEUM OVARY                          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"
D55V4, binary
                              cls
clus                             0   1
  DEL PEAK 22(11Q25) MUTATED   186   2
  DEL PEAK 22(11Q25) WILD-TYPE 355   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11Q25) MUTATED    186    2
  DEL PEAK 22(11Q25) WILD-TYPE  355    3
     clus
vv    DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE
  NO                         186                          355
  YES                          2                            3
[1] 2 2
[1] FALSE
D55V5, continuous
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 22(11Q25) MUTATED    5  6  2  1
  DEL PEAK 22(11Q25) WILD-TYPE 10 20  3  2
D55V6, multiclass
    clus
vv   DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE
  R0                          5                           10
  R1                          6                           20
  R2                          2                            3
  RX                          1                            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"
D55V7, binary
                              cls
clus                             0   1
  DEL PEAK 22(11Q25) MUTATED     7 113
  DEL PEAK 22(11Q25) WILD-TYPE   3 214
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11Q25) MUTATED      7  113
  DEL PEAK 22(11Q25) WILD-TYPE    3  214
                        clus
vv                       DEL PEAK 22(11Q25) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                        113
                        clus
vv                       DEL PEAK 22(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          214
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 23(12Q23.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(12Q23.1) MUTATED    78 111
  DEL PEAK 23(12Q23.1) WILD-TYPE 150 220
  DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE 
                           189                            370 
  DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE 
                           111                            220 
$`DEL PEAK 23(12Q23.1) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1335 TCGA-04-1346 TCGA-04-1356 TCGA-04-1361 
       13.81        20.52         1.81        65.52        49.28        32.52 
TCGA-04-1371 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-09-1659 
       82.39       119.08        84.20        55.43        27.88         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1674 
       38.43        89.33        57.60        61.87        55.36         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 
       97.55         6.12        81.17        28.54        55.23        81.01 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1483 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       17.46        87.06        29.42        70.82        83.93        52.44 
TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
      127.27        43.20        65.52        80.15        44.68        14.53 
TCGA-13-2059 TCGA-13-A5FU TCGA-20-0987 TCGA-20-1682 TCGA-20-1685 TCGA-20-1687 
       78.48         8.42        23.05        27.52        16.70         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1027 TCGA-23-1117 TCGA-23-1120 TCGA-23-1122 
       47.54        40.54        32.09        33.30         4.27        39.09 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-24-0970 TCGA-24-0979 
        0.53       115.89        87.48        77.00        11.64        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1418 TCGA-24-1425 
        7.66        22.32        63.55        47.41         7.99         5.95 
TCGA-24-1431 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1556 TCGA-24-1557 
       18.64        45.14         9.11         1.18        70.62        39.88 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1849 
       88.37        48.33         8.32         3.72        11.28         5.79 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-2023 TCGA-24-2026 TCGA-24-2035 
        9.80        30.21        16.44        44.84        34.82        28.18 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       64.01        57.07        47.54         0.82        67.36        36.23 
TCGA-24-2297 TCGA-25-1313 TCGA-25-1314 TCGA-25-1320 TCGA-25-1625 TCGA-25-1877 
       55.86        26.96        33.01        37.97        27.62        24.00 
TCGA-25-2391 TCGA-25-2397 TCGA-25-2400 TCGA-25-2401 TCGA-25-2409 TCGA-29-1691 
       49.05        12.00        42.02         2.96        26.99        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 
      101.79        39.02        40.41        23.93        59.67        31.27 
TCGA-29-1711 TCGA-29-1763 TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 
       34.62        66.81        31.30        24.36        12.36        11.84 
TCGA-29-1777 TCGA-29-2425 TCGA-29-2427 TCGA-29-2432 TCGA-29-2434 TCGA-30-1718 
       12.30        65.00        62.47        21.47        11.47        51.91 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1891 TCGA-30-1892 
       36.26        15.68         0.26        34.78        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1577 
       45.57        30.18        44.12         2.20        29.10        25.74 
TCGA-36-1578 TCGA-36-2537 TCGA-36-2538 TCGA-36-2545 TCGA-42-2582 TCGA-42-2587 
       27.85        25.91        25.08        18.31        47.57        23.74 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 
       42.02        10.42        40.77        24.03        21.14         1.74 
TCGA-59-2350 TCGA-59-2363 TCGA-61-1727 TCGA-61-1734 TCGA-61-1738 TCGA-61-1895 
       22.32         5.42        18.54        28.47        35.80         1.45 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1913 TCGA-61-1917 TCGA-61-1919 
       11.41        13.02         9.07        48.92        43.43        38.17 
TCGA-61-2008 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2104 TCGA-61-2612 
       30.64        45.40         4.80        71.74        76.87         6.35 
TCGA-10-0928 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 
       18.51        44.55        12.39        31.20        15.19        55.17 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 
        2.50        11.38        11.54        38.01       111.78        56.71 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 
      118.42       107.28        63.09        45.99        43.86        35.31 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0888 TCGA-13-0891 TCGA-13-0893 TCGA-13-0903 
       13.61       111.39        92.42       102.84        43.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0911 TCGA-13-0913 TCGA-13-0919 
       50.37       123.16        60.59        44.55       109.32        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       48.79        48.76        83.74 

$`DEL PEAK 23(12Q23.1) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       11.87        43.92        41.00        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
        1.08        18.51        11.87        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       63.98        65.46         0.53        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
      103.40        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1536 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       29.10        48.89        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1664 TCGA-09-1665 TCGA-09-1669 TCGA-09-1670 
       47.70        45.37        74.93        41.62        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
        5.85         3.02         6.18        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1407 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
       77.10        83.31        57.27        32.35        54.64        61.71 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
      124.44        20.68        22.39       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
        4.24        66.15       115.07        13.97        34.82        65.69 
TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       34.16        54.25        80.02        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
       70.45        25.94        26.20        72.20        25.38        19.10 
TCGA-20-1686 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 
        2.93        49.68        15.39        26.83        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 
       31.20        68.68        19.46        86.01       129.96         6.38 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 
       33.47        58.13        24.95        91.66        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-1103 TCGA-24-1413 
        4.70         4.50         7.63        21.80        54.12         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.38         7.82         7.86         0.76         6.25         6.02 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        28.37        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 
        8.55        72.92        12.46       105.99         3.45        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 
       51.91        41.39        58.09        88.50        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 TCGA-24-1923 
       38.24         3.48         3.81         4.37         5.52        22.68 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 
       11.05        81.11         4.87       152.02        58.16       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
       14.43        55.92        18.48        44.52        36.16         0.79 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2293 TCGA-24-2295 
        0.36        31.63        70.45        44.61        16.64        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26         1.02        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       17.03        12.95        20.61        38.20         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
       62.17        35.87        52.04        14.96        24.99        85.05 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 
       13.02         1.02        38.04         3.02        45.01        19.99 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1696 TCGA-29-1697 
       29.03        31.00        78.90        47.61        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1707 TCGA-29-1761 
       68.32        36.36        16.93        18.25        41.98        17.36 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 
       86.60        62.93        39.42        22.98        22.55        17.33 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       45.11        13.84        42.25         9.76        35.77        38.07 
TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
        2.47        48.10        44.91         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       57.57        24.26        18.77        22.49         6.71        42.51 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       28.77        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 
       23.80        21.60         2.24        20.98        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2588 TCGA-42-2593 TCGA-57-1583 
        6.05        16.18        11.47        28.93         1.48        11.38 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 
      116.12         9.40        34.39         2.14        44.81        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        8.09        20.94        31.43        27.88         4.34        31.79 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
       48.79        44.84         2.43        33.67        43.69         8.42 
TCGA-61-1900 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 
        5.79        34.13        31.30        37.05        42.51        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        15.75         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2088 
        4.01        39.85        30.64         1.18        45.96         4.77 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       51.72        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 
        6.48        20.68        44.52       125.75        22.22        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
        8.61        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
        9.47        57.76        17.98        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.86        34.19        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 
       36.92        19.99        20.91         6.21        24.59        39.58 
TCGA-13-0724 TCGA-13-0730 TCGA-13-0757 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 
        2.73        17.82        11.18        61.84        58.65        40.24 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 
       20.35        69.73        83.34        87.48        51.02        35.28 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
       68.94       107.18       153.37        66.67        95.15       145.45 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0906 TCGA-13-0910 
       71.74        66.15       134.04        19.36       118.98       116.65 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0924 TCGA-13-2071 
       37.64        58.68        85.94        25.41 

  DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE 
                          0.26                           0.30 
  DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE 
                        127.79                         180.20 
  DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE 
                         36.23                          31.20 
[1] "0.3 - 127.8 (36.2)" "0.3 - 180.2 (31.2)"
[1] "hr=" "1.1"
D56V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 23(12Q23.1) MUTATED         1   190                0
  DEL PEAK 23(12Q23.1) WILD-TYPE       2   368                2
D56V3, multiclass
                  clus
vv                 DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     190                            368
  PERITONEUM OVARY                            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"
D56V4, binary
                                cls
clus                               0   1
  DEL PEAK 23(12Q23.1) MUTATED   185   2
  DEL PEAK 23(12Q23.1) WILD-TYPE 356   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(12Q23.1) MUTATED    185    2
  DEL PEAK 23(12Q23.1) WILD-TYPE  356    3
     clus
vv    DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE
  NO                           185                            356
  YES                            2                              3
[1] 2 2
[1] FALSE
D56V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 23(12Q23.1) MUTATED    5 10  1  1
  DEL PEAK 23(12Q23.1) WILD-TYPE 10 16  4  2
D56V6, multiclass
    clus
vv   DEL PEAK 23(12Q23.1) MUTATED DEL PEAK 23(12Q23.1) WILD-TYPE
  R0                            5                             10
  R1                           10                             16
  R2                            1                              4
  RX                            1                              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"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(12Q23.1) MUTATED     3 116
  DEL PEAK 23(12Q23.1) WILD-TYPE   7 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(12Q23.1) MUTATED      3  116
  DEL PEAK 23(12Q23.1) WILD-TYPE    7  211
                        clus
vv                       DEL PEAK 23(12Q23.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       DEL PEAK 23(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            211
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 24(12Q24.33) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(12Q24.33) MUTATED    80 128
  DEL PEAK 24(12Q24.33) WILD-TYPE 148 203
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                            208                             351 
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                            128                             203 
$`DEL PEAK 24(12Q24.33) MUTATED`
TCGA-3P-A9WA TCGA-04-1335 TCGA-04-1341 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       13.81         1.81         1.08        65.46        49.28        32.52 
TCGA-04-1371 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 
       82.39        19.99        29.10        84.20        55.43        27.88 
TCGA-04-1651 TCGA-04-1654 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1666 
       36.23        47.70         9.99        38.43        89.33        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2051 
       61.87        55.36         8.55         6.12        35.15        63.09 
TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
       12.46        81.17        28.54        55.23        81.01        17.46 
TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       32.35        61.71        29.42        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 
      125.56        93.90        43.20        65.52        80.15        14.53 
TCGA-13-2059 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-1687 
       78.48        76.90        70.45         8.42        23.05         2.66 
TCGA-23-1022 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1110 TCGA-23-1117 
       49.68        26.83        32.09        49.41        54.51        33.30 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1124 TCGA-23-2077 TCGA-23-2078 
       86.01         4.27        39.09        58.13       115.89        87.48 
TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 
        4.50        11.64        21.80         7.66        22.32        63.55 
TCGA-24-1105 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 
       47.41         7.99         0.76         6.25         5.95         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 
       17.39        18.64         8.55        72.92        45.14         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1550 TCGA-24-1557 TCGA-24-1562 TCGA-24-1567 
        3.45         1.18        41.06        39.88        45.50        17.23 
TCGA-24-1614 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1924 
       48.33         3.72         4.37        11.28         5.79        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 
       16.44        81.11       152.02        44.84        34.82       109.71 
TCGA-24-2035 TCGA-24-2254 TCGA-24-2267 TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 
       28.18        57.07        47.54        70.45        36.23        16.64 
TCGA-24-2297 TCGA-25-1313 TCGA-25-1318 TCGA-25-1321 TCGA-25-1625 TCGA-25-1630 
       55.86        26.96        34.98        33.96        27.62        38.20 
TCGA-25-1632 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 
       59.15        24.00        13.02        49.05        38.04        12.00 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1694 
       42.02         2.96        26.99        78.90        48.33        39.02 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1768 
       16.93        59.67        34.62        17.36        66.81        31.30 
TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 
       24.36        12.36        11.84        12.30         8.38         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2432 TCGA-30-1853 TCGA-30-1857 
       86.17        65.00        62.47        21.47        36.26         0.26 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1891 TCGA-31-1956 TCGA-31-1959 TCGA-36-1574 
       44.91        34.78        30.05        44.12         2.20        22.55 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       29.82        25.91        25.08        21.60         2.24        20.98 
TCGA-36-2549 TCGA-42-2589 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 
        6.05        42.02        40.77        24.03        21.14         1.74 
TCGA-59-2350 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1738 TCGA-61-1740 
       22.32         8.09        20.94        18.54        35.80         2.43 
TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1917 TCGA-61-1919 
        1.45        11.41        13.02         9.07        43.43        38.17 
TCGA-61-2008 TCGA-61-2018 TCGA-61-2096 TCGA-61-2102 TCGA-61-2109 TCGA-61-2612 
       30.64        45.40        58.39         6.48        20.68         6.35 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0928 TCGA-10-0937 TCGA-13-0720 TCGA-13-0724 
       17.98        54.31        18.51        19.99        44.55         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 
       12.39        31.20        55.17         2.50        11.38        38.01 
TCGA-13-0762 TCGA-13-0793 TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 
      111.78       107.28        69.73        45.99        43.86        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 
       13.61        68.94       107.18       111.39        66.67        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 
      102.84        43.36        71.74       123.16        60.59       116.65 
TCGA-13-0911 TCGA-13-0913 TCGA-13-0919 TCGA-13-0923 
       44.55       109.32        84.53        83.74 

$`DEL PEAK 24(12Q24.33) WILD-TYPE`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 
       20.52        11.87        43.92        41.00        49.15         2.01 
TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
       46.62        18.51        11.87        65.52        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       21.57        63.98         0.53        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
      103.40        56.55        41.59         0.79        38.37       119.08 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1664 
       48.89        28.64        64.64        31.86        45.37        74.93 
TCGA-09-1665 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       41.62        30.51        17.98         5.85         3.02        97.55 
TCGA-09-2043 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
        6.18         4.54       112.41        71.11        39.75        20.94 
TCGA-09-2055 TCGA-13-1403 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1481 
       26.93        77.10        83.31        57.27        54.64        87.06 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
      124.44        20.68        22.39        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15       115.07        13.97        34.82        65.69        34.16 
TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 TCGA-20-0990 
       44.68        54.25        80.02        77.88        65.52        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1029 TCGA-23-1030 
        2.93        47.54        40.54        15.39         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
       18.90         2.76        51.35         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 
       19.46       129.96         6.38        33.47         0.53        24.95 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.70         7.63 
TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 
       41.56        54.12         6.31         6.38         7.82         7.86 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1464 
        6.02         5.36        28.37        18.67        43.53        12.46 
TCGA-24-1467 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
      105.99        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 
       19.53        44.09        47.70        25.87        10.26        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1850 
       88.37        38.24         8.32         3.48         3.81         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1928 TCGA-24-2019 TCGA-24-2024 TCGA-24-2029 
        9.80        22.68        11.05         4.87        58.16        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
       55.92        18.48        64.01        44.52        36.16         0.79 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 
        0.36        31.63        44.61         0.82        67.36        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       53.26         1.02        33.01        52.04        42.05         2.01 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        37.97         2.99        12.99        15.02        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       17.03        12.95        20.61         0.30        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 
       52.04        14.96        24.99        85.05         1.02         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1693 
       45.01        19.99        29.03        31.00        47.61       101.79 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 
       40.41        33.93        31.20        68.32        36.36        23.93 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       18.25        41.98        31.27        86.60        62.93        39.42 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 
       22.98        22.55        17.33        14.93         7.23        36.30 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11        13.84        42.25        11.47         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1862 
       38.07        51.91         2.47        15.68        48.10         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
       36.62         1.22        57.57        24.26        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-36-1568 
       30.18        18.77        22.49         6.71        42.51        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       29.10        21.53        22.85         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       27.85        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2540 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 
       23.80        18.31        20.52        14.17        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 
       47.57        23.74        28.93        10.42         1.48        11.38 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       11.11        31.43        27.88         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 
       48.79        44.84        33.67        43.69         8.42         5.79 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
       34.13        31.30        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        15.75         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
        4.01        39.85        30.64         1.18        45.96         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 
        4.77        51.72        71.74        61.64        60.62        65.52 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 
       55.50        76.87        44.52       125.75        22.22        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
        8.61        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 
        9.47        57.76        35.57        25.91        81.86        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 
       32.88        14.66         6.71        35.44        36.92        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 
        6.21        24.59        39.58        15.19        17.82        11.18 
TCGA-13-0760 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       11.54        61.84        56.71        58.65        40.24       118.42 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 
       63.09        20.35        83.34        87.48        51.02        35.28 
TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
      153.37        92.42       145.45        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 
      127.79        50.37       118.98        37.64        58.68        48.79 
TCGA-13-0921 TCGA-13-0924 TCGA-13-2071 
       48.76        85.94        25.41 

  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                           0.26                            0.30 
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                         152.02                          180.20 
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                          34.80                           31.43 
[1] "0.3 - 152.0 (34.8)" "0.3 - 180.2 (31.4)"
[1] "hr=" "1"  
D57V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 24(12Q24.33) MUTATED         2   208                0
  DEL PEAK 24(12Q24.33) WILD-TYPE       1   350                2
D57V3, multiclass
                  clus
vv                 DEL PEAK 24(12Q24.33) MUTATED
  OMENTUM                                      2
  OVARY                                      208
  PERITONEUM OVARY                             0
                  clus
vv                 DEL PEAK 24(12Q24.33) WILD-TYPE
  OMENTUM                                        1
  OVARY                                        350
  PERITONEUM OVARY                               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"
D57V4, binary
                                 cls
clus                                0   1
  DEL PEAK 24(12Q24.33) MUTATED   205   1
  DEL PEAK 24(12Q24.33) WILD-TYPE 336   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(12Q24.33) MUTATED    205    1
  DEL PEAK 24(12Q24.33) WILD-TYPE  336    4
     clus
vv    DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE
  NO                            205                             336
  YES                             1                               4
[1] 2 2
[1] FALSE
D57V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 24(12Q24.33) MUTATED    2 13  1  2
  DEL PEAK 24(12Q24.33) WILD-TYPE 13 13  4  1
D57V6, multiclass
    clus
vv   DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE
  R0                             2                              13
  R1                            13                              13
  R2                             1                               4
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 24(12Q24.33) MUTATED     7 111
  DEL PEAK 24(12Q24.33) WILD-TYPE   3 216
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(12Q24.33) MUTATED      7  111
  DEL PEAK 24(12Q24.33) WILD-TYPE    3  216
                        clus
vv                       DEL PEAK 24(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           111
                        clus
vv                       DEL PEAK 24(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             216
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 25(13Q14.2) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(13Q14.2) MUTATED   149 199
  DEL PEAK 25(13Q14.2) WILD-TYPE  79 132
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                           348                            211 
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                           199                            132 
$`DEL PEAK 25(13Q14.2) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 
       46.62         1.08        18.51        11.87        63.09        21.57 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 
        0.53        32.52        76.57       103.40        56.55        41.59 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 
       38.37       119.08        29.10        84.20        55.43        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       38.43        41.62        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2048 
       17.98         5.85         3.02         8.55         6.12         4.54 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-13-1404 TCGA-13-1409 
       71.11        63.09        20.94        26.93        81.17        57.27 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       87.06        61.71        29.42        22.39        70.82        83.93 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
      125.56        93.90        90.38       127.27       115.07        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       43.20        34.82        65.69        80.15        44.68        54.25 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       80.02        77.88        76.90        65.52        70.45         8.42 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 
       26.20        27.52        19.10        16.70         2.66        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       40.54        15.39        32.09        49.41         8.81        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
        2.76        54.51        68.68        19.46        86.01       129.96 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 
        4.27        39.09        33.47         0.53       115.89        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 
       49.84         2.76         4.70         7.63        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 
        7.66        54.12        63.55        47.41         6.31         7.82 
TCGA-24-1419 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        7.86         6.02         5.95         5.36        17.39        28.37 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1464 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 
       18.67        43.53        12.46         9.11        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        56.58        51.91        41.39 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 
       88.50        70.62        39.88        19.53        44.09        47.70 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       25.87        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
        8.32         3.48         3.72         3.81         4.37        11.28 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        5.52         9.80        30.21        16.44        11.05         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2036 
      152.02        44.84        58.16        34.82       109.71        64.01 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 
       57.07        36.16         0.79         0.36        47.54        70.45 
TCGA-24-2289 TCGA-24-2290 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 
       67.36        36.23        26.96        52.04        34.98        65.00 
TCGA-25-1321 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       33.96        15.02        12.95        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 
       62.17        35.87        52.04        85.05        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        12.00        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       29.03        26.99        78.90        48.33       101.79        39.02 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.93        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       59.67        41.98        86.60        66.81        62.93        39.42 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       31.30        22.55        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 
        8.38         5.36        86.17        62.47        42.25        21.47 
TCGA-29-2434 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1891 TCGA-31-1946 
       11.47        44.91        34.78        36.62        30.05        30.18 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 
       18.77         6.71        42.51         2.20        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
       22.85        22.55         8.55        27.85        24.69        35.05 
TCGA-36-2532 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-42-2582 
       29.49        21.60         2.24        18.31        20.52        47.57 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2350 
       10.42        40.77        21.14         1.74        29.00        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 
      116.12         9.40        34.39        44.81         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       31.43        18.54         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80         2.43        43.69         1.45         8.42 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 
       11.41        13.02         9.07        34.13        31.30        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 
       56.61        67.76        38.17         2.01         5.52        17.98 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64        30.64         1.18        45.40         4.80         4.77 
TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 
       71.74        60.62         6.48        76.87        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0366 
       22.22         6.35         8.61        39.68        18.94        57.76 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        54.31        81.86        18.51        34.19        32.88 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 
       36.92        19.99        20.91        24.59        44.55         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 
       12.39        31.20        17.82        55.17         2.50        11.38 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       61.84        56.71        58.65       118.42       107.28        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
       69.73        83.34        87.48        51.02        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       92.42       145.45       102.84        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
      134.04        19.36       127.79        50.37       123.16       118.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        84.53        48.79        83.74        85.94        25.41 

$`DEL PEAK 25(13Q14.2) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1337 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 
       11.87         2.01        65.52        48.76        63.98        65.46 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 
       49.28        44.32        33.67        82.39        19.99         0.79 
TCGA-04-1644 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1675 TCGA-09-2043 
       48.89        47.70        89.33        74.93        97.55         6.18 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 TCGA-13-1405 
       35.15       112.41        39.75        12.46        77.10        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       83.31        55.23        81.01        17.46        32.35        54.64 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1491 TCGA-13-1496 TCGA-13-1498 TCGA-13-1506 
      124.44        20.68        52.44         4.24        66.15        34.16 
TCGA-13-1507 TCGA-13-1512 TCGA-13-2059 TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 
       65.52        14.53        78.48        23.05        25.94        72.20 
TCGA-20-1683 TCGA-20-1686 TCGA-23-1022 TCGA-23-1026 TCGA-23-1030 TCGA-23-1109 
       25.38         2.93        49.68        26.83        29.13        51.35 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1121 TCGA-23-1124 TCGA-23-2072 
        3.22        31.20        33.30         6.38        58.13        24.95 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2645 TCGA-24-0970 TCGA-24-0982 TCGA-24-1416 
       87.48        91.66         4.50        11.64        22.32         6.38 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1427 TCGA-24-1431 TCGA-24-1436 
        7.99         0.76         6.25         4.83        18.64         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1550 
       72.92        45.14       105.99         3.45         1.18        41.06 
TCGA-24-1553 TCGA-24-1562 TCGA-24-1565 TCGA-24-1849 TCGA-24-1923 TCGA-24-1930 
       58.09        45.50        10.26         5.79        22.68        81.11 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2271 
       14.43        55.92        18.48        28.18        44.52        31.63 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       44.61         0.82        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 
        1.02        33.01        42.05         2.01        37.97         2.99 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1870 
       12.99        18.58        27.62        17.03        38.20        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2398 TCGA-25-2408 TCGA-29-1690 
       24.99        24.00        13.02        45.01        31.00        47.61 
TCGA-29-1695 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1769 
       40.41        18.25        31.27        34.62        17.36        22.98 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 
       24.36        17.33         7.23        36.30        65.00        45.11 
TCGA-29-2429 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       13.84         9.76        35.77        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1867 
        2.47        15.68         0.26        48.10         6.12         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1951 TCGA-31-1956 
       57.57        24.26        48.79        45.57        22.49        44.12 
TCGA-36-1568 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2534 
       28.77        30.08        25.74        24.23        33.01        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 
       25.91        25.08        23.80        20.98        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2593 
       16.18        11.47        23.74        28.93        42.02         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       24.03        11.38        22.32        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1728 TCGA-61-1741 
       80.12         2.14         5.42        11.11        27.88        33.67 
TCGA-61-1900 TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 
        5.79        37.05        42.51        43.43        15.75        14.50 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
        4.01        39.85        45.96        51.72        61.64        58.39 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2109 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       65.52        55.50        20.68        31.07         0.79         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 
       29.16         9.47        17.98        25.91        14.66         6.71 
TCGA-10-0935 TCGA-13-0714 TCGA-13-0723 TCGA-13-0727 TCGA-13-0757 TCGA-13-0760 
       35.44         6.21        39.58        15.19        11.18        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0791 TCGA-13-0794 TCGA-13-0801 TCGA-13-0803 
       38.01       111.78        40.24        63.09        45.99        43.86 
TCGA-13-0889 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       95.15        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0921 
       48.76 

  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                        153.37                         180.20 
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                         34.82                          29.16 
[1] "0.3 - 153.4 (34.8)" "0.3 - 180.2 (29.2)"
[1] "hr=" "1.3"
D58V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 25(13Q14.2) MUTATED         1   349                2
  DEL PEAK 25(13Q14.2) WILD-TYPE       2   209                0
D58V3, multiclass
                  clus
vv                 DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     349                            209
  PERITONEUM OVARY                            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"
D58V4, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q14.2) MUTATED   338   2
  DEL PEAK 25(13Q14.2) WILD-TYPE 203   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q14.2) MUTATED    338    2
  DEL PEAK 25(13Q14.2) WILD-TYPE  203    3
     clus
vv    DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE
  NO                           338                            203
  YES                            2                              3
[1] 2 2
[1] FALSE
D58V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 25(13Q14.2) MUTATED    8 10  2  3
  DEL PEAK 25(13Q14.2) WILD-TYPE  7 16  3  0
D58V6, multiclass
    clus
vv   DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE
  R0                            8                              7
  R1                           10                             16
  R2                            2                              3
  RX                            3                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q14.2) MUTATED     7 198
  DEL PEAK 25(13Q14.2) WILD-TYPE   3 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q14.2) MUTATED      7  198
  DEL PEAK 25(13Q14.2) WILD-TYPE    3  129
                        clus
vv                       DEL PEAK 25(13Q14.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          198
                        clus
vv                       DEL PEAK 25(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            129
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 26(14Q23.3) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(14Q23.3) MUTATED   119 176
  DEL PEAK 26(14Q23.3) WILD-TYPE 109 155
  DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE 
                           295                            264 
  DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE 
                           176                            155 
$`DEL PEAK 26(14Q23.3) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 
       20.52        11.87        41.00         1.81         2.01        46.62 
TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 
        1.08        11.87        65.52        63.09        48.76        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
        0.53        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       82.39        41.59        38.37       119.08        84.20        55.43 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       28.64        64.64        36.23        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       38.43        57.60        61.87        55.36        17.98         5.85 
TCGA-09-1675 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
       97.55         4.54        71.11        63.09        39.75        20.94 
TCGA-09-2056 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1411 TCGA-13-1481 
       12.46        28.54        83.31        55.23        17.46        87.06 
TCGA-13-1482 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
       61.71        22.39        70.82        83.93        52.44        93.90 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24       127.27        66.15       115.07        43.20        34.82 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 
       65.69        65.52        44.68        14.53        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       76.90        65.52         8.42        25.38        19.10        16.70 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
        2.66        47.54        15.39        26.83        32.09        49.41 
TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 
       29.13        51.35        54.51         3.22        68.68        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 
       86.01       129.96        39.09        33.47         0.53        24.95 
TCGA-23-2077 TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 
      115.89        77.00         4.70         4.50        11.64        21.80 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1422 
       41.56        22.32        63.55        47.41         7.82         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 
        6.25         6.02         5.95         4.83        18.64        18.67 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 
        8.55        72.92        12.46        45.14         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        64.27        16.21        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 TCGA-24-1565 
       51.91        41.39        70.62        39.88        25.87        10.26 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1924 
       88.37        48.33         3.48         3.81         4.37        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
       16.44        11.05        81.11         4.87        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 
       34.82        14.43        57.07        36.16         0.36        47.54 
TCGA-24-2288 TCGA-24-2295 TCGA-24-2298 TCGA-25-1313 TCGA-25-1320 TCGA-25-1321 
        0.82        33.11        53.26        26.96        37.97        33.96 
TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 
       17.03        38.20         0.30        59.15        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       14.96        24.99        24.00        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2400 TCGA-25-2404 TCGA-29-1691 
       38.04         3.02        12.00        42.02        29.03        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 TCGA-29-1705 TCGA-29-1707 
      101.79        39.02        40.41        68.32        18.25        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1771 
       31.27        17.36        86.60        66.81        39.42        22.55 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2434 
       11.84        12.30         5.36        36.30        62.47        11.47 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
       51.91         2.47        15.68        48.10        44.91        34.78 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
        1.22        24.26        30.05        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       22.49         6.71         2.20        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       30.08        29.82        25.91        25.08        21.60         2.24 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 
       20.52        14.17        16.18        11.47        23.74        42.02 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       40.77         1.48        29.00        25.08        25.02       180.20 
TCGA-59-2351 TCGA-59-2372 TCGA-61-1724 TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 
      116.12        44.81        20.94        18.54        31.79        28.47 
TCGA-61-1736 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1904 
       48.79        33.67        43.69         1.45        11.41         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 
       34.13        31.30        67.76        43.43        15.75        14.50 
TCGA-61-2009 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2097 
       39.85        45.40         4.80         4.77        51.72        60.62 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2111 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        6.48        20.68       125.75         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 
        0.79        35.57        54.31        25.91        18.51        32.88 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       35.44        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
        2.73        31.20        15.19        17.82        55.17        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.38        11.54        38.01        61.84        56.71        40.24 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 
      118.42        63.09        20.35        83.34        45.99        43.86 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 
      107.18       111.39       153.37        66.67        92.42       102.84 
TCGA-13-0893 TCGA-13-0906 TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       43.36       118.98       109.32        84.53        48.76        83.74 
TCGA-13-2071 
       25.41 

$`DEL PEAK 26(14Q23.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1336 TCGA-04-1342 TCGA-04-1349 TCGA-04-1350 
       13.81        43.92        49.15        18.51        21.57        63.98 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1644 
      103.40        56.55        19.99         0.79        29.10        48.89 
TCGA-04-1646 TCGA-04-1652 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1669 
       27.88        31.86        89.33        74.93        41.62        30.51 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        3.02         8.55         6.18         6.12        35.15       112.41 
TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
       26.93        77.10        81.17        57.27        81.01        32.35 
TCGA-13-1477 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1492 TCGA-13-1495 
       54.64        29.42       124.44        20.68       125.56        90.38 
TCGA-13-1500 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-2057 TCGA-13-A5FT 
       13.97        34.16        80.15        54.25        80.02        70.45 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1686 
       23.05        25.94        26.20        72.20        27.52         2.93 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 
       49.68        40.54         8.81        18.90         2.76        31.20 
TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 
       19.46         4.27         6.38        58.13        87.48        91.66 
TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0980 TCGA-24-1103 TCGA-24-1413 
       49.84         2.76         7.63         7.66        54.12         6.31 
TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        6.38         7.99         7.86         5.36        17.39        28.37 
TCGA-24-1435 TCGA-24-1467 TCGA-24-1545 TCGA-24-1550 TCGA-24-1553 TCGA-24-1555 
       43.53       105.99        57.40        41.06        58.09        88.50 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 
       19.53        44.09        45.50        47.70        17.23        90.15 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
       38.24         8.32         3.72        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-2020 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 
        9.80        22.68       152.02       109.71        55.92        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2261 TCGA-24-2271 TCGA-24-2280 
       28.18        64.01        44.52         0.79        31.63        70.45 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 
       44.61        67.36        36.23        16.64        55.86         1.02 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       33.01        52.04        42.05         2.01        34.98        65.00 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 
        2.99        12.99        15.02        18.58        27.62        12.95 
TCGA-25-1628 TCGA-25-1633 TCGA-25-1878 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 
       20.61        62.17        85.05        45.01        19.99         2.96 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1696 TCGA-29-1697 
       31.00        26.99        78.90        47.61        33.93        31.20 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 TCGA-29-1764 
       36.36        16.93        23.93        59.67        34.62        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 
       31.30        22.98        24.36        17.33        12.36        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
        8.38         7.23        86.17        65.00        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 
       42.25        21.47         9.76        35.77        38.07        36.26 
TCGA-30-1857 TCGA-30-1862 TCGA-30-1866 TCGA-30-1880 TCGA-30-1892 TCGA-31-1955 
        0.26         6.12        36.62        57.57        48.79        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1577 TCGA-36-1578 
       44.12        28.77        29.10        21.53        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2540 
       24.23        24.69        35.05        33.01        29.49        23.80 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 
       20.98        18.31         6.05        47.57        28.93        10.42 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-59-2349 
       24.03        11.38        21.14         1.74        22.32        80.12 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 
       22.32         9.40        34.39         2.14         5.42        11.11 
TCGA-61-1722 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1737 TCGA-61-1738 
        8.09        31.43        27.88         4.34        44.84        35.80 
TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1910 TCGA-61-1911 
        2.43         8.42         5.79        13.02        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 
       48.92        56.61        38.17         2.01         5.52        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2094 
        4.01        30.64        30.64         1.18        45.96        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 
       61.64        58.39        65.52        55.50        76.87        44.52 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       22.22         6.35        31.07         9.99        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 
       57.76        17.98        81.86        34.19        14.66         6.71 
TCGA-10-0936 TCGA-10-0937 TCGA-13-0725 TCGA-13-0755 TCGA-13-0762 TCGA-13-0768 
       36.92        19.99        12.39         2.50       111.78        58.65 
TCGA-13-0793 TCGA-13-0797 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
      107.28        69.73        87.48        51.02        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 
       13.61        68.94        95.15       145.45        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 
      134.04        19.36       127.79        50.37       123.16        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 
      116.65        44.55        37.64        58.68        48.79        85.94 

  DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE 
                        180.20                         152.02 
  DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE 
                        33.670                         31.365 
[1] "0.3 - 180.2 (33.7)" "0.3 - 152.0 (31.4)"
[1] "hr=" "1"  
D59V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 26(14Q23.3) MUTATED         0   298                1
  DEL PEAK 26(14Q23.3) WILD-TYPE       3   260                1
D59V3, multiclass
                  clus
vv                 DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE
  OMENTUM                                     0                              3
  OVARY                                     298                            260
  PERITONEUM OVARY                            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"
D59V4, binary
                                cls
clus                               0   1
  DEL PEAK 26(14Q23.3) MUTATED   289   2
  DEL PEAK 26(14Q23.3) WILD-TYPE 252   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(14Q23.3) MUTATED    289    2
  DEL PEAK 26(14Q23.3) WILD-TYPE  252    3
     clus
vv    DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE
  NO                           289                            252
  YES                            2                              3
[1] 2 2
[1] FALSE
D59V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 26(14Q23.3) MUTATED    8 10  4  1
  DEL PEAK 26(14Q23.3) WILD-TYPE  7 16  1  2
D59V6, multiclass
    clus
vv   DEL PEAK 26(14Q23.3) MUTATED DEL PEAK 26(14Q23.3) WILD-TYPE
  R0                            8                              7
  R1                           10                             16
  R2                            4                              1
  RX                            1                              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"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(14Q23.3) MUTATED     8 174
  DEL PEAK 26(14Q23.3) WILD-TYPE   2 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(14Q23.3) MUTATED      8  174
  DEL PEAK 26(14Q23.3) WILD-TYPE    2  153
                        clus
vv                       DEL PEAK 26(14Q23.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          174
                        clus
vv                       DEL PEAK 26(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            153
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 27(15Q11.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q11.2) MUTATED   114 176
  DEL PEAK 27(15Q11.2) WILD-TYPE 114 155
  DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE 
                           290                            269 
  DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE 
                           176                            155 
$`DEL PEAK 27(15Q11.2) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       43.92        49.15         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1350 TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       63.09        63.98        33.67        82.39        56.55        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
        0.79        38.37        29.10        84.20        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1661 TCGA-09-1667 
       28.64        64.64        31.86        45.37        38.43        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-2050 
       55.36        30.51        17.98         3.02         8.55        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       63.09        39.75        12.46        81.17        28.54        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1482 TCGA-13-1484 
       55.23        57.27        81.01        17.46        61.71       124.44 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1496 
       22.39        70.82        83.93        52.44        93.90         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
      127.27        66.15       115.07        34.82        34.16        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU 
       80.15        44.68        78.48        76.90        65.52         8.42 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1686 TCGA-23-1022 
       25.94        26.20        27.52        25.38         2.93        49.68 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       29.13        18.90         2.76        51.35        54.51        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 
       68.68        19.46        39.09        33.47         0.53        24.95 
TCGA-23-2077 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0979 
      115.89        49.84         2.76         4.70         4.50        41.56 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 
       22.32        54.12        47.41         6.31         6.38         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 
        7.86         0.76         6.25         6.02         5.36        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
       28.37        18.64        18.67         8.55        72.92        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 
      105.99         9.11         1.18        26.96        16.21        56.58 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1557 TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 
       41.39        58.09        39.88        25.87        90.15        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       38.24         8.32         3.48         3.72         3.81        11.28 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
        5.52        22.68        16.44        81.11         4.87       152.02 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       34.82        55.92        18.48        57.07        36.16         0.79 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        0.82        36.23        16.64        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 
       26.96        33.01        52.04        42.05        65.00        37.97 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 TCGA-25-1628 
       33.96        12.99        15.02        18.58        12.95        20.61 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 
        0.30        59.15        62.17        35.87        52.04        24.99 
TCGA-25-1877 TCGA-25-2393 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 
       24.00        38.04        48.33       101.79        40.41        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       68.32        36.36        16.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1774 
       31.27        17.36        66.81        39.42        22.98        17.33 
TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 
       12.30         7.23         5.36        65.00        45.11        21.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 
       38.07        51.91         2.47        15.68        48.10        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 
       34.78        36.62         1.22        24.26        48.79        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1575 TCGA-36-1577 TCGA-36-1581 
       22.49         6.71         2.20         8.55        25.74        24.69 
TCGA-36-2529 TCGA-36-2534 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       35.05        29.82        21.60        18.31        20.52        14.17 
TCGA-36-2551 TCGA-42-2587 TCGA-42-2589 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       16.18        23.74        42.02         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02       180.20        22.32       116.12         9.40 
TCGA-59-2363 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
        5.42        27.88        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 
       35.80         2.43        33.67        11.41         9.07        34.13 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-2003 
       42.51        48.92        56.61        43.43        38.17         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2087 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 
       30.64        30.64         4.80        71.74        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
      125.75        22.22         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 
       18.94        29.16         9.47        25.91        81.86        34.19 
TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
       35.44        36.92        24.59        39.58         2.73        12.39 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 
       17.82        55.17        11.18        11.38        11.54        61.84 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0801 TCGA-13-0802 
      118.42       107.28        63.09        20.35        45.99        51.02 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       43.86        35.31        13.61        68.94       107.18       111.39 
TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 TCGA-13-0904 TCGA-13-0910 
       66.67       145.45       102.84        66.15        50.37       116.65 
TCGA-13-0920 TCGA-13-0921 
       48.79        48.76 

$`DEL PEAK 27(15Q11.2) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 
       13.81        20.52        11.87        41.00         1.81         2.01 
TCGA-04-1338 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       46.62        48.76        21.57        65.46         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 TCGA-04-1530 
       32.52        44.32        76.57       103.40        41.59       119.08 
TCGA-04-1638 TCGA-04-1651 TCGA-04-1654 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
       55.43        36.23        47.70         9.99        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       41.62        57.60         5.85        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 
       35.15         4.54       112.41        20.94        26.93        77.10 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1492 
       32.35        54.64        87.06        29.42        20.68       125.56 
TCGA-13-1495 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1511 TCGA-13-1512 
       90.38        13.97        43.20        65.69        54.25        14.53 
TCGA-13-2057 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1684 
       80.02        77.88        70.45        23.05        72.20        19.10 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       16.70         2.66        47.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1111 TCGA-23-1117 TCGA-23-1118 
       32.09        49.41         8.81         3.22        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 
      129.96         4.27         6.38        58.13        87.48        91.66 
TCGA-23-2081 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1104 
       77.00         7.63        11.64        21.80         7.66        63.55 
TCGA-24-1417 TCGA-24-1425 TCGA-24-1427 TCGA-24-1435 TCGA-24-1464 TCGA-24-1470 
        7.82         5.95         4.83        43.53        12.46         3.45 
TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 
       22.22        57.40        64.27        41.06        51.91        88.50 
TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 
       70.62        19.53        44.09        45.50        47.70        10.26 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 
       17.23        88.37         4.37         5.79         9.80        30.21 
TCGA-24-1928 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 
       11.05        44.84        58.16       109.71        14.43        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       64.01        44.52         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2295 TCGA-25-1317 TCGA-25-1318 TCGA-25-1322 
       44.61        67.36        33.11         2.01        34.98         2.99 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 
       27.62        17.03        38.20        14.96        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05         1.02         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 
       47.61        39.02        33.93        23.93        34.62        86.60 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       62.93        31.30        24.36        22.55        12.36        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 
       14.93         8.38        36.30        86.17        62.47        13.84 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1857 
       42.25        11.47         9.76        35.77        36.26         0.26 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1955 
        6.12        57.57        30.05        45.57        30.18        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 
       30.08        27.85        24.23        33.01        29.49        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2549 TCGA-36-2552 
       25.08        23.80         2.24        20.98         6.05        11.47 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       47.57        28.93        10.42        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 
       11.38        21.14        80.12        34.39         2.14        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
       11.11         8.09        20.94        31.43        18.54         4.34 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 
       43.69         1.45         8.42         5.79        13.02        31.30 
TCGA-61-1910 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       37.05        67.76        15.75         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 
       17.98        39.85         1.18        45.96        45.40         4.77 
TCGA-61-2092 TCGA-61-2095 TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 
       51.72        61.64         0.79         9.99        57.76        17.98 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       35.57        54.31        18.51        32.88        14.66         6.71 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0726 TCGA-13-0727 
       19.99        20.91         6.21        44.55        31.20        15.19 
TCGA-13-0755 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
        2.50        38.01       111.78        56.71        58.65        40.24 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0804 TCGA-13-0886 TCGA-13-0888 
       69.73        83.34        87.48        35.28       153.37        92.42 
TCGA-13-0889 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       95.15        43.36        71.74       134.04        19.36       127.79 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      123.16       118.98        60.59        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        84.53        83.74        85.94        25.41 

  DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE 
                        180.20                         153.37 
  DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE 
                         33.67                          32.09 
[1] "0.3 - 180.2 (33.7)" "0.3 - 153.4 (32.1)"
[1] "hr=" "1.1"
D60V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 27(15Q11.2) MUTATED         2   287                2
  DEL PEAK 27(15Q11.2) WILD-TYPE       1   271                0
D60V3, multiclass
                  clus
vv                 DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     287                            271
  PERITONEUM OVARY                            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"
D60V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q11.2) MUTATED   278   3
  DEL PEAK 27(15Q11.2) WILD-TYPE 263   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q11.2) MUTATED    278    3
  DEL PEAK 27(15Q11.2) WILD-TYPE  263    2
     clus
vv    DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE
  NO                           278                            263
  YES                            3                              2
[1] 2 2
[1] FALSE
D60V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 27(15Q11.2) MUTATED    5 15  2  1
  DEL PEAK 27(15Q11.2) WILD-TYPE 10 11  3  2
D60V6, multiclass
    clus
vv   DEL PEAK 27(15Q11.2) MUTATED DEL PEAK 27(15Q11.2) WILD-TYPE
  R0                            5                             10
  R1                           15                             11
  R2                            2                              3
  RX                            1                              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"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q11.2) MUTATED     6 169
  DEL PEAK 27(15Q11.2) WILD-TYPE   4 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q11.2) MUTATED      6  169
  DEL PEAK 27(15Q11.2) WILD-TYPE    4  158
                        clus
vv                       DEL PEAK 27(15Q11.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          169
                        clus
vv                       DEL PEAK 27(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            158
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 28(15Q15.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(15Q15.1) MUTATED   139 211
  DEL PEAK 28(15Q15.1) WILD-TYPE  89 120
  DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE 
                           350                            209 
  DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE 
                           211                            120 
$`DEL PEAK 28(15Q15.1) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       43.92        49.15        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1371 TCGA-04-1514 
       65.52        63.98        49.28        44.32        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       41.59        19.99         0.79        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 
       84.20        27.88        28.64        64.64        31.86        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
        9.99        38.43        61.87        55.36        30.51        17.98 
TCGA-09-1674 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        8.55         6.12       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2056 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       20.94        12.46        28.54        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 
       81.01        17.46        87.06        61.71       124.44        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       70.82        83.93        52.44        93.90        90.38         4.24 
TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
      127.27       115.07        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
       65.52        80.15        44.68        80.02        78.48        76.90 
TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
       65.52         8.42        25.94        26.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1686 TCGA-23-1022 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       19.10         2.93        49.68        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
       54.51        31.20        68.68        19.46        86.01       129.96 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0979 
       49.84         2.76         4.70         4.50        11.64        41.56 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       22.32        54.12        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36        17.39        28.37        18.64        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 
        8.55        72.92        45.14         9.11         1.18        26.96 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 
       16.21        56.58        41.06        41.39        70.62        39.88 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       25.87        17.23        90.15        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 
        3.48         3.72         3.81         4.37        11.28         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2030 TCGA-24-2035 
        4.87       152.02        44.84        34.82        55.92        28.18 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 
       57.07        36.16         0.79        47.54        70.45         0.82 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       36.23        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       26.96        33.01        52.04        42.05        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       37.97        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       12.95        20.61         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       52.04        24.00         1.02        38.04         3.02        12.00 
TCGA-25-2404 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       29.03        48.33       101.79        40.41        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       36.36        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       31.27        34.62        17.36        86.60        66.81        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       39.42        22.98        24.36        17.33        12.36        12.30 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 
       14.93         7.23         5.36        86.17        65.00        45.11 
TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       21.47        11.47        38.07        51.91         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 
        0.26        48.10        44.91        34.78        36.62         1.22 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       24.26        30.05        48.79        18.77        22.49         6.71 
TCGA-31-1959 TCGA-36-1575 TCGA-36-1577 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 
        2.20         8.55        25.74        24.69        35.05        29.82 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 
        2.24        18.31        14.17        16.18        11.47        42.02 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        24.03        11.38         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02       180.20        22.32       116.12         9.40 
TCGA-59-2363 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 
        5.42        20.94        18.54        27.88        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       48.79        44.84        35.80         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 
        1.45         5.79         9.07        34.13        31.30        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-1998 TCGA-61-2003 
       48.92        56.61        43.43        38.17         5.52         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 
       30.64        30.64         1.18        45.40         4.80        71.74 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       58.39        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
       44.52       125.75        22.22         6.35         8.61        39.68 
TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 
       18.94        29.16         9.47        17.98        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 
       81.86        18.51        34.19        35.44        36.92        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        12.39        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0793 
       11.18        11.38        11.54       111.78        61.84       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       20.35        69.73        87.48        45.99        51.02        43.86 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 
       35.31        13.61        68.94       107.18       111.39        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       92.42       145.45       102.84        43.36        71.74        66.15 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
       50.37       123.16       116.65        44.55        37.64        58.68 
TCGA-13-0921 TCGA-13-0923 
       48.76        83.74 

$`DEL PEAK 28(15Q15.1) WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 
       13.81        20.52        11.87        41.00         1.81         2.01 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 
       63.09        48.76        21.57        65.46         0.53        32.52 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1638 TCGA-04-1644 TCGA-04-1651 
       33.67        76.57       103.40        55.43        48.89        36.23 
TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1672 
       47.70        89.33        74.93        41.62        57.60         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2055 
        3.02        97.55         6.18        35.15         4.54        26.93 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 
       77.10        81.17        32.35        54.64        29.42        20.68 
TCGA-13-1492 TCGA-13-1498 TCGA-13-1500 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 
      125.56        66.15        13.97        54.25        14.53        77.88 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 
       70.45        23.05        72.20        16.70         2.66        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1111 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-2078 
       29.13         3.22        33.30         4.27         6.38        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0975 TCGA-24-0980 TCGA-24-1104 
       91.66        77.00         7.63        21.80         7.66        63.55 
TCGA-24-1427 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 
        4.83        12.46       105.99         3.45        22.22        57.40 
TCGA-24-1546 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 
       64.27        51.91        58.09        88.50        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1604 TCGA-24-1849 TCGA-24-2024 
       45.50        47.70        10.26        88.37         5.79        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 
      109.71        14.43        18.48        64.01        44.52         0.36 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-25-1317 TCGA-25-1625 TCGA-25-1626 
       31.63        44.61        67.36         2.01        27.62        17.03 
TCGA-25-1630 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       38.20        14.96        24.99        85.05        13.02        49.05 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99        42.02         2.96        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 TCGA-29-1768 TCGA-29-1771 
       78.90        47.61        39.02        33.93        31.30        22.55 
TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
       11.84         8.38        36.30        62.47        13.84        42.25 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1862 TCGA-30-1880 TCGA-31-1944 
        9.76        35.77        36.26         6.12        57.57        45.57 
TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       30.18        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 
       22.85        22.55        30.08        27.85        24.23        33.01 
TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       29.49        25.91        25.08        23.80        21.60        20.98 
TCGA-36-2547 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       20.52         6.05        47.57        23.74        28.93        10.42 
TCGA-42-2591 TCGA-57-1584 TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 
       40.77        21.14        80.12        34.39         2.14        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 TCGA-61-1899 TCGA-61-1901 
       11.11         8.09        31.43         4.34         8.42        11.41 
TCGA-61-1903 TCGA-61-1910 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 
       13.02        37.05        67.76        15.75         2.01        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2017 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 
       17.98        39.85        45.96         4.77        51.72        61.64 
TCGA-61-2109 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 TCGA-09-0369 
       20.68        31.07         0.79         9.99        57.76        35.57 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       32.88        14.66         6.71        19.99        20.91         6.21 
TCGA-13-0720 TCGA-13-0726 TCGA-13-0755 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 
       44.55        31.20         2.50        38.01        56.71        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0799 TCGA-13-0804 TCGA-13-0886 
       40.24       118.42        63.09        83.34        35.28       153.37 
TCGA-13-0889 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 
       95.15       134.04        19.36       127.79       118.98        60.59 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
      109.32        84.53        48.79        85.94        25.41 

  DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE 
                          0.26                           0.36 
  DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE 
                        180.20                         153.37 
  DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE 
                         33.57                          32.09 
[1] "0.3 - 180.2 (33.6)" "0.4 - 153.4 (32.1)"
[1] "hr=" "1"  
D61V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 28(15Q15.1) MUTATED         2   349                2
  DEL PEAK 28(15Q15.1) WILD-TYPE       1   209                0
D61V3, multiclass
                  clus
vv                 DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     349                            209
  PERITONEUM OVARY                            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"
D61V4, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q15.1) MUTATED   339   3
  DEL PEAK 28(15Q15.1) WILD-TYPE 202   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q15.1) MUTATED    339    3
  DEL PEAK 28(15Q15.1) WILD-TYPE  202    2
     clus
vv    DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE
  NO                           339                            202
  YES                            3                              2
[1] 2 2
[1] FALSE
D61V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 28(15Q15.1) MUTATED    7 13  3  1
  DEL PEAK 28(15Q15.1) WILD-TYPE  8 13  2  2
D61V6, multiclass
    clus
vv   DEL PEAK 28(15Q15.1) MUTATED DEL PEAK 28(15Q15.1) WILD-TYPE
  R0                            7                              8
  R1                           13                             13
  R2                            3                              2
  RX                            1                              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"
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q15.1) MUTATED     8 198
  DEL PEAK 28(15Q15.1) WILD-TYPE   2 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q15.1) MUTATED      8  198
  DEL PEAK 28(15Q15.1) WILD-TYPE    2  129
                        clus
vv                       DEL PEAK 28(15Q15.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          198
                        clus
vv                       DEL PEAK 28(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            129
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 29(16P13.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16P13.3) MUTATED   126 176
  DEL PEAK 29(16P13.3) WILD-TYPE 102 155
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           302                            257 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           176                            155 
$`DEL PEAK 29(16P13.3) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       20.52        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 
        2.01        46.62         1.08        11.87        48.76        21.57 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1516 
       63.98        49.28        44.32        33.67       103.40        41.59 
TCGA-04-1517 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1654 
       19.99        29.10        55.43        48.89        64.64        47.70 
TCGA-09-1659 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 
        9.99        57.60        61.87        30.51        17.98         3.02 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
        6.18         6.12        35.15        71.11        39.75        20.94 
TCGA-09-2055 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 
       26.93        28.54        83.31        55.23        81.01        87.06 
TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
      124.44        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 
       90.38       127.27        66.15        13.97        43.20        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 
       65.52        80.15        14.53        80.02        76.90        65.52 
TCGA-13-A5FT TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-23-1024 TCGA-23-1028 
       70.45        25.94        26.20        25.38        15.39        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 
        8.81        29.13         2.76        51.35         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       68.68        19.46        33.30        86.01       129.96        39.09 
TCGA-23-1123 TCGA-23-2072 TCGA-23-2078 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       33.47        24.95        87.48        11.64        21.80        41.56 
TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       63.55         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 
        6.25         6.02         5.95         5.36        17.39        18.64 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1471 TCGA-24-1545 TCGA-24-1548 
        8.55        72.92        45.14         1.18        57.40        16.21 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 TCGA-24-1567 
       41.39        88.50        19.53        44.09        25.87        17.23 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 
        8.32         3.48         3.72         4.37        11.28         5.52 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 
       22.68        30.21        16.44        11.05        81.11       152.02 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 
       44.84       109.71        14.43        36.16         0.36        47.54 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       70.45        44.61         0.82        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       42.05         2.01        34.98        37.97         2.99        12.99 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1631 TCGA-25-1635 TCGA-25-1870 TCGA-25-2391 
       17.03        12.95         0.30        52.04        14.96        49.05 
TCGA-25-2392 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        1.02        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1697 TCGA-29-1698 
       29.03        26.99        78.90       101.79        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       36.36        16.93        18.25        34.62        17.36        86.60 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 
       62.93        39.42        22.98        24.36        22.55        12.36 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 
       12.30         8.38         7.23        36.30        65.00        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       13.84        42.25        21.47        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 
       15.68         0.26        34.78         6.12        36.62        24.26 
TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       45.57        18.77        22.49         6.71        42.51         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
       28.77        29.10        21.53        22.85        22.55        30.08 
TCGA-36-2532 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-42-2589 TCGA-42-2590 
       29.49         2.24        18.31        14.17        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 
       40.77         1.48         1.74        29.00        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1722 
       22.32       116.12         9.40         2.14         5.42         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       20.94        31.43         4.34        28.47        48.79        44.84 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
       33.67         1.45         8.42        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 
       31.30        37.05        48.92        56.61        43.43        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 TCGA-61-2008 TCGA-61-2087 TCGA-61-2088 
        2.01         5.52         4.01        30.64         4.80         4.77 
TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2109 TCGA-61-2113 
       71.74        58.39        60.62        65.52        20.68        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
        6.35        31.07         8.61        39.68         0.79         9.99 
TCGA-09-0367 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 
       17.98        35.44        19.99        20.91        24.59        44.55 
TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
        2.73        15.19        17.82        55.17        11.18        11.38 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       61.84        56.71        40.24       107.28        63.09        20.35 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 
       83.34        87.48        45.99        43.86        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18       111.39       153.37        66.67        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
      102.84        43.36        66.15       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
      118.98       116.65        37.64       109.32        58.68        48.79 
TCGA-13-0923 TCGA-13-0924 
       83.74        85.94 

$`DEL PEAK 29(16P13.3) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1353 
       13.81        18.51        65.52        63.09        65.46         0.53 
TCGA-04-1361 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1519 TCGA-04-1525 
       32.52        76.57        82.39        56.55         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
      119.08        84.20        27.88        28.64        36.23        31.86 
TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1668 
       45.37        38.43        89.33        74.93        41.62        55.36 
TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 
        5.85         8.55        97.55         4.54       112.41        63.09 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 
       12.46        77.10        81.17        57.27        17.46        32.35 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1496 
       54.64        61.71        29.42        20.68        22.39         4.24 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1510 TCGA-13-1511 TCGA-13-2059 
      115.07        34.82        65.69        44.68        54.25        78.48 
TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 
       77.88         8.42        23.05        72.20        27.52        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        49.68        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1031 TCGA-23-1110 TCGA-23-1120 TCGA-23-1121 
       26.83        32.09        18.90        54.51         4.27         6.38 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       58.13         0.53       115.89        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0980 TCGA-24-0982 
        2.76         4.70         4.50         7.63         7.66        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 
       54.12        47.41         6.31         4.83        28.37        18.67 
TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 
       43.53        12.46       105.99         9.11         3.45        22.22 
TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 
       26.96        64.27        56.58        41.06        51.91        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 
       70.62        39.88        45.50        47.70        10.26        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 
       88.37        48.33        38.24         3.81         5.79         9.80 
TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
        4.87        58.16        34.82        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2271 TCGA-24-2289 
       64.01        44.52        57.07         0.79        31.63        67.36 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 
       65.00        33.96        15.02        18.58        27.62        20.61 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 
       38.20        59.15        62.17        35.87        24.99        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2393 TCGA-25-2396 TCGA-25-2408 TCGA-29-1690 
       85.05        13.02        38.04         3.02        31.00        47.61 
TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1702 TCGA-29-1703 
       48.33        39.02        40.41        33.93        23.93        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1763 TCGA-29-1768 TCGA-29-1774 TCGA-29-1776 
       41.98        31.27        66.81        31.30        17.33        11.84 
TCGA-29-1778 TCGA-29-1784 TCGA-29-2414 TCGA-29-2427 TCGA-29-2434 TCGA-29-2436 
       14.93         5.36        86.17        62.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-30-1867 TCGA-30-1880 
       35.77        36.26        48.10        44.91         1.22        57.57 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1956 TCGA-36-1575 TCGA-36-1577 
       30.05        48.79        30.18        44.12         8.55        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 
       27.85        24.23        24.69        35.05        33.01        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 
       25.91        25.08        23.80        21.60        20.98        20.52 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        11.47        47.57        23.74        28.93 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1994 TCGA-59-2349 
       24.03        11.38        21.14        22.32        25.02        80.12 
TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
       34.39        44.81        11.11        18.54        27.88        31.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 TCGA-61-1911 
       35.80         2.43        43.69         5.79        11.41        42.51 
TCGA-61-1915 TCGA-61-1918 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 
       67.76        15.75        14.50        17.98        39.85        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-61-2095 TCGA-61-2101 
        1.18        45.96        45.40        51.72        61.64        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-OY-A56Q TCGA-09-0364 
        6.48        76.87        44.52       125.75        18.94        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        9.47        57.76        35.57        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 
       18.51        34.19        32.88        14.66         6.71        36.92 
TCGA-13-0714 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0760 
        6.21        39.58        12.39        31.20         2.50        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0768 TCGA-13-0792 TCGA-13-0797 TCGA-13-0802 
       38.01       111.78        58.65       118.42        69.73        51.02 
TCGA-13-0804 TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
       35.28        92.42       145.45        71.74       134.04        19.36 
TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-2071 
       60.59        44.55        84.53        48.76        25.41 

  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                        180.20                         145.45 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                         31.20                          33.96 
[1] "0.3 - 180.2 (31.2)" "0.5 - 145.4 (34.0)"
[1] "hr=" "1"  
D62V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 29(16P13.3) MUTATED         2   300                1
  DEL PEAK 29(16P13.3) WILD-TYPE       1   258                1
D62V3, multiclass
                  clus
vv                 DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     300                            258
  PERITONEUM OVARY                            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"
D62V4, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED   291   2
  DEL PEAK 29(16P13.3) WILD-TYPE 250   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED    291    2
  DEL PEAK 29(16P13.3) WILD-TYPE  250    3
     clus
vv    DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  NO                           291                            250
  YES                            2                              3
[1] 2 2
[1] FALSE
D62V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 29(16P13.3) MUTATED    8 12  3  1
  DEL PEAK 29(16P13.3) WILD-TYPE  7 14  2  2
D62V6, multiclass
    clus
vv   DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  R0                            8                              7
  R1                           12                             14
  R2                            3                              2
  RX                            1                              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"
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED     4 180
  DEL PEAK 29(16P13.3) WILD-TYPE   6 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED      4  180
  DEL PEAK 29(16P13.3) WILD-TYPE    6  147
                        clus
vv                       DEL PEAK 29(16P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          180
                        clus
vv                       DEL PEAK 29(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            147
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 30(16Q22.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(16Q22.1) MUTATED   181 264
  DEL PEAK 30(16Q22.1) WILD-TYPE  47  67
  DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE 
                           445                            114 
  DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE 
                           264                             67 
$`DEL PEAK 30(16Q22.1) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       20.52        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        2.01         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       48.76        21.57        63.98        65.46        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 TCGA-04-1517 
       44.32        33.67        76.57       103.40        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 
       38.37       119.08        55.43        48.89        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 TCGA-09-1666 
       31.86        47.70        45.37        38.43        89.33        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 
       61.87        55.36        30.51        17.98         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.18         6.12         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       39.75        20.94        26.93        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
       83.31        55.23        81.01        17.46        32.35        87.06 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42       124.44        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
      115.07        13.97        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       65.52        80.15        54.25        14.53        80.02        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       77.88        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 
       25.94        26.20        27.52        25.38        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 
        2.66        47.54        49.68        40.54        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 
       49.41         8.81        29.13        18.90        51.35         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68        19.46        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 
        4.27         6.38        39.09        33.47        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 
        4.50         7.63        11.64        41.56        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        7.86         0.76         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       28.37        18.64        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       26.96        57.40        16.21        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        70.62        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1842 TCGA-24-1843 
       25.87        10.26        17.23        90.15         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
        3.72         3.81         4.37        11.28         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
       22.68        30.21        16.44        11.05        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 
      152.02        44.84        58.16        34.82        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       18.48        28.18        64.01        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 
       47.54        31.63        70.45        44.61         0.82        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       33.11        55.86        53.26         1.02        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       52.04        42.05         2.01        34.98        65.00        37.97 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.99        12.99        15.02        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 
       38.20         0.30        59.15        62.17        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        24.00        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       29.03        26.99        48.33       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.93        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       59.67        18.25        17.36        86.60        66.81        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 
       31.30        22.98        24.36        22.55        12.36        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        36.30        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11        13.84        42.25        21.47        11.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       35.77        38.07        36.26         2.47        15.68         0.26 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       44.91        34.78        36.62         1.22        57.57        24.26 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 
        8.55        30.08        25.74        27.85        24.23        35.05 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 
       33.01        29.82        25.91        21.60         2.24        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 
       20.52        14.17        16.18        11.47        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 
       42.02        10.42         1.48        24.03        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2351 
       22.32        29.00        25.08        25.02        22.32       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        9.40         2.14         5.42         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 
       18.54        27.88         4.34        31.79        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        5.79        11.41         9.07        34.13        31.30        37.05 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        43.43        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2087 TCGA-61-2088 
       14.50         4.01        30.64        30.64         4.80         4.77 
TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       71.74        60.62        65.52         6.48        76.87        20.68 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
      125.75        22.22         6.35        31.07         8.61        39.68 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 
        0.79         9.99        57.76        17.98        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0935 TCGA-10-0936 
       81.86        18.51        34.19        32.88        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       19.99        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
        2.73        31.20        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        38.01       111.78        61.84 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 
      118.42       107.28        63.09        20.35        69.73        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       51.02        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      111.39       153.37        66.67        92.42        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
      102.84        43.36        71.74        66.15       134.04       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       37.64       109.32        58.68        84.53        48.79        83.74 
TCGA-13-0924 
       85.94 

$`DEL PEAK 30(16Q22.1) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1338 TCGA-04-1353 TCGA-04-1371 TCGA-04-1514 TCGA-04-1519 
       13.81        46.62         0.53        82.39        56.55         0.79 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-09-1659 TCGA-09-1664 
       29.10        84.20        27.88        28.64         9.99        74.93 
TCGA-09-1665 TCGA-09-1672 TCGA-09-1673 TCGA-09-2045 TCGA-09-2056 TCGA-13-1409 
       41.62         5.85         3.02        35.15        12.46        57.27 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 TCGA-13-1510 TCGA-20-0996 TCGA-20-1684 
       54.64        61.71        20.68        44.68        72.20        19.10 
TCGA-23-1024 TCGA-23-1032 TCGA-23-1110 TCGA-23-1124 TCGA-23-1809 TCGA-24-0975 
       15.39         2.76        54.51        58.13         0.53        21.80 
TCGA-24-0980 TCGA-24-1423 TCGA-24-1424 TCGA-24-1467 TCGA-24-1546 TCGA-24-1549 
        7.66         6.25         6.02       105.99        64.27        56.58 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1849 
       58.09        39.88        88.37        48.33        38.24         5.79 
TCGA-24-2027 TCGA-24-2038 TCGA-24-2254 TCGA-24-2289 TCGA-24-2290 TCGA-25-1321 
      109.71        44.52        57.07        67.36        36.23        33.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1634 TCGA-25-2397 TCGA-25-2408 TCGA-29-1688 
       18.58        27.62        35.87        12.00        31.00        78.90 
TCGA-29-1690 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1766 TCGA-29-1774 
       47.61        41.98        31.27        34.62        39.42        17.33 
TCGA-29-1776 TCGA-29-1778 TCGA-29-2436 TCGA-30-1718 TCGA-30-1859 TCGA-30-1862 
       11.84        14.93         9.76        51.91        48.10         6.12 
TCGA-30-1891 TCGA-31-1956 TCGA-36-1574 TCGA-36-1581 TCGA-36-2532 TCGA-36-2538 
       30.05        44.12        22.55        24.69        29.49        25.08 
TCGA-36-2540 TCGA-36-2544 TCGA-36-2549 TCGA-42-2582 TCGA-42-2591 TCGA-57-1583 
       23.80        20.98         6.05        47.57        40.77        11.38 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 TCGA-61-1734 
      180.20        80.12        34.39        44.81        11.11        28.47 
TCGA-61-1903 TCGA-61-1911 TCGA-61-1915 TCGA-61-1918 TCGA-61-2002 TCGA-61-2009 
       13.02        42.51        67.76        15.75        17.98        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
        1.18        45.96        45.40        51.72        61.64        58.39 
TCGA-61-2101 TCGA-61-2110 TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 
       55.50        44.52        18.94        29.16         9.47        35.57 
TCGA-10-0933 TCGA-10-0934 TCGA-13-0725 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       14.66         6.71        12.39        56.71        58.65        40.24 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0803 TCGA-13-0901 TCGA-13-0921 TCGA-13-2071 
       83.34        87.48        43.86        19.36        48.76        25.41 

  DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE 
                        153.37                         180.20 
  DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE 
                         31.86                          35.36 
[1] "0.3 - 153.4 (31.9)" "0.5 - 180.2 (35.4)"
[1] "hr=" "1"  
D63V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 30(16Q22.1) MUTATED         2   444                1
  DEL PEAK 30(16Q22.1) WILD-TYPE       1   114                1
D63V3, multiclass
                  clus
vv                 DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     444                            114
  PERITONEUM OVARY                            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"
D63V4, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q22.1) MUTATED   432   5
  DEL PEAK 30(16Q22.1) WILD-TYPE 109   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q22.1) MUTATED    432    5
  DEL PEAK 30(16Q22.1) WILD-TYPE  109    0
     clus
vv    DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE
  NO                           432                            109
  YES                            5                              0
[1] 2 2
[1] FALSE
D63V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 30(16Q22.1) MUTATED   10 23  5  1
  DEL PEAK 30(16Q22.1) WILD-TYPE  5  3  0  2
D63V6, multiclass
    clus
vv   DEL PEAK 30(16Q22.1) MUTATED DEL PEAK 30(16Q22.1) WILD-TYPE
  R0                           10                              5
  R1                           23                              3
  R2                            5                              0
  RX                            1                              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"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q22.1) MUTATED     7 262
  DEL PEAK 30(16Q22.1) WILD-TYPE   3  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q22.1) MUTATED      7  262
  DEL PEAK 30(16Q22.1) WILD-TYPE    3   65
                        clus
vv                       DEL PEAK 30(16Q22.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          262
                        clus
vv                       DEL PEAK 30(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             65
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 31(16Q23.1) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(16Q23.1) MUTATED   172 265
  DEL PEAK 31(16Q23.1) WILD-TYPE  56  66
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                           437                            122 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                           265                             66 
$`DEL PEAK 31(16Q23.1) MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 
       20.52        11.87        43.92        41.00        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       46.62         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       48.76        21.57        63.98        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 
       33.67        76.57       103.40        82.39        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 
       38.37       119.08        55.43        48.89        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2048 
        3.02         8.55        97.55         6.18         6.12         4.54 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-13-1403 TCGA-13-1404 
      112.41        63.09        39.75        20.94        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       28.54        83.31        55.23        81.01        17.46        32.35 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       87.06        29.42       124.44        22.39        70.82        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44       125.56        93.90        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15       115.07        13.97        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 
       65.52        80.15        54.25        14.53        80.02        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 
       76.90        65.52        70.45         8.42        23.05        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       27.52        25.38        16.70         2.93         2.66        49.68 
TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       40.54        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.76        51.35         3.22        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       33.47        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 
       16.21        41.06        51.91        41.39        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       39.88        19.53        44.09        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       17.23        90.15        48.33         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.81         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       22.68        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       18.48        28.18        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       52.04        42.05         2.01        34.98        65.00        37.97 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 
        2.99        12.99        15.02        18.58        17.03        12.95 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 
       20.61         0.30        59.15        62.17        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        24.00        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       38.04         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
        2.96        29.03        26.99        48.33       101.79        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       40.41        33.93        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       23.93        59.67        31.27        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       62.93        39.42        31.30        22.98        22.55        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       11.84        12.30         8.38         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       86.17        65.00        45.11        13.84        42.25        21.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
       35.77        38.07        36.26        15.68         0.26        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       34.78        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85         8.55        30.08        25.74        27.85        24.23 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2547 
       35.05        33.01        29.82        21.60         2.24        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       14.17        16.18        11.47        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 
       10.42        40.77         1.48        24.03        21.14         1.74 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 TCGA-59-2355 
       29.00        25.08        25.02        22.32         9.40         2.14 
TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
        5.42         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 
        4.34        31.79        48.79        44.84         2.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 
       43.69         1.45         8.42         5.79         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 
       31.30        37.05        48.92        56.61        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2087 
        5.52        14.50         4.01        30.64        30.64         4.80 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 
        4.77        71.74        60.62        65.52         6.48        76.87 
TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       20.68       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 
       39.68         0.79         9.99        57.76        17.98        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0935 
       25.91        81.86        18.51        34.19        32.88        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       36.92        19.99        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
        2.50        11.18        11.38        11.54        38.01       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       61.84        56.71        40.24       107.28        63.09        20.35 
TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       69.73        45.99        51.02        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18       111.39       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       95.15       145.45        43.36        71.74        66.15       134.04 
TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
      127.79       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       58.68        84.53        48.79        83.74        85.94 

$`DEL PEAK 31(16Q23.1) WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1335 TCGA-04-1351 TCGA-04-1353 TCGA-04-1514 TCGA-04-1519 
       13.81         1.81        65.46         0.53        56.55         0.79 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-09-1664 TCGA-09-1672 
       29.10        84.20        27.88        28.64        74.93         5.85 
TCGA-09-2045 TCGA-09-2050 TCGA-09-2055 TCGA-09-2056 TCGA-13-1409 TCGA-13-1477 
       35.15        71.11        26.93        12.46        57.27        54.64 
TCGA-13-1482 TCGA-13-1485 TCGA-13-1501 TCGA-13-1510 TCGA-13-2059 TCGA-20-0990 
       61.71        20.68        43.20        44.68        78.48        25.94 
TCGA-20-0996 TCGA-20-1684 TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1110 
       72.20        19.10        47.54        15.39        26.83        54.51 
TCGA-23-1124 TCGA-23-1809 TCGA-24-0980 TCGA-24-1423 TCGA-24-1424 TCGA-24-1467 
       58.13         0.53         7.66         6.25         6.02       105.99 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1553 TCGA-24-1562 TCGA-24-1604 TCGA-24-1616 
       64.27        56.58        58.09        45.50        88.37        38.24 
TCGA-24-1924 TCGA-24-2036 TCGA-24-2038 TCGA-24-2290 TCGA-25-1314 TCGA-25-1321 
       30.21        64.01        44.52        36.23        33.01        33.96 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1634 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       27.62        38.20        35.87        31.00        78.90        47.61 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 
       18.25        41.98        34.62        24.36        17.33        14.93 
TCGA-29-2427 TCGA-29-2434 TCGA-29-2436 TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 
       62.47        11.47         9.76        51.91         2.47        48.10 
TCGA-30-1862 TCGA-36-1574 TCGA-36-1581 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
        6.12        22.55        24.69        29.49        25.91        25.08 
TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-57-1583 
       23.80        20.98        18.31         6.05        47.57        11.38 
TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2354 TCGA-59-2372 
       22.32       180.20        80.12       116.12        34.39        44.81 
TCGA-61-1721 TCGA-61-1734 TCGA-61-1738 TCGA-61-1901 TCGA-61-1903 TCGA-61-1911 
       11.11        28.47        35.80        11.41        13.02        42.51 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 
       67.76        43.43        15.75        17.98        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 
       45.96        45.40        51.72        61.64        58.39        55.50 
TCGA-61-2110 TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-10-0933 
       44.52        18.94        29.16         9.47        35.57        14.66 
TCGA-10-0934 TCGA-13-0725 TCGA-13-0768 TCGA-13-0792 TCGA-13-0799 TCGA-13-0800 
        6.71        12.39        58.65       118.42        83.34        87.48 
TCGA-13-0803 TCGA-13-0891 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0913 
       43.86       102.84        19.36        50.37       123.16       109.32 
TCGA-13-0921 TCGA-13-2071 
       48.76        25.41 

  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                        153.37                         180.20 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                         31.79                          35.36 
[1] "0.3 - 153.4 (31.8)" "0.5 - 180.2 (35.4)"
[1] "hr=" "1.2"
D64V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 31(16Q23.1) MUTATED         2   435                2
  DEL PEAK 31(16Q23.1) WILD-TYPE       1   123                0
D64V3, multiclass
                  clus
vv                 DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     435                            123
  PERITONEUM OVARY                            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"
D64V4, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q23.1) MUTATED   425   5
  DEL PEAK 31(16Q23.1) WILD-TYPE 116   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q23.1) MUTATED    425    5
  DEL PEAK 31(16Q23.1) WILD-TYPE  116    0
     clus
vv    DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  NO                           425                            116
  YES                            5                              0
[1] 2 2
[1] FALSE
D64V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 31(16Q23.1) MUTATED    8 21  5  1
  DEL PEAK 31(16Q23.1) WILD-TYPE  7  5  0  2
D64V6, multiclass
    clus
vv   DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  R0                            8                              7
  R1                           21                              5
  R2                            5                              0
  RX                            1                              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"
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q23.1) MUTATED     6 253
  DEL PEAK 31(16Q23.1) WILD-TYPE   4  74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q23.1) MUTATED      6  253
  DEL PEAK 31(16Q23.1) WILD-TYPE    4   74
                        clus
vv                       DEL PEAK 31(16Q23.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          253
                        clus
vv                       DEL PEAK 31(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             74
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 32(17P12) MUTATION ANALYSIS
D65V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 32(17P12) MUTATED   185 288
  DEL PEAK 32(17P12) WILD-TYPE  43  43
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                         473                           86 
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                         288                           43 
$`DEL PEAK 32(17P12) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       46.62        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       63.98        65.46         0.53        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
      103.40        82.39        56.55        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
      119.08        29.10        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
        9.99        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       55.36        30.51        17.98         5.85         3.02        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
        6.12        35.15       112.41        71.11        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       26.93        12.46        77.10        81.17        28.54        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 
       55.23        57.27        81.01        17.46        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42       124.44        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1509 TCGA-13-1510 
      115.07        13.97        43.20        34.82        80.15        44.68 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       54.25        14.53        76.90        65.52        70.45         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       23.05        25.94        26.20        27.52        19.10        16.70 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.66        47.54        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        31.20        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       24.95       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
        2.76         4.70         4.50         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        6.25         6.02         5.95         5.36         4.83        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       18.64        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 
       45.14       105.99         9.11         3.45         1.18        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       41.39        58.09        88.50        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       45.50        47.70        25.87        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       16.44        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       58.16        34.82       109.71        14.43        55.92        18.48 
TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       64.01        36.16         0.79        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       44.61         0.82        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       53.26         1.02        26.96        33.01        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       15.02        27.62        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       24.00        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 
       19.99        42.02         2.96        29.03        26.99        78.90 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 
       41.98        34.62        17.36        86.60        62.93        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       22.98        24.36        22.55        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 
       65.00        62.47        45.11        42.25        21.47        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       51.91        36.26         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.23        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       25.08         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        6.05        47.57        23.74        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1993 
        1.48        24.03        11.38        21.14         1.74        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
      180.20        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
        5.42        44.81        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 
        2.43        33.67        43.69         1.45         8.42        11.41 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       13.02        34.13        31.30        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 
       17.98         4.01        30.64        30.64         1.18        45.40 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
        4.77        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
        0.79         9.99        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0936 
       35.57        25.91        81.86        34.19        14.66        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       19.99        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 
        2.73        12.39        31.20        15.19        17.82         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       11.18        11.38        11.54        38.01        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       58.65        40.24       118.42       107.28        63.09        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       69.73        83.34        45.99        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.31        13.61        68.94       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        92.42        95.15       145.45       102.84        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       71.74       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       60.59       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.76        83.74        85.94        25.41 

$`DEL PEAK 32(17P12) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1341 TCGA-04-1342 TCGA-04-1356 TCGA-04-1361 
       11.87        41.00         1.08        18.51        49.28        32.52 
TCGA-04-1516 TCGA-09-1661 TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-09-2051 
       41.59        38.43         8.55         6.18         4.54        63.09 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       32.35        54.64        20.68        65.69        34.16        65.52 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-20-0996 TCGA-20-1683 TCGA-20-1686 
       80.02        78.48        77.88        72.20        25.38         2.93 
TCGA-23-1022 TCGA-23-1114 TCGA-23-1809 TCGA-24-1428 TCGA-24-1474 TCGA-24-1556 
       49.68        68.68         0.53        17.39        22.22        70.62 
TCGA-24-1565 TCGA-24-1924 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 
       10.26        30.21        28.18        44.52        57.07         0.36 
TCGA-24-2289 TCGA-25-1315 TCGA-25-1623 TCGA-25-1626 TCGA-25-1878 TCGA-25-2397 
       67.36        52.04        18.58        17.03        85.05        12.00 
TCGA-25-2398 TCGA-25-2408 TCGA-29-1690 TCGA-29-1710 TCGA-29-1763 TCGA-29-1766 
       45.01        31.00        47.61        31.27        66.81        39.42 
TCGA-29-1774 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-36-1569 
       17.33        13.84        11.47         9.76        35.77        29.10 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2540 TCGA-36-2542 TCGA-36-2551 TCGA-36-2552 
       27.85        24.69        23.80        21.60        16.18        11.47 
TCGA-42-2588 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2349 TCGA-61-1721 
       28.93        22.32        29.00        25.02        80.12        11.11 
TCGA-61-1722 TCGA-61-1900 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-2009 
        8.09         5.79         9.07        37.05        42.51        39.85 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 
       45.96         4.80        51.72        54.31        18.51        32.88 
TCGA-10-0934 TCGA-10-0935 TCGA-13-0751 TCGA-13-0762 TCGA-13-0800 TCGA-13-0899 
        6.71        35.44        55.17       111.78        87.48        66.15 
TCGA-13-0906 TCGA-13-0920 
      118.98        48.79 

  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                        0.26                         0.36 
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                      180.20                       118.98 
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                       33.11                        31.81 
[1] "0.3 - 180.2 (33.1)" "0.4 - 119.0 (31.8)"
[1] "hr=" "1.1"
D65V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 32(17P12) MUTATED         2   474                1
  DEL PEAK 32(17P12) WILD-TYPE       1    84                1
D65V3, multiclass
                  clus
vv                 DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE
  OMENTUM                                   2                            1
  OVARY                                   474                           84
  PERITONEUM OVARY                          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"
D65V4, binary
                              cls
clus                             0   1
  DEL PEAK 32(17P12) MUTATED   457   5
  DEL PEAK 32(17P12) WILD-TYPE  84   0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(17P12) MUTATED    457    5
  DEL PEAK 32(17P12) WILD-TYPE   84    0
     clus
vv    DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE
  NO                         457                           84
  YES                          5                            0
[1] 2 2
[1] FALSE
D65V5, continuous
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 32(17P12) MUTATED   10 22  4  3
  DEL PEAK 32(17P12) WILD-TYPE  5  4  1  0
D65V6, multiclass
    clus
vv   DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE
  R0                         10                            5
  R1                         22                            4
  R2                          4                            1
  RX                          3                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                              cls
clus                             0   1
  DEL PEAK 32(17P12) MUTATED     8 277
  DEL PEAK 32(17P12) WILD-TYPE   2  50
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(17P12) MUTATED      8  277
  DEL PEAK 32(17P12) WILD-TYPE    2   50
                        clus
vv                       DEL PEAK 32(17P12) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                        277
                        clus
vv                       DEL PEAK 32(17P12) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           50
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 33(17Q11.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(17Q11.2) MUTATED   182 271
  DEL PEAK 33(17Q11.2) WILD-TYPE  46  60
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                           453                            106 
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                           271                             60 
$`DEL PEAK 33(17Q11.2) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
        2.01        46.62        11.87        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       63.98        65.46         0.53        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       33.67        76.57       103.40        82.39        56.55        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 
       38.37       119.08        29.10        84.20        55.43        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1664 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
        9.99        74.93        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        5.85         3.02         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       39.75        20.94        26.93        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
       83.31        57.27        81.01        17.46        32.35        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42       124.44        22.39        70.82        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44       125.56        93.90        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       66.15       115.07        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       34.16        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       78.48        76.90        65.52         8.42        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        18.90         2.76        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
        3.22        31.20        68.68        19.46        86.01       129.96 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
        4.27        39.09        33.47        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.31         6.38         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       72.92        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        1.18        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 
       41.06        51.91        41.39        58.09        88.50        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 
       19.53        44.09        45.50        47.70        25.87        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       90.15        88.37        48.33        38.24         8.32         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.81         4.37        11.28         5.79         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 
       58.16       109.71        14.43        55.92        18.48        64.01 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
       57.07         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 
        0.82        67.36        36.23        16.64        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       34.98        37.97        33.96         2.99        12.99        15.02 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       27.62        12.95        20.61        38.20         0.30        59.15 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 
       62.17        52.04        14.96        24.99        13.02        49.05 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       29.03        26.99        78.90       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 
       33.93        31.20        68.32        36.36        59.67        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        34.62        17.36        86.60        66.81        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       31.30        22.98        24.36        22.55        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       65.00        62.47        45.11        13.84        42.25        21.47 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       11.47        38.07        36.26         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       48.10        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       18.77         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       25.08         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        6.05        47.57        28.93        42.02        10.42        40.77 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       11.38        21.14         1.74       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1724 TCGA-61-1725 
        9.40        34.39         5.42        44.81        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 
        8.42         5.79        11.41        13.02        34.13        31.30 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       37.05        48.92        56.61        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64        30.64         1.18        45.40         4.80         4.77 
TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       71.74        58.39        60.62        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q 
       20.68        44.52       125.75        22.22        31.07        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
        0.79         9.99        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       19.99        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
        2.73        12.39        31.20        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 
       11.18        11.38        11.54        38.01       111.78        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       58.65        40.24       118.42       107.28        20.35        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18       111.39       153.37        66.67        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
      145.45       102.84        43.36        71.74       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      127.79        50.37       123.16       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       44.55        37.64       109.32        58.68        84.53        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

$`DEL PEAK 33(17Q11.2) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1516 TCGA-04-1519 
       11.87         1.08        18.51        65.52        41.59         0.79 
TCGA-04-1644 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1674 
       48.89        38.43        89.33        41.62        57.60         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2056 TCGA-13-1408 
       97.55         6.18        35.15         4.54        12.46        55.23 
TCGA-13-1477 TCGA-13-1485 TCGA-13-2057 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0987 
       54.64        20.68        80.02        77.88        70.45        23.05 
TCGA-20-0996 TCGA-23-1030 TCGA-23-1117 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 
       72.20        29.13        33.30         6.38        58.13         0.53 
TCGA-23-2079 TCGA-24-1417 TCGA-24-1474 TCGA-24-1556 TCGA-24-1565 TCGA-24-1844 
       91.66         7.82        22.22        70.62        10.26         3.72 
TCGA-24-1850 TCGA-24-2023 TCGA-24-2026 TCGA-24-2035 TCGA-24-2038 TCGA-24-2260 
        5.52        44.84        34.82        28.18        44.52        36.16 
TCGA-24-2261 TCGA-24-2295 TCGA-25-1319 TCGA-25-1623 TCGA-25-1626 TCGA-25-1634 
        0.79        33.11        65.00        18.58        17.03        35.87 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 TCGA-25-2408 TCGA-29-1690 
       24.00        85.05         1.02         3.02        31.00        47.61 
TCGA-29-1691 TCGA-29-1701 TCGA-29-1702 TCGA-29-1710 TCGA-29-1766 TCGA-29-1774 
       48.33        16.93        23.93        31.27        39.42        17.33 
TCGA-29-2414 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-31-1951 TCGA-36-1569 
       86.17         9.76        35.77        51.91        22.49        29.10 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2540 TCGA-36-2542 TCGA-36-2551 TCGA-36-2552 
       24.69        35.05        23.80        21.60        16.18        11.47 
TCGA-42-2587 TCGA-42-2593 TCGA-57-1582 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       23.74         1.48        24.03        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2355 TCGA-61-1721 TCGA-61-1722 TCGA-61-1904 
       25.02        80.12         2.14        11.11         8.09         9.07 
TCGA-61-1911 TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2098 
       42.51        39.85        45.96        51.72        61.64        65.52 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-10-0925 TCGA-10-0933 TCGA-10-0934 
        6.35         8.61        39.68        54.31        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-13-0755 TCGA-13-0764 TCGA-13-0794 TCGA-13-0800 
       35.44        36.92         2.50        61.84        63.09        87.48 
TCGA-13-0807 TCGA-13-0888 TCGA-13-0899 TCGA-13-0920 
       13.61        92.42        66.15        48.79 

  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                        180.20                          97.55 
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                        33.010                         30.065 
[1] "0.3 - 180.2 (33.0)" "0.5 - 97.5 (30.1)" 
[1] "hr=" "1.1"
D66V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 33(17Q11.2) MUTATED         2   455                0
  DEL PEAK 33(17Q11.2) WILD-TYPE       1   103                2
D66V3, multiclass
                  clus
vv                 DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE
  OMENTUM                                     2                              1
  OVARY                                     455                            103
  PERITONEUM OVARY                            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"
D66V4, binary
                                cls
clus                               0   1
  DEL PEAK 33(17Q11.2) MUTATED   439   4
  DEL PEAK 33(17Q11.2) WILD-TYPE 102   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(17Q11.2) MUTATED    439    4
  DEL PEAK 33(17Q11.2) WILD-TYPE  102    1
     clus
vv    DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE
  NO                           439                            102
  YES                            4                              1
[1] 2 2
[1] FALSE
D66V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 33(17Q11.2) MUTATED   10 16  3  2
  DEL PEAK 33(17Q11.2) WILD-TYPE  5 10  2  1
D66V6, multiclass
    clus
vv   DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE
  R0                           10                              5
  R1                           16                             10
  R2                            3                              2
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(17Q11.2) MUTATED     9 267
  DEL PEAK 33(17Q11.2) WILD-TYPE   1  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(17Q11.2) MUTATED      9  267
  DEL PEAK 33(17Q11.2) WILD-TYPE    1   60
                        clus
vv                       DEL PEAK 33(17Q11.2) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          267
                        clus
vv                       DEL PEAK 33(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             60
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 34(18Q23) MUTATION ANALYSIS
D67V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 34(18Q23) MUTATED   155 214
  DEL PEAK 34(18Q23) WILD-TYPE  73 117
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         369                          190 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         214                          117 
$`DEL PEAK 34(18Q23) MUTATED`
TCGA-59-A5PD TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 
       20.52        41.00         1.81        49.15        46.62         1.08 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       65.46         0.53        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1644 
       76.57        41.59        19.99         0.79       119.08        48.89 
TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1665 
       27.88        36.23        31.86        47.70        45.37        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        61.87        30.51         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
       97.55         6.18         6.12         4.54       112.41        71.11 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 
       28.54        83.31        55.23        57.27        17.46        32.35 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 
       29.42       124.44        22.39        70.82        83.93        90.38 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
      127.27        66.15       115.07        13.97        43.20        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       34.16        65.52        80.15        54.25        14.53        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 TCGA-20-0990 
       78.48        77.88        76.90        65.52        23.05        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 
        2.66        47.54        49.68        40.54        32.09        49.41 
TCGA-23-1030 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       29.13         3.22        31.20        68.68        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       86.01       129.96         4.27        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
        0.53        24.95        87.48        91.66        77.00        49.84 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 
        4.70         4.50         7.63        11.64        41.56        22.32 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 
       63.55         6.31         6.38         7.82         7.99         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 
       18.64        43.53         8.55        72.92        12.46         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1552 
        1.18        22.22        57.40        64.27        16.21        41.39 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       47.70        25.87        17.23        90.15        88.37        48.33 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
      152.02        44.84        58.16       109.71        14.43        55.92 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 
       28.18        64.01        57.07         0.79        47.54        31.63 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 
        0.82        67.36        16.64        55.86         1.02        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
       52.04        42.05         2.01        34.98        37.97        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
        2.99        12.99        15.02        27.62        17.03        12.95 
TCGA-25-1628 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 
       20.61        59.15        62.17        35.87        24.00        85.05 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 
       13.02         1.02        38.04        19.99         2.96        29.03 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1697 TCGA-29-1701 
       26.99        48.33       101.79        39.02        31.20        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1763 TCGA-29-1764 
       23.93        59.67        18.25        41.98        66.81        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 
       31.30        22.98        24.36        12.36        12.30         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        7.23         5.36        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       13.84        11.47        35.77        38.07        51.91        36.26 
TCGA-30-1856 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 
       15.68        34.78        36.62         1.22        57.57        30.05 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       45.57        30.18        22.49        42.51        44.12         2.20 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 
       21.53        22.85        22.55         8.55        25.74        27.85 
TCGA-36-1580 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       24.23        29.49        29.82        25.08        21.60         2.24 
TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 
       20.98        20.52        14.17         6.05        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
       24.03        11.38        21.14         1.74        29.00        25.08 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       22.32       116.12        34.39         2.14         5.42        44.81 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
        8.09        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1736 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 
       48.79         2.43        33.67        43.69         5.79        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 
        9.07        34.13        31.30        42.51        56.61        67.76 
TCGA-61-1919 TCGA-61-1995 TCGA-61-2002 TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 
       38.17         2.01        17.98        45.40         4.77        71.74 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       58.39        60.62         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
      125.75         6.35        31.07        39.68         0.79         9.99 
TCGA-09-0367 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 
       17.98        81.86        18.51        34.19        32.88        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 
       19.99        20.91         6.21        44.55         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 
       15.19        17.82        55.17         2.50        11.18        11.54 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 
       61.84        56.71        40.24       118.42        63.09        20.35 
TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       69.73        87.48        45.99        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
      145.45        66.15       134.04       127.79       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 
       60.59       116.65        44.55        37.64       109.32        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

$`DEL PEAK 34(18Q23) WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1337 TCGA-04-1342 TCGA-04-1367 
       13.81        11.87        43.92         2.01        18.51       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       82.39        56.55        38.37        29.10        84.20        55.43 
TCGA-04-1648 TCGA-04-1649 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       28.64        64.64         9.99        38.43        89.33        74.93 
TCGA-09-1668 TCGA-09-1670 TCGA-09-2045 TCGA-09-2051 TCGA-13-1410 TCGA-13-1477 
       55.36        17.98        35.15        63.09        81.01        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       87.06        61.71        20.68        52.44       125.56        93.90 
TCGA-13-1496 TCGA-13-1504 TCGA-13-1510 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0996 
        4.24        34.82        44.68        70.45         8.42        72.20 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       15.39        26.83         8.81        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1121 TCGA-23-2077 TCGA-23-2641 TCGA-24-0975 TCGA-24-0980 
       54.51         6.38       115.89         2.76        21.80         7.66 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1419 TCGA-24-1430 TCGA-24-1434 TCGA-24-1466 
       54.12        47.41         7.86        28.37        18.67        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1544 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
      105.99         9.11        26.96        56.58        41.06        51.91 
TCGA-24-1553 TCGA-24-1565 TCGA-24-1616 TCGA-24-1845 TCGA-24-1930 TCGA-24-2019 
       58.09        10.26        38.24         3.81        81.11         4.87 
TCGA-24-2026 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2280 
       34.82        18.48        44.52        36.16         0.36        70.45 
TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 TCGA-24-2298 TCGA-25-1313 TCGA-25-1319 
       44.61        36.23        33.11        53.26        26.96        65.00 
TCGA-25-1623 TCGA-25-1630 TCGA-25-1631 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       18.58        38.20         0.30        52.04        14.96        24.99 
TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2408 
       49.05         3.02        12.00        45.01        42.02        31.00 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 
       78.90        47.61        40.41        33.93        68.32        36.36 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 TCGA-29-1771 
       31.27        34.62        17.36        86.60        39.42        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1785 TCGA-29-2431 TCGA-29-2432 
       17.33        11.84        14.93        36.30        42.25        21.47 
TCGA-29-2436 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 
        9.76         2.47         0.26        48.10        44.91         6.12 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 TCGA-31-1953 TCGA-36-1568 TCGA-36-1569 
       24.26        48.79        18.77         6.71        28.77        29.10 
TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 
       30.08        24.69        35.05        33.01        25.91        23.80 
TCGA-36-2545 TCGA-36-2551 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       18.31        16.18        22.32        25.02       180.20        80.12 
TCGA-59-2352 TCGA-61-1721 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 
        9.40        11.11        31.79        28.47        44.84        35.80 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1903 TCGA-61-1910 TCGA-61-1913 TCGA-61-1917 
        1.45         8.42        13.02        37.05        48.92        43.43 
TCGA-61-1918 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
       15.75         5.52        14.50         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 
       30.64         1.18        45.96         4.80        51.72        61.64 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56Q TCGA-09-0364 
       65.52        55.50        22.22         8.61        18.94        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0933 
        9.47        57.76        35.57        54.31        25.91        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-13-0717 TCGA-13-0723 TCGA-13-0725 TCGA-13-0758 
        6.71        35.44        24.59        39.58        12.39        11.38 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0768 TCGA-13-0793 TCGA-13-0799 TCGA-13-0802 
       38.01       111.78        58.65       107.28        83.34        51.02 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 
       92.42        95.15       102.84        43.36        71.74        19.36 
TCGA-13-0904 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       50.37        58.68        84.53        48.76 

  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                        0.53                         0.26 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                      153.37                       180.20 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                      31.430                       34.935 
[1] "0.5 - 153.4 (31.4)" "0.3 - 180.2 (34.9)"
[1] "hr=" "1.1"
D67V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 34(18Q23) MUTATED         2   367                0
  DEL PEAK 34(18Q23) WILD-TYPE       1   191                2
D67V3, multiclass
                  clus
vv                 DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  OMENTUM                                   2                            1
  OVARY                                   367                          191
  PERITONEUM OVARY                          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"
D67V4, binary
                              cls
clus                             0   1
  DEL PEAK 34(18Q23) MUTATED   355   3
  DEL PEAK 34(18Q23) WILD-TYPE 186   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 34(18Q23) MUTATED    355    3
  DEL PEAK 34(18Q23) WILD-TYPE  186    2
     clus
vv    DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  NO                         355                          186
  YES                          3                            2
[1] 2 2
[1] FALSE
D67V5, continuous
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 34(18Q23) MUTATED   11 18  4  0
  DEL PEAK 34(18Q23) WILD-TYPE  4  8  1  3
D67V6, multiclass
    clus
vv   DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  R0                         11                            4
  R1                         18                            8
  R2                          4                            1
  RX                          0                            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"
D67V7, binary
                              cls
clus                             0   1
  DEL PEAK 34(18Q23) MUTATED     7 218
  DEL PEAK 34(18Q23) WILD-TYPE   3 109
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 34(18Q23) MUTATED      7  218
  DEL PEAK 34(18Q23) WILD-TYPE    3  109
                        clus
vv                       DEL PEAK 34(18Q23) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                        218
                        clus
vv                       DEL PEAK 34(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          109
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 35(19P13.3) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(19P13.3) MUTATED   202 291
  DEL PEAK 35(19P13.3) WILD-TYPE  26  40
  DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE 
                           493                             66 
  DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE 
                           291                             40 
$`DEL PEAK 35(19P13.3) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       49.15        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       63.09        21.57        63.98        65.46         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       32.52        44.32        33.67        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       56.55        41.59        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       74.93        41.62        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 
       17.98         5.85         3.02         8.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       12.46        77.10        81.17        28.54        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
       57.27        81.01        17.46        32.35        87.06        61.71 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       29.42        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       93.90        90.38         4.24        66.15       115.07        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       44.68        54.25        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       76.90        65.52        70.45         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       26.20        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
       18.90         2.76        54.51         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       19.46        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       87.48        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 
        7.63        11.64        21.80        41.56        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.86         0.76         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       72.92        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        1.18        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 
       56.58        41.06        51.91        41.39        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 
       10.26        17.23        48.33        38.24         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.81         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        11.05         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       18.48        28.18        64.01        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       47.54        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       33.01        52.04        42.05         2.01        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       37.97        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       27.62        17.03        12.95        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       62.17        35.87        52.04        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       12.00        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       26.99        48.33       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        36.36        16.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       17.33        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        5.36        36.30        86.17        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       42.25        21.47        11.47        35.77        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       36.26         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       34.78        36.62         1.22        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       45.57        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2591 TCGA-57-1582 
       16.18        11.47        47.57        28.93        40.77        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
       25.02       180.20        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        2.14         5.42        44.81         8.09        20.94        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 
        5.79        13.02         9.07        34.13        31.30        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 
       48.92        56.61        67.76        43.43        38.17         2.01 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98         4.01        30.64        30.64         1.18 
TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       45.40         4.77        71.74        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        0.79         9.99        29.16        57.76        17.98        35.57 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.86        18.51        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        36.92        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        12.39        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 
       55.17         2.50        11.18        11.38        38.01       111.78 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       56.71        58.65        40.24       118.42       107.28        63.09 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       20.35        69.73        83.34        87.48        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      111.39       153.37        92.42        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       43.36        66.15       134.04        19.36       127.79        50.37 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      118.98        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       58.68        84.53        48.79        48.76        83.74        85.94 
TCGA-13-2071 
       25.41 

$`DEL PEAK 35(19P13.3) WILD-TYPE`
TCGA-04-1337 TCGA-04-1348 TCGA-04-1654 TCGA-09-1662 TCGA-09-1675 TCGA-09-2043 
        2.01        48.76        47.70        89.33        97.55         6.18 
TCGA-09-2048 TCGA-13-1477 TCGA-13-1484 TCGA-13-1485 TCGA-13-1497 TCGA-20-0996 
        4.54        54.64       124.44        20.68       127.27        72.20 
TCGA-20-1682 TCGA-23-1021 TCGA-23-1022 TCGA-23-1026 TCGA-23-1109 TCGA-23-2079 
       27.52        47.54        49.68        26.83        51.35        91.66 
TCGA-24-0980 TCGA-24-1423 TCGA-24-1553 TCGA-24-1603 TCGA-24-1604 TCGA-24-1842 
        7.66         6.25        58.09        90.15        88.37         8.32 
TCGA-24-1930 TCGA-24-2038 TCGA-24-2254 TCGA-24-2271 TCGA-25-1630 TCGA-25-2408 
       81.11        44.52        57.07        31.63        38.20        31.00 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1702 TCGA-29-1775 TCGA-29-2425 TCGA-29-2436 
       78.90        47.61        23.93        12.36        65.00         9.76 
TCGA-30-1862 TCGA-30-1880 TCGA-31-1946 TCGA-36-2540 TCGA-36-2542 TCGA-42-2587 
        6.12        57.57        30.18        23.80        21.60        23.74 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-59-2349 TCGA-61-1721 TCGA-61-1727 
       42.02        10.42         1.48        80.12        11.11        18.54 
TCGA-61-1901 TCGA-61-1910 TCGA-61-1918 TCGA-61-1998 TCGA-61-2009 TCGA-61-2017 
       11.41        37.05        15.75         5.52        39.85        45.96 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-09-0365 TCGA-10-0925 TCGA-10-0930 
        4.80        51.72        61.64         9.47        54.31        34.19 
TCGA-13-0726 TCGA-13-0760 TCGA-13-0764 TCGA-13-0887 TCGA-13-0897 TCGA-13-0905 
       31.20        11.54        61.84        66.67        71.74       123.16 

  DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE 
                          0.26                           1.48 
  DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE 
                        180.20                         127.27 
  DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE 
                        32.090                         39.025 
[1] "0.3 - 180.2 (32.1)" "1.5 - 127.3 (39.0)"
[1] "hr=" "1.1"
D68V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 35(19P13.3) MUTATED         3   491                2
  DEL PEAK 35(19P13.3) WILD-TYPE       0    67                0
D68V3, multiclass
                  clus
vv                 DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE
  OMENTUM                                     3                              0
  OVARY                                     491                             67
  PERITONEUM OVARY                            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"
D68V4, binary
                                cls
clus                               0   1
  DEL PEAK 35(19P13.3) MUTATED   475   5
  DEL PEAK 35(19P13.3) WILD-TYPE  66   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(19P13.3) MUTATED    475    5
  DEL PEAK 35(19P13.3) WILD-TYPE   66    0
     clus
vv    DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE
  NO                           475                             66
  YES                            5                              0
[1] 2 2
[1] FALSE
D68V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 35(19P13.3) MUTATED   13 21  4  3
  DEL PEAK 35(19P13.3) WILD-TYPE  2  5  1  0
D68V6, multiclass
    clus
vv   DEL PEAK 35(19P13.3) MUTATED DEL PEAK 35(19P13.3) WILD-TYPE
  R0                           13                              2
  R1                           21                              5
  R2                            4                              1
  RX                            3                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(19P13.3) MUTATED     9 284
  DEL PEAK 35(19P13.3) WILD-TYPE   1  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(19P13.3) MUTATED      9  284
  DEL PEAK 35(19P13.3) WILD-TYPE    1   43
                        clus
vv                       DEL PEAK 35(19P13.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          284
                        clus
vv                       DEL PEAK 35(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             43
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 36(19Q13.33) MUTATION ANALYSIS
D69V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 36(19Q13.33) MUTATED   127 163
  DEL PEAK 36(19Q13.33) WILD-TYPE 101 168
  DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE 
                            290                             269 
  DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE 
                            163                             168 
$`DEL PEAK 36(19Q13.33) MUTATED`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1341 TCGA-04-1348 TCGA-04-1349 
       13.81        11.87         1.81         1.08        48.76        21.57 
TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 
       63.98         0.53        49.28        44.32        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        41.59         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       29.10        84.20        55.43        48.89        28.64        64.64 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 
       31.86        47.70        45.37         9.99        38.43        74.93 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       41.62        61.87        55.36         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       97.55         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 
       20.94        26.93        12.46        77.10        81.17        83.31 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       17.46        32.35        87.06        29.42       124.44        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       83.93        52.44        93.90        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 TCGA-13-2059 
       66.15       115.07        65.69        34.16        44.68        78.48 
TCGA-13-2060 TCGA-13-2065 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 
       77.88        65.52        25.94        26.20        27.52        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 
       16.70         2.93         2.66        47.54        49.68        15.39 
TCGA-23-1026 TCGA-23-1028 TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1118 
       26.83        49.41        29.13         2.76        54.51        86.01 
TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
      129.96         6.38        33.47        58.13        24.95       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0979 
       91.66        77.00         2.76         4.70         7.63        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1413 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.66        22.32         6.31         0.76         6.25         6.02 
TCGA-24-1426 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
        5.36        18.67        43.53        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1548 TCGA-24-1549 
      105.99         9.11         3.45        22.22        16.21        56.58 
TCGA-24-1552 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 TCGA-24-1565 
       41.39        70.62        19.53        44.09        25.87        10.26 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1920 
       90.15        48.33         3.48         3.72         4.37         9.80 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2036 
       81.11         4.87        44.84        58.16        34.82        64.01 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2280 TCGA-24-2281 TCGA-24-2293 TCGA-25-1312 
       57.07        36.16        70.45        44.61        16.64         1.02 
TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1627 TCGA-25-1631 
       42.05        65.00        37.97        33.96        12.95         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       24.00        85.05        49.05         1.02        38.04         3.02 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1697 
       19.99        42.02        26.99        48.33        39.02        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       68.32        36.36        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1763 TCGA-29-1771 TCGA-29-1775 TCGA-29-1778 TCGA-29-1784 
       31.27        66.81        22.55        12.36        14.93         5.36 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 
       65.00        62.47        42.25        11.47        38.07        36.26 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1861 TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 
        2.47         0.26        34.78        36.62        24.26        30.05 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1956 TCGA-36-1569 
       45.57        30.18        18.77         6.71        44.12        29.10 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       22.85        22.55        30.08        25.74        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 
       35.05        33.01        29.82        25.91        25.08        21.60 
TCGA-36-2543 TCGA-36-2547 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2589 
        2.24        20.52        16.18        11.47        47.57        42.02 
TCGA-42-2590 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-57-1994 TCGA-59-2355 
       10.42        11.38        21.14        25.08        25.02         2.14 
TCGA-59-2372 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       44.81        20.94        31.43        27.88         4.34        31.79 
TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1907 
       35.80        33.67         1.45         8.42        11.41        31.30 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 
       67.76        43.43        15.75         2.01        14.50        17.98 
TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
        4.01        30.64         1.18        45.96         4.80         4.77 
TCGA-61-2094 TCGA-61-2096 TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
       71.74        58.39         6.48         6.35         8.61        39.68 
TCGA-OY-A56Q TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       18.94        57.76        54.31        25.91        81.86        18.51 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 
       32.88         6.71        36.92        19.99        20.91        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
        2.73        31.20        17.82        55.17         2.50        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 
       38.01       111.78        61.84        56.71        58.65       118.42 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 
       63.09        69.73        83.34        87.48        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0886 TCGA-13-0897 TCGA-13-0899 TCGA-13-0903 
       35.31        13.61       153.37        71.74        66.15       127.79 
TCGA-13-0908 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       60.59        44.55       109.32        58.68        84.53        48.76 
TCGA-13-0923 TCGA-13-2071 
       83.74        25.41 

$`DEL PEAK 36(19Q13.33) WILD-TYPE`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       20.52        43.92        41.00        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1361 
       18.51        11.87        65.52        63.09        65.46        32.52 
TCGA-04-1364 TCGA-04-1517 TCGA-04-1646 TCGA-04-1651 TCGA-09-1662 TCGA-09-1666 
       33.67        19.99        27.88        36.23        89.33        57.60 
TCGA-09-1669 TCGA-09-1670 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-13-1405 
       30.51        17.98         6.18         6.12        35.15        28.54 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 
       55.23        57.27        81.01        54.64        61.71        20.68 
TCGA-13-1488 TCGA-13-1492 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1507 
       70.82       125.56        13.97        43.20        34.82        65.52 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-A5FT 
       80.15        54.25        14.53        80.02        76.90        70.45 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 TCGA-23-1023 TCGA-23-1027 
        8.42        23.05        72.20        25.38        40.54        32.09 
TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
        8.81        18.90        51.35         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1122 TCGA-23-1809 TCGA-23-2078 
       19.46        33.30         4.27        39.09         0.53        87.48 
TCGA-23-2084 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-1103 TCGA-24-1104 
       49.84         4.50        11.64        21.80        54.12        63.55 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1425 
       47.41         6.38         7.82         7.99         7.86         5.95 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1436 TCGA-24-1471 
        4.83        17.39        28.37        18.64         8.55         1.18 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 
       26.96        57.40        64.27        41.06        51.91        58.09 
TCGA-24-1555 TCGA-24-1557 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1604 
       88.50        39.88        45.50        47.70        17.23        88.37 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
       38.24         8.32         3.81        11.28         5.79         5.52 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 TCGA-24-2027 
       22.68        30.21        16.44        11.05       152.02       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2261 
       14.43        55.92        18.48        28.18        44.52         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
        0.36        47.54        31.63         0.82        67.36        36.23 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86        53.26        26.96        33.01        52.04 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
        2.01        34.98         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-2042 TCGA-25-2397 
       27.62        17.03        20.61        38.20        13.02        12.00 
TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       45.01         2.96        29.03        31.00        78.90        47.61 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 TCGA-29-1701 TCGA-29-1711 TCGA-29-1761 
      101.79        40.41        33.93        16.93        34.62        17.36 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       86.60        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 
       17.33        11.84        12.30         8.38         7.23        36.30 
TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ 
       86.17        45.11        13.84        21.47         9.76        35.77 
TCGA-30-1718 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 
       51.91        15.68        48.10        44.91         6.12         1.22 
TCGA-30-1880 TCGA-30-1892 TCGA-31-1951 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 
       57.57        48.79        22.49        42.51         2.20        28.77 
TCGA-36-1570 TCGA-36-1575 TCGA-36-1578 TCGA-36-2532 TCGA-36-2540 TCGA-36-2544 
       21.53         8.55        27.85        29.49        23.80        20.98 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 
       18.31        14.17         6.05        23.74        28.93        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 
        1.48        24.03         1.74        22.32        29.00       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
       80.12        22.32       116.12         9.40        34.39         5.42 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       11.11         8.09        18.54        28.47        48.79        44.84 
TCGA-61-1740 TCGA-61-1743 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        2.43        43.69         5.79        13.02         9.07        34.13 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1998 
       37.05        42.51        48.92        56.61        38.17         5.52 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2018 TCGA-61-2092 TCGA-61-2095 TCGA-61-2097 
       30.64        39.85        45.40        51.72        61.64        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       65.52        55.50        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       22.22        31.07         0.79         9.99        29.16         9.47 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 TCGA-13-0714 
       17.98        35.57        34.19        14.66        35.44         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0727 TCGA-13-0757 TCGA-13-0758 
       24.59        44.55        12.39        15.19        11.18        11.38 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0801 TCGA-13-0802 TCGA-13-0883 
       40.24       107.28        20.35        45.99        51.02        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      107.18       111.39        66.67        92.42        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 
      102.84        43.36       134.04        19.36        50.37       123.16 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0920 TCGA-13-0924 
      118.98       116.65        37.64        48.79        85.94 

  DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE 
                           0.26                            0.36 
  DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE 
                         153.37                          180.20 
  DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE 
                          33.57                           31.63 
[1] "0.3 - 153.4 (33.6)" "0.4 - 180.2 (31.6)"
[1] "hr=" "1.2"
D69V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 36(19Q13.33) MUTATED         1   289                1
  DEL PEAK 36(19Q13.33) WILD-TYPE       2   269                1
D69V3, multiclass
                  clus
vv                 DEL PEAK 36(19Q13.33) MUTATED
  OMENTUM                                      1
  OVARY                                      289
  PERITONEUM OVARY                             1
                  clus
vv                 DEL PEAK 36(19Q13.33) WILD-TYPE
  OMENTUM                                        2
  OVARY                                        269
  PERITONEUM OVARY                               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"
D69V4, binary
                                 cls
clus                                0   1
  DEL PEAK 36(19Q13.33) MUTATED   282   3
  DEL PEAK 36(19Q13.33) WILD-TYPE 259   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(19Q13.33) MUTATED    282    3
  DEL PEAK 36(19Q13.33) WILD-TYPE  259    2
     clus
vv    DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE
  NO                            282                             259
  YES                             3                               2
[1] 2 2
[1] FALSE
D69V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 36(19Q13.33) MUTATED   10 16  1  2
  DEL PEAK 36(19Q13.33) WILD-TYPE  5 10  4  1
D69V6, multiclass
    clus
vv   DEL PEAK 36(19Q13.33) MUTATED DEL PEAK 36(19Q13.33) WILD-TYPE
  R0                            10                               5
  R1                            16                              10
  R2                             1                               4
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                                 cls
clus                                0   1
  DEL PEAK 36(19Q13.33) MUTATED     8 173
  DEL PEAK 36(19Q13.33) WILD-TYPE   2 154
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(19Q13.33) MUTATED      8  173
  DEL PEAK 36(19Q13.33) WILD-TYPE    2  154
                        clus
vv                       DEL PEAK 36(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           173
                        clus
vv                       DEL PEAK 36(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             154
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 37(19Q13.43) MUTATION ANALYSIS
D70V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 37(19Q13.43) MUTATED   114 162
  DEL PEAK 37(19Q13.43) WILD-TYPE 114 169
  DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE 
                            276                             283 
  DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE 
                            162                             169 
$`DEL PEAK 37(19Q13.43) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1336 TCGA-04-1341 
       13.81        20.52        11.87         1.81        49.15         1.08 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       65.52        63.09        48.76        21.57        63.98         0.53 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        44.32        33.67        76.57       103.40        82.39 
TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       41.59         0.79        38.37       119.08        29.10        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       48.89        28.64        64.64        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 TCGA-09-1667 TCGA-09-1668 TCGA-09-1672 
        9.99        38.43        74.93        61.87        55.36         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        3.02         8.55        97.55         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       63.09        39.75        20.94        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 
       81.17        83.31        17.46        32.35        87.06        29.42 
TCGA-13-1484 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
      124.44        83.93        52.44        93.90        90.38         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1505 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 
       66.15       115.07        65.69        44.68        80.02        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       76.90        65.52        23.05        25.94        26.20        27.52 
TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1030 TCGA-23-1032 
       19.10         2.93         2.66        47.54        29.13         2.76 
TCGA-23-1110 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       54.51       129.96         6.38        39.09        33.47        58.13 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2643 TCGA-24-0966 TCGA-24-0979 TCGA-24-0980 
       91.66        77.00         4.70         7.63        41.56         7.66 
TCGA-24-0982 TCGA-24-1413 TCGA-24-1424 TCGA-24-1426 TCGA-24-1434 TCGA-24-1435 
       22.32         6.31         6.02         5.36        18.67        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1549 
       72.92        12.46       105.99         9.11         3.45        56.58 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 
       41.39        88.50        70.62        19.53        44.09        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1843 
       25.87        10.26        90.15        88.37        48.33         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1930 TCGA-24-2019 TCGA-24-2024 
        3.72         4.37        11.28        81.11         4.87        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2260 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       34.82        14.43        36.16        70.45        44.61         0.82 
TCGA-24-2293 TCGA-24-2298 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1321 
       16.64        53.26        52.04        42.05        65.00        33.96 
TCGA-25-1627 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       12.95         0.30        59.15        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2393 
       14.96        24.99        24.00        85.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2409 TCGA-29-1691 
        3.02        45.01        19.99        42.02        26.99        48.33 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       16.93        23.93        59.67        18.25        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       17.36        86.60        31.30        22.55        17.33        12.36 
TCGA-29-1778 TCGA-29-1784 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 
       14.93         5.36        65.00        62.47        42.25        21.47 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 
       11.47        38.07        51.91        36.26         0.26        34.78 
TCGA-30-1862 TCGA-30-1887 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
        6.12        24.26        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        6.71        44.12        29.10        21.53        22.85        22.55 
TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 TCGA-36-2537 
       30.08        24.23        24.69        35.05        29.82        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2547 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       25.08        21.60        20.52        16.18        11.47        47.57 
TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 TCGA-57-1993 TCGA-57-1994 TCGA-59-2355 
       42.02        10.42        21.14        25.08        25.02         2.14 
TCGA-59-2372 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       44.81        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1738 TCGA-61-1741 TCGA-61-1901 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 
       35.80        33.67        11.41        67.76        43.43        38.17 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       14.50        17.98         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2102 TCGA-61-2612 
        4.77        71.74        58.39        60.62         6.48         6.35 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0365 TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 
       39.68        18.94         9.47        57.76        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       81.86        18.51        32.88         6.71        36.92        19.99 
TCGA-10-0938 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 
       20.91        39.58         2.73        31.20        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
        2.50        11.18        11.54        38.01       111.78        61.84 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 
       56.71        58.65        63.09        20.35        83.34        87.48 
TCGA-13-0804 TCGA-13-0807 TCGA-13-0886 TCGA-13-0888 TCGA-13-0897 TCGA-13-0899 
       35.28        13.61       153.37        92.42        71.74        66.15 
TCGA-13-0903 TCGA-13-0908 TCGA-13-0911 TCGA-13-0912 TCGA-13-0919 TCGA-13-0921 
      127.79        60.59        44.55        37.64        84.53        48.76 

$`DEL PEAK 37(19Q13.43) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       43.92        41.00         2.01        46.62        18.51        11.87 
TCGA-04-1351 TCGA-04-1361 TCGA-04-1514 TCGA-04-1517 TCGA-04-1542 TCGA-04-1646 
       65.46        32.52        56.55        19.99        84.20        27.88 
TCGA-04-1651 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       36.23        89.33        41.62        57.60        30.51        17.98 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 
        6.18         6.12        35.15        28.54        55.23        57.27 
TCGA-13-1410 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       81.01        54.64        61.71        20.68        22.39        70.82 
TCGA-13-1492 TCGA-13-1497 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 
      125.56       127.27        13.97        43.20        34.82        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-A5FT 
       65.52        80.15        54.25        14.53        78.48        70.45 
TCGA-13-A5FU TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 TCGA-23-1022 TCGA-23-1023 
        8.42        72.20        25.38        16.70        49.68        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       15.39        26.83        32.09        49.41         8.81        18.90 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       51.35         3.22        31.20        68.68        19.46        33.30 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       86.01         4.27         0.53        24.95       115.89        87.48 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-1103 
       49.84         2.76         4.50        11.64        21.80        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        0.76         6.25         5.95         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1436 TCGA-24-1466 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       18.64         8.55        45.14         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 
       57.40        64.27        16.21        41.06        51.91        58.09 
TCGA-24-1557 TCGA-24-1562 TCGA-24-1567 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 
       39.88        45.50        17.23        38.24         8.32         3.81 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 
       11.05       152.02        44.84       109.71        55.92        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 
       28.18        64.01        44.52        57.07         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 
       47.54        31.63        67.36        36.23        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 
        1.02        26.96        33.01         2.01        34.98        37.97 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.99        15.02        18.58        27.62        17.03 
TCGA-25-1628 TCGA-25-1630 TCGA-25-2042 TCGA-25-2391 TCGA-25-2397 TCGA-25-2401 
       20.61        38.20        13.02        49.05        12.00         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1707 
       29.03        31.00        78.90        47.61       101.79        41.98 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 
       66.81        62.93        39.42        22.98        24.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 
       12.30         8.38         7.23        36.30        86.17        45.11 
TCGA-29-2429 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       13.84         9.76        35.77         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       44.91        36.62         1.22        57.57        30.05        48.79 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 
       42.51         2.20        28.77         8.55        25.74        27.85 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       33.01        29.49        23.80         2.24        20.98        18.31 
TCGA-36-2548 TCGA-36-2549 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-42-2593 
       14.17         6.05        23.74        28.93        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 
       24.03        11.38         1.74        22.32        29.00       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
       80.12        22.32       116.12         9.40        34.39         5.42 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       11.11         8.09        20.94        28.47        48.79        44.84 
TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 
        2.43        43.69         1.45         8.42         5.79        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
        9.07        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 TCGA-61-2008 
       56.61        15.75         2.01         5.52         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2092 TCGA-61-2095 TCGA-61-2098 TCGA-61-2101 
       39.85        30.64        51.72        61.64        65.52        55.50 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 
       76.87        20.68        44.52       125.75        22.22        31.07 
TCGA-61-2614 TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0367 TCGA-09-0369 
        8.61         0.79         9.99        29.16        17.98        35.57 
TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       34.19        14.66        35.44         6.21        24.59        44.55 
TCGA-13-0725 TCGA-13-0727 TCGA-13-0758 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       12.39        15.19        11.38        40.24       118.42       107.28 
TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0883 
       69.73        45.99        51.02        43.86        35.31        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      107.18       111.39        66.67        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       43.36       134.04        19.36        50.37       123.16       118.98 
TCGA-13-0910 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      116.65       109.32        58.68        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE 
                           0.26                            0.36 
  DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE 
                         153.37                          180.20 
  DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE 
                          34.29                           31.07 
[1] "0.3 - 153.4 (34.3)" "0.4 - 180.2 (31.1)"
[1] "hr=" "1.1"
D70V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 37(19Q13.43) MUTATED         1   276                1
  DEL PEAK 37(19Q13.43) WILD-TYPE       2   282                1
D70V3, multiclass
                  clus
vv                 DEL PEAK 37(19Q13.43) MUTATED
  OMENTUM                                      1
  OVARY                                      276
  PERITONEUM OVARY                             1
                  clus
vv                 DEL PEAK 37(19Q13.43) WILD-TYPE
  OMENTUM                                        2
  OVARY                                        282
  PERITONEUM OVARY                               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"
D70V4, binary
                                 cls
clus                                0   1
  DEL PEAK 37(19Q13.43) MUTATED   271   1
  DEL PEAK 37(19Q13.43) WILD-TYPE 270   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(19Q13.43) MUTATED    271    1
  DEL PEAK 37(19Q13.43) WILD-TYPE  270    4
     clus
vv    DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE
  NO                            271                             270
  YES                             1                               4
[1] 2 2
[1] FALSE
D70V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 37(19Q13.43) MUTATED   10 14  1  2
  DEL PEAK 37(19Q13.43) WILD-TYPE  5 12  4  1
D70V6, multiclass
    clus
vv   DEL PEAK 37(19Q13.43) MUTATED DEL PEAK 37(19Q13.43) WILD-TYPE
  R0                            10                               5
  R1                            14                              12
  R2                             1                               4
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                                 cls
clus                                0   1
  DEL PEAK 37(19Q13.43) MUTATED     7 157
  DEL PEAK 37(19Q13.43) WILD-TYPE   3 170
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(19Q13.43) MUTATED      7  157
  DEL PEAK 37(19Q13.43) WILD-TYPE    3  170
                        clus
vv                       DEL PEAK 37(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           157
                        clus
vv                       DEL PEAK 37(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             170
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 38(21Q22.3) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(21Q22.3) MUTATED    93 126
  DEL PEAK 38(21Q22.3) WILD-TYPE 135 205
  DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE 
                           219                            340 
  DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE 
                           126                            205 
$`DEL PEAK 38(21Q22.3) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1335 TCGA-04-1341 TCGA-04-1347 TCGA-04-1350 
       13.81        20.52         1.81         1.08        63.09        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1365 TCGA-04-1638 
       65.46         0.53        49.28        44.32        76.57        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 
       48.89        28.64        64.64        36.23        31.86        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1667 TCGA-09-1669 
        9.99        38.43        89.33        41.62        61.87        30.51 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 
        3.02        97.55         6.18         6.12       112.41        71.11 
TCGA-09-2051 TCGA-09-2056 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 
       63.09        12.46        81.17        55.23        57.27        17.46 
TCGA-13-1412 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       32.35        61.71       124.44        22.39        70.82        83.93 
TCGA-13-1491 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 
       52.44        90.38       127.27       115.07        43.20        65.69 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
       65.52        44.68        14.53        80.02        78.48        76.90 
TCGA-13-2065 TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       65.52        27.52        19.10         2.93         2.66        49.68 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 
       49.41        29.13        18.90         2.76        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1121 TCGA-23-2072 TCGA-23-2078 TCGA-23-2641 
       19.46        33.30         6.38        24.95        87.48         2.76 
TCGA-24-0975 TCGA-24-0980 TCGA-24-1105 TCGA-24-1413 TCGA-24-1418 TCGA-24-1422 
       21.80         7.66        47.41         6.31         7.99         0.76 
TCGA-24-1425 TCGA-24-1430 TCGA-24-1431 TCGA-24-1467 TCGA-24-1471 TCGA-24-1548 
        5.95        28.37        18.64       105.99         1.18        16.21 
TCGA-24-1549 TCGA-24-1553 TCGA-24-1557 TCGA-24-1563 TCGA-24-1603 TCGA-24-1845 
       56.58        58.09        39.88        47.70        90.15         3.81 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 
        5.79         5.52         9.80        44.84        34.82       109.71 
TCGA-24-2029 TCGA-24-2035 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 
       14.43        28.18        47.54        44.61         0.82        36.23 
TCGA-24-2298 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1627 
       53.26        42.05        34.98        37.97        33.96        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       38.20         0.30        59.15        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2396 TCGA-29-1691 TCGA-29-1695 
       14.96        24.99        24.00         3.02        48.33        40.41 
TCGA-29-1699 TCGA-29-1702 TCGA-29-1705 TCGA-29-1761 TCGA-29-1763 TCGA-29-1769 
       36.36        23.93        18.25        17.36        66.81        22.98 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       24.36        17.33        12.36         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       65.00        62.47        11.47        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-30-1891 
        2.47        15.68        48.10        44.91        36.62        30.05 
TCGA-31-1950 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 TCGA-36-1575 
       18.77        44.12        28.77        29.10        22.55         8.55 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2538 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       24.69        33.01        25.08        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2552 TCGA-42-2587 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
       14.17        11.47        23.74         1.74        29.00        25.08 
TCGA-57-1994 TCGA-59-2354 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       25.02        34.39        18.54         4.34        31.79        28.47 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 
       44.84         2.43         8.42         5.79        13.02         9.07 
TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       31.30        48.92        56.61        43.43        15.75        38.17 
TCGA-61-2000 TCGA-61-2008 TCGA-61-2016 TCGA-61-2094 TCGA-61-2113 TCGA-61-2613 
       14.50        30.64         1.18        71.74        22.22        31.07 
TCGA-WR-A838 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
        9.99        35.57        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0937 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0761 
       32.88        19.99        15.19        17.82        55.17        38.01 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 
       56.71        40.24       118.42        63.09        87.48        43.86 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0891 TCGA-13-0904 
       68.94       107.18       153.37        66.67       102.84        50.37 
TCGA-13-0906 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      118.98        44.55        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       48.79        48.76        83.74 

$`DEL PEAK 38(21Q22.3) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       11.87        43.92        41.00        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1361 
       18.51        11.87        65.52        48.76        21.57        32.52 
TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       33.67       103.40        82.39        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 
        0.79        38.37       119.08        29.10        84.20        27.88 
TCGA-04-1654 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       47.70        74.93        57.60        55.36        17.98         5.85 
TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        8.55        35.15         4.54        39.75        20.94        26.93 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 
       77.10        28.54        83.31        81.01        54.64        87.06 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 
       29.42        20.68       125.56        93.90         4.24        66.15 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-2060 
       13.97        34.82        34.16        80.15        54.25        77.88 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       70.45         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1683 TCGA-20-1685 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       25.38        16.70        47.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1029 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1118 
       32.09         8.81        51.35        54.51         3.22        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
      129.96         4.27        39.09        33.47        58.13         0.53 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 
      115.89        91.66        77.00        49.84         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
        7.63        11.64        41.56        22.32        54.12        63.55 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 
        6.38         7.82         7.86         6.25         6.02         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
        4.83        17.39        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       12.46        45.14         9.11         3.45        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
       57.40        64.27        41.06        51.91        41.39        88.50 
TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       70.62        19.53        44.09        45.50        25.87        10.26 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       17.23        88.37        48.33        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        3.72         4.37        11.28        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2030 
       11.05        81.11         4.87       152.02        58.16        55.92 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       18.48        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 
        0.36        31.63        70.45        67.36        16.64        33.11 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1317 
       55.86         1.02        26.96        33.01        52.04         2.01 
TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       65.00         2.99        12.99        15.02        18.58        27.62 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       17.03        20.61        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       29.03        31.00        26.99        78.90        47.61       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1703 
       39.02        33.93        31.20        68.32        16.93        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       41.98        31.27        34.62        86.60        62.93        39.42 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       31.30        22.55        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
        7.23        45.11        13.84        42.25        21.47         9.76 
TCGA-29-A5NZ TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 
       35.77         0.26        34.78         6.12         1.22        57.57 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       24.26        48.79        45.57        30.18        22.49         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-1577 
       42.51         2.20        21.53        22.85        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        35.05        29.49        29.82        25.91 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 
       23.80        21.60         2.24         6.05        16.18        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       28.93        42.02        10.42        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       11.38        21.14        22.32       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
      116.12         9.40         2.14         5.42        44.81        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 TCGA-61-1738 
        8.09        20.94        31.43        27.88        48.79        35.80 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1906 TCGA-61-1910 
       33.67        43.69         1.45        11.41        34.13        37.05 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 
       42.51        67.76         2.01         5.52        17.98         4.01 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       39.85        30.64        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       51.72        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 
        6.48        76.87        20.68        44.52       125.75         6.35 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 
        8.61        39.68        18.94         0.79        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       57.76        17.98        54.31        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       36.92        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
        2.73        12.39        31.20         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0793 TCGA-13-0795 
       11.54       111.78        61.84        58.65       107.28        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
       69.73        83.34        45.99        51.02        35.28        35.31 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 
       13.61       111.39        92.42        95.15       145.45        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 
       71.74        66.15       134.04        19.36       127.79       123.16 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0924 TCGA-13-2071 
       60.59       116.65        85.94        25.41 

  DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE 
                        153.37                         180.20 
  DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE 
                        34.820                         31.235 
[1] "0.3 - 153.4 (34.8)" "0.3 - 180.2 (31.2)"
[1] "hr=" "1.1"
D71V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 38(21Q22.3) MUTATED         1   220                0
  DEL PEAK 38(21Q22.3) WILD-TYPE       2   338                2
D71V3, multiclass
                  clus
vv                 DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE
  OMENTUM                                     1                              2
  OVARY                                     220                            338
  PERITONEUM OVARY                            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"
D71V4, binary
                                cls
clus                               0   1
  DEL PEAK 38(21Q22.3) MUTATED   214   2
  DEL PEAK 38(21Q22.3) WILD-TYPE 327   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(21Q22.3) MUTATED    214    2
  DEL PEAK 38(21Q22.3) WILD-TYPE  327    3
     clus
vv    DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE
  NO                           214                            327
  YES                            2                              3
[1] 2 2
[1] FALSE
D71V5, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 38(21Q22.3) MUTATED    5 11  0  1
  DEL PEAK 38(21Q22.3) WILD-TYPE 10 15  5  2
D71V6, multiclass
    clus
vv   DEL PEAK 38(21Q22.3) MUTATED DEL PEAK 38(21Q22.3) WILD-TYPE
  R0                            5                             10
  R1                           11                             15
  R2                            0                              5
  RX                            1                              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"
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(21Q22.3) MUTATED     6 135
  DEL PEAK 38(21Q22.3) WILD-TYPE   4 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(21Q22.3) MUTATED      6  135
  DEL PEAK 38(21Q22.3) WILD-TYPE    4  192
                        clus
vv                       DEL PEAK 38(21Q22.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          135
                        clus
vv                       DEL PEAK 38(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            192
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 39(22Q13.32) MUTATION ANALYSIS
D72V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 39(22Q13.32) MUTATED   199 286
  DEL PEAK 39(22Q13.32) WILD-TYPE  29  45
  DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE 
                            485                              74 
  DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE 
                            286                              45 
$`DEL PEAK 39(22Q13.32) MUTATED`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 
       13.81        11.87        43.92        41.00        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
       46.62         1.08        18.51        65.52        63.09        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       63.98        65.46         0.53        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       33.67        76.57       103.40        82.39        56.55        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
        0.79        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        3.02         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2056 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       12.46        81.17        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       17.46        32.35        87.06        61.71        29.42       124.44 
TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       22.39        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
      127.27        66.15       115.07        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       65.69        34.16        65.52        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       14.53        80.02        78.48        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
       70.45         8.42        25.94        26.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       19.10        16.70         2.93         2.66        47.54        49.68 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       18.90         2.76        51.35        54.51        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
       19.46        33.30        86.01       129.96         4.27        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 
       33.47        58.13        24.95       115.89        87.48        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
       28.37        18.64        18.67        43.53         8.55        12.46 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
      105.99         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 
       64.27        16.21        56.58        41.06        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 
       25.87        10.26        17.23        90.15        88.37        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
        8.32         3.48         3.72         3.81         4.37        11.28 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 
       81.11         4.87       152.02        44.84        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 
       14.43        55.92        18.48        64.01        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       53.26         1.02        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       15.02        18.58        17.03        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       62.17        35.87        52.04        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 
       85.05        13.02        49.05         1.02        38.04        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       26.99        78.90       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 
       41.98        34.62        17.36        86.60        66.81        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       31.30        22.98        17.33        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        45.11        13.84        42.25        21.47        11.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       35.77        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       48.10        44.91         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       24.26        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       42.02        10.42        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
       21.14        29.00        25.08        25.02       180.20        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        8.09        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       28.47        48.79        44.84        35.80         2.43        33.67 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 
       43.69         8.42         5.79        11.41        13.02        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       31.30        37.05        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 
        4.01        30.64        39.85        30.64         1.18        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
        4.80         4.77        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
        6.48        20.68        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 
       29.16         9.47        57.76        17.98        35.57        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       36.92        19.99        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        12.39        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.18        11.38        38.01        61.84        56.71        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       40.24       118.42       107.28        63.09        20.35        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       83.34        87.48        45.99        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.31        13.61        68.94       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 
       66.67        92.42       145.45       102.84        71.74       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36       127.79        50.37       123.16       118.98        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      116.65        44.55        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.79        48.76        83.74        85.94        25.41 

$`DEL PEAK 39(22Q13.32) WILD-TYPE`
TCGA-59-A5PD TCGA-04-1335 TCGA-04-1343 TCGA-04-1348 TCGA-04-1516 TCGA-09-1672 
       20.52         1.81        11.87        48.76        41.59         5.85 
TCGA-09-2055 TCGA-13-1403 TCGA-13-1405 TCGA-13-1477 TCGA-13-1485 TCGA-13-1488 
       26.93        77.10        28.54        54.64        20.68        70.82 
TCGA-13-1489 TCGA-20-0987 TCGA-20-0996 TCGA-23-1026 TCGA-23-1111 TCGA-23-1121 
       83.93        23.05        72.20        26.83         3.22         6.38 
TCGA-23-1809 TCGA-23-2079 TCGA-24-0980 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 
        0.53        91.66         7.66        72.92        45.14         9.11 
TCGA-24-1551 TCGA-24-1563 TCGA-24-1614 TCGA-24-1849 TCGA-24-2024 TCGA-24-2035 
       51.91        47.70        48.33         5.79        58.16        28.18 
TCGA-24-2038 TCGA-25-1313 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-2396 
       44.52        26.96        27.62        12.95        38.20         3.02 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1699 TCGA-29-1710 TCGA-29-1764 TCGA-29-1770 
       47.61        48.33        36.36        31.27        62.93        24.36 
TCGA-29-1771 TCGA-29-2427 TCGA-29-2436 TCGA-30-1857 TCGA-30-1861 TCGA-30-1891 
       22.55        62.47         9.76         0.26        34.78        30.05 
TCGA-30-1892 TCGA-31-1956 TCGA-36-1574 TCGA-36-2529 TCGA-57-1585 TCGA-57-1586 
       48.79        44.12        22.55        35.05         1.74        22.32 
TCGA-59-2349 TCGA-61-1721 TCGA-61-1724 TCGA-61-1895 TCGA-61-1904 TCGA-61-1911 
       80.12        11.11        20.94         1.45         9.07        42.51 
TCGA-61-2017 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2104 TCGA-10-0934 
       45.96        51.72        71.74        61.64        76.87         6.71 
TCGA-10-0935 TCGA-13-0726 TCGA-13-0755 TCGA-13-0760 TCGA-13-0762 TCGA-13-0889 
       35.44        31.20         2.50        11.54       111.78        95.15 
TCGA-13-0893 TCGA-13-0899 
       43.36        66.15 

  DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE 
                           0.30                            0.26 
  DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE 
                         180.20                          111.78 
  DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE 
                         32.880                          33.025 
[1] "0.3 - 180.2 (32.9)" "0.3 - 111.8 (33.0)"
[1] "hr=" "1.1"
D72V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 39(22Q13.32) MUTATED         3   485                1
  DEL PEAK 39(22Q13.32) WILD-TYPE       0    73                1
D72V3, multiclass
                  clus
vv                 DEL PEAK 39(22Q13.32) MUTATED
  OMENTUM                                      3
  OVARY                                      485
  PERITONEUM OVARY                             1
                  clus
vv                 DEL PEAK 39(22Q13.32) WILD-TYPE
  OMENTUM                                        0
  OVARY                                         73
  PERITONEUM OVARY                               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"
D72V4, binary
                                 cls
clus                                0   1
  DEL PEAK 39(22Q13.32) MUTATED   471   5
  DEL PEAK 39(22Q13.32) WILD-TYPE  70   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(22Q13.32) MUTATED    471    5
  DEL PEAK 39(22Q13.32) WILD-TYPE   70    0
     clus
vv    DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE
  NO                            471                              70
  YES                             5                               0
[1] 2 2
[1] FALSE
D72V5, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 39(22Q13.32) MUTATED   13 24  5  3
  DEL PEAK 39(22Q13.32) WILD-TYPE  2  2  0  0
D72V6, multiclass
    clus
vv   DEL PEAK 39(22Q13.32) MUTATED DEL PEAK 39(22Q13.32) WILD-TYPE
  R0                            13                               2
  R1                            24                               2
  R2                             5                               0
  RX                             3                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                 cls
clus                                0   1
  DEL PEAK 39(22Q13.32) MUTATED     9 280
  DEL PEAK 39(22Q13.32) WILD-TYPE   1  47
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(22Q13.32) MUTATED      9  280
  DEL PEAK 39(22Q13.32) WILD-TYPE    1   47
                        clus
vv                       DEL PEAK 39(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           280
                        clus
vv                       DEL PEAK 39(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              47
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 40(XP21.1) MUTATION ANALYSIS
D73V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 40(XP21.1) MUTATED   145 202
  DEL PEAK 40(XP21.1) WILD-TYPE  83 129
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                          347                           212 
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                          202                           129 
$`DEL PEAK 40(XP21.1) MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1335 TCGA-04-1336 TCGA-04-1346 TCGA-04-1347 
       13.81        20.52         1.81        49.15        65.52        63.09 
TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       65.46        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 
       29.10        84.20        55.43        48.89        28.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 
       74.93        57.60        61.87        30.51        17.98         3.02 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 
       97.55         6.18         6.12       112.41        71.11        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       20.94        26.93        12.46        81.17        28.54        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 
       55.23        57.27        32.35        61.71        29.42        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 
       83.93        52.44       125.56        93.90         4.24        66.15 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       13.97        34.82        65.69        80.15        44.68        14.53 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       78.48        77.88        65.52        70.45         8.42        23.05 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
        2.66        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 
       51.35         3.22        31.20       129.96         6.38        33.47 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 
      115.89        91.66        77.00         2.76         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56         7.66        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.31         6.38         7.99         0.76         6.25         6.02 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        5.36         4.83        17.39        28.37        18.64        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1474 TCGA-24-1545 
        8.55        72.92        12.46        45.14        22.22        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 
       64.27        41.06        51.91        41.39        88.50        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 
       45.50        47.70        25.87        17.23        90.15        48.33 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1928 
        3.81         4.37        11.28         5.79         9.80        11.05 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
       81.11        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       55.92        18.48        64.01        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 
        0.36        47.54        31.63        70.45         0.82        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1316 TCGA-25-1318 
       36.23        55.86        53.26        33.01        42.05        34.98 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1625 TCGA-25-1631 TCGA-25-1632 
       37.97         2.99        15.02        27.62         0.30        59.15 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 
       35.87        52.04        14.96        24.99        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       49.05         1.02        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 
       19.99        42.02         2.96        26.99        78.90       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 
       39.02        33.93        31.20        36.36        23.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 
       66.81        62.93        22.98        22.55        12.36        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       14.93         8.38         5.36        36.30        86.17        62.47 
TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       21.47        11.47        35.77        38.07        51.91        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       15.68         0.26        34.78        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       24.26        30.05        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 
        6.71        42.51        44.12        29.10        21.53        22.55 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
        8.55        25.74        27.85        24.23        24.69        35.05 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       29.49        29.82        25.91        25.08        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-42-2582 TCGA-42-2593 
       20.98        18.31        20.52         6.05        47.57         1.48 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 
       11.38        21.14         1.74        22.32        29.00        25.02 
TCGA-59-2350 TCGA-59-2363 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       22.32         5.42        20.94        31.43        18.54        27.88 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 
       31.79        28.47        48.79        44.84        35.80        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       43.69         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-2000 
       37.05        48.92        56.61        67.76        38.17        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 
       17.98         4.01        30.64         1.18        45.40         4.80 
TCGA-61-2088 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 
        4.77        58.39        65.52        55.50        76.87        44.52 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        6.35        31.07         8.61        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0938 
       54.31        25.91        81.86        34.19        32.88        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 
        6.21        24.59        44.55        39.58        12.39        15.19 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
        2.50        11.18        11.38        11.54        38.01       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       61.84        56.71       118.42        63.09        20.35        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        87.48        45.99        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 TCGA-13-0891 TCGA-13-0900 
       13.61        68.94       153.37        95.15       102.84       134.04 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      127.79        50.37       123.16       118.98        60.59       116.65 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 
      109.32        58.68        84.53        48.76        85.94 

$`DEL PEAK 40(XP21.1) WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       11.87        43.92        41.00         2.01        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       18.51        11.87        48.76        21.57        63.98         0.53 
TCGA-04-1356 TCGA-04-1516 TCGA-04-1646 TCGA-04-1649 TCGA-09-1665 TCGA-09-1668 
       49.28        41.59        27.88        64.64        41.62        55.36 
TCGA-09-1672 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2051 TCGA-13-1403 
        5.85         8.55        35.15         4.54        63.09        77.10 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 
       81.01        17.46        54.64        87.06       124.44        20.68 
TCGA-13-1488 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 TCGA-13-1506 
       70.82        90.38       127.27       115.07        43.20        34.16 
TCGA-13-1507 TCGA-13-1511 TCGA-13-2057 TCGA-13-2061 TCGA-20-0990 TCGA-20-0996 
       65.52        54.25        80.02        76.90        25.94        72.20 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1032 
       47.54        49.68        40.54        15.39        26.83         2.76 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
       54.51        68.68        19.46        33.30        86.01         4.27 
TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 
       39.09        58.13         0.53        24.95        87.48        49.84 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0982 TCGA-24-1417 TCGA-24-1419 TCGA-24-1425 
        4.70         4.50        22.32         7.82         7.86         5.95 
TCGA-24-1434 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 
       18.67       105.99         9.11         3.45         1.18        26.96 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       16.21        56.58        58.09        70.62        39.88        19.53 
TCGA-24-1565 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       10.26        88.37        38.24         8.32         3.48         3.72 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 
        5.52        22.68        30.21        16.44         4.87       152.02 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2281 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 
       28.18        44.52        44.61        16.64        33.11         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 
       26.96        52.04         2.01        65.00        33.96        12.99 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 
       18.58        17.03        12.95        20.61        38.20        62.17 
TCGA-25-1877 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 
       24.00        29.03        31.00        47.61        48.33        40.41 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 
       68.32        16.93        39.42        31.30        24.36        17.33 
TCGA-29-1776 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       11.84         7.23        65.00        45.11        13.84        42.25 
TCGA-29-2436 TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1892 
        9.76         2.47        48.10        44.91         6.12        48.79 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 TCGA-36-1576 TCGA-36-2530 TCGA-36-2540 
        2.20        28.77        22.85        30.08        33.01        23.80 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       14.17        16.18        11.47        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 
       10.42        40.77        24.03        25.08       180.20        80.12 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 
      116.12         9.40        34.39         2.14        44.81        11.11 
TCGA-61-1722 TCGA-61-1730 TCGA-61-1740 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.09         4.34         2.43         9.07        34.13        31.30 
TCGA-61-1911 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2008 
       42.51        43.43        15.75         2.01         5.52        30.64 
TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
       39.85        45.96        51.72        71.74        61.64        60.62 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-OY-A56P TCGA-OY-A56Q 
        6.48        20.68       125.75        22.22        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-10-0928 TCGA-10-0933 
        0.79         9.99        29.16         9.47        18.51        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0724 TCGA-13-0726 
        6.71        35.44        36.92        19.99         2.73        31.20 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0802 
       17.82        55.17        58.65        40.24       107.28        51.02 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 
      107.18       111.39        66.67        92.42       145.45        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0911 TCGA-13-0912 TCGA-13-0920 
       71.74        66.15        19.36        44.55        37.64        48.79 
TCGA-13-0923 TCGA-13-2071 
       83.74        25.41 

  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                         0.26                          0.53 
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                       153.37                        180.20 
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                        33.47                         31.25 
[1] "0.3 - 153.4 (33.5)" "0.5 - 180.2 (31.2)"
[1] "hr=" "1.1"
D73V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 40(XP21.1) MUTATED         2   344                1
  DEL PEAK 40(XP21.1) WILD-TYPE       1   214                1
D73V3, multiclass
                  clus
vv                 DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE
  OMENTUM                                    2                             1
  OVARY                                    344                           214
  PERITONEUM OVARY                           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"
D73V4, binary
                               cls
clus                              0   1
  DEL PEAK 40(XP21.1) MUTATED   337   4
  DEL PEAK 40(XP21.1) WILD-TYPE 204   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 40(XP21.1) MUTATED    337    4
  DEL PEAK 40(XP21.1) WILD-TYPE  204    1
     clus
vv    DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE
  NO                          337                           204
  YES                           4                             1
[1] 2 2
[1] FALSE
D73V5, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 40(XP21.1) MUTATED    7 16  2  2
  DEL PEAK 40(XP21.1) WILD-TYPE  8 10  3  1
D73V6, multiclass
    clus
vv   DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE
  R0                           7                             8
  R1                          16                            10
  R2                           2                             3
  RX                           2                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                               cls
clus                              0   1
  DEL PEAK 40(XP21.1) MUTATED     5 193
  DEL PEAK 40(XP21.1) WILD-TYPE   5 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 40(XP21.1) MUTATED      5  193
  DEL PEAK 40(XP21.1) WILD-TYPE    5  134
                        clus
vv                       DEL PEAK 40(XP21.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         193
                        clus
vv                       DEL PEAK 40(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           134
[1] 2 2
[1] FALSE
